Stefanie S. Jeffrey, MD

Abstract

Triple-negative breast cancer (TNBC) is aggressive and lacks targeted therapies. Phosphatidylinositide 3-kinase (PI3K) / mammalian target of rapamycin (mTOR) pathways are frequently activated in TNBC patient tumors at the genome, gene expression and protein levels, and mTOR inhibitors have been shown to inhibit growth in TNBC cell lines. We describe a panel of patient-derived xenografts representing multiple TNBC subtypes and use them to test preclinical drug efficacy of two mTOR inhibitors, sirolimus (rapamycin) and temsirolimus (CCI-779).We generated a panel of seven patient-derived orthotopic xenografts from six primary TNBC tumors and one metastasis. Patient tumors and corresponding xenografts were compared by histology, immunohistochemistry, array comparative genomic hybridization (aCGH) and phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA) sequencing; TNBC subtypes were determined. Using a previously published logistic regression approach, we generated a rapamycin response signature from Connectivity Map gene expression data and used it to predict rapamycin sensitivity in 1401 human breast cancers of different intrinsic subtypes, prompting in vivo testing of mTOR inhibitors and doxorubicin in our TNBC xenografts.Patient-derived xenografts recapitulated histology, biomarker expression and global genomic features of patient tumors. Two primary tumors had PIK3CA coding mutations, and 5/6 primary tumors showed flanking intron single nucleotide polymorphisms (SNPs) with conservation of sequence variations between primary tumors and xenografts, even on subsequent xenograft passages. Gene expression profiling showed that our models represent at least four of six TNBC subtypes. The rapamycin response signature predicted sensitivity for 94% of basal-like breast cancers in a large dataset. Drug testing of mTOR inhibitors in our xenografts showed 77 to 99% growth inhibition, significantly more than doxorubicin; protein phosphorylation studies indicated constitutive activation of the mTOR pathway that decreased with treatment. However, no tumor was completely eradicated.A panel of patient-derived xenograft models covering a spectrum of TNBC subtypes was generated that histologically and genomically matched original patient tumors. Consistent with in silico predictions, mTOR inhibitor testing in our TNBC xenografts showed significant tumor growth inhibition in all, suggesting that mTOR inhibitors can be effective in TNBC, but will require use with additional therapies, warranting investigation of optimal drug combinations.

View details for DOI 10.1186/bcr3640

View details for PubMedID 24708766

Abstract

Dysregulation of the Akt/PKB pathway has been associated with poor prognosis in several human carcinomas. Current approaches to assess Akt activation rely on intensity-based methods, which are limited by the subjectivity of manual scoring and poor specificity. Here, we report the development of a novel assay using amplified, time-resolved Förster resonance energy transfer (FRET), which is highly specific and sensitive and can be adapted to any protein. Using this approach to analyze primary breast tissue microarrays, we quantified levels of activated pAkt at a spatial resolution that revealed molecular heterogeneity within tumors. High pAkt status assessed by amplified FRET correlated with worse disease-free survival. Our findings support the use of amplified FRET to determine pAkt status in cancer tissues as candidate biomarker for the identification of high-risk patients. Cancer Res; 74(18); 4983-95. ©2014 AACR.

View details for DOI 10.1158/0008-5472.CAN-13-3382

View details for PubMedID 24970478

Abstract

Therapeutic decisions in cancer are generally guided by molecular biomarkers or, for some newer therapeutics, primary tumor genotype. However, because biomarkers or genotypes may change as new metastases emerge, circulating tumor cells (CTCs) from blood are being investigated for a role in guiding real-time drug selection during disease progression, expecting that CTCs will comprehensively represent the full spectrum of genomic changes in metastases. However, information is limited regarding mutational heterogeneity among CTCs and metastases in breast cancer as discerned by single cell analysis. The presence of disseminated tumor cells (DTCs) in bone marrow also carry prognostic significance in breast cancer, but with variability between CTC and DTC detection. Here we analyze a series of single tumor cells, CTCs, and DTCs for PIK3CA mutations and report CTC and corresponding metastatic genotypes.We used the MagSweeper, an immunomagnetic separation device, to capture live single tumor cells from breast cancer patients' primary and metastatic tissues, blood, and bone marrow. Single cells were screened for known hotspot mutations in exons 9 and 20 of the PIK3CA gene. Captured DTCs grown in cell culture were also sequenced for PIK3CA mutations.Among 242 individual tumor cells isolated from 17 patients and tested for mutations, 48 mutated tumor cells were identified in three patients. Single cell analyses revealed mutational heterogeneity among CTCs and tumor cells in tissues. In a patient followed serially, there was mutational discordance between CTCs, DTCs, and metastases, and among CTCs isolated at different time points. DTCs from this patient propagated in vitro contained a PIK3CA mutation, which was maintained despite morphological changes during 21 days of cell culture.Single cell analysis of CTCs can demonstrate genotypic heterogeneity, changes over time, and discordance from DTCs and distant metastases. We present a cautionary case showing that CTCs from any single blood draw do not always reflect metastatic genotype, and that CTC and DTC analyses may provide independent clinical information. Isolated DTCs remain viable and can be propagated in culture while maintaining their original mutational status, potentially serving as a future resource for investigating new drug therapies.

View details for DOI 10.1186/1471-2407-14-456

View details for PubMedID 24947048

Abstract

Detection and characterization of circulating tumor cells (CTCs) may reveal insights into the diagnosis and treatment of malignant disease. Technologies for isolating CTCs developed thus far suffer from one or more limitations, such as low throughput, inability to release captured cells, and reliance on expensive instrumentation for enrichment or subsequent characterization. We report a continuing development of a magnetic separation device, the magnetic sifter, which is a miniature microfluidic chip with a dense array of magnetic pores. It offers high efficiency capture of tumor cells, labeled with magnetic nanoparticles, from whole blood with high throughput and efficient release of captured cells. For subsequent characterization of CTCs, an assay, using a protein chip with giant magnetoresistive nanosensors, has been implemented for mutational analysis of CTCs enriched with the magnetic sifter. The use of these magnetic technologies, which are separate devices, may lead the way to routine preparation and characterization of "liquid biopsies" from cancer patients.

View details for DOI 10.1039/c3lc50580d

View details for PubMedID 23969419

View details for DOI 10.1186/gm474

View details for Web of Science ID 000323065600001

Abstract

Reliable biomarkers are needed to guide treatment of colorectal cancer, as well as for surveillance to detect recurrence and monitor therapeutic response. In this review, the authors discuss the use of various biomarkers in addition to serum carcinoembryonic antigen, the current surveillance method for metastatic recurrence after resection. The clinical relevance of mutations including microsatellite instability, KRAS, BRAF and SMAD4 is addressed. The role of circulating tumor cells and cell-free DNA with regards to their implementation into clinical use is discussed, as well as how single-cell analysis may fit into a monitoring program. The detection and characterization of circulating tumor cells and cell-free DNA in colorectal cancer patients will not only improve the understanding of the development of metastasis, but may also supplant the use of other biomarkers.

View details for DOI 10.1586/14737159.2013.811896

View details for Web of Science ID 000331285900014

View details for PubMedID 23895128

Abstract

Cellular stress responses are frequently governed by the subcellular localization of critical effector proteins. Apoptosis-inducing Factor (AIF) or Glyceraldehyde 3-Phosphate Dehydrogenase (GAPDH), for example, can translocate from mitochondria to the nucleus, where they modulate apoptotic death pathways. Hypoxia-inducible gene domain 1A (HIGD1A) is a mitochondrial protein regulated by Hypoxia-inducible Factor-1α (HIF1α). Here we show that while HIGD1A resides in mitochondria during physiological hypoxia, severe metabolic stress, such as glucose starvation coupled with hypoxia, in addition to DNA damage induced by etoposide, triggers its nuclear accumulation. We show that nuclear localization of HIGD1A overlaps with that of AIF, and is dependent on the presence of BAX and BAK. Furthermore, we show that AIF and HIGD1A physically interact. Additionally, we demonstrate that nuclear HIGD1A is a potential marker of metabolic stress in vivo, frequently observed in diverse pathological states such as myocardial infarction, hypoxic-ischemic encephalopathy (HIE), and different types of cancer. In summary, we demonstrate a novel nuclear localization of HIGD1A that is commonly observed in human disease processes in vivo.

View details for DOI 10.1371/journal.pone.0062758

View details for Web of Science ID 000319077300094

View details for PubMedID 23646141

Abstract

Racial, ethnic and economic disparities in cancer rates, outcomes, and clinical trials participation persist despite significant research. We examined barriers to clinical trials enrollment among Chinese patients, and developed a navigation program for Chinese gynecologic and breast cancer patients. Six bilingual navigators were trained and a navigator assigned to each patient for at least 2 months. All patients received a clinical trials booklet in Chinese and English. Data collection included pre-and post-navigation surveys, intake forms, and documentation of navigation encounters. Between July 2010 and May 31, 2011, we recruited 28 breast and gynecologic cancer patients. Patients averaged 317 min of navigation (range 63-1,852) during 8 sessions (range 3-28). They improved in 4 of 10 true-false knowledge statements about clinical trials. A patient navigation program for Chinese-speaking cancer patients is feasible. It results in high patient satisfaction rates and modest improvements in clinical trials knowledge and participation.

View details for DOI 10.1007/s10903-013-9901-x

View details for PubMedID 23963874

Abstract

To improve cancer therapy, it is critical to target metastasizing cells. Circulating tumor cells (CTCs) are rare cells found in the blood of patients with solid tumors and may play a key role in cancer dissemination. Uncovering CTC phenotypes offers a potential avenue to inform treatment. However, CTC transcriptional profiling is limited by leukocyte contamination; an approach to surmount this problem is single cell analysis. Here we demonstrate feasibility of performing high dimensional single CTC profiling, providing early insight into CTC heterogeneity and allowing comparisons to breast cancer cell lines widely used for drug discovery.We purified CTCs using the MagSweeper, an immunomagnetic enrichment device that isolates live tumor cells from unfractionated blood. CTCs that met stringent criteria for further analysis were obtained from 70% (14/20) of primary and 70% (21/30) of metastatic breast cancer patients; none were captured from patients with non-epithelial cancer (n = 20) or healthy subjects (n = 25). Microfluidic-based single cell transcriptional profiling of 87 cancer-associated and reference genes showed heterogeneity among individual CTCs, separating them into two major subgroups, based on 31 highly expressed genes. In contrast, single cells from seven breast cancer cell lines were tightly clustered together by sample ID and ER status. CTC profiles were distinct from those of cancer cell lines, questioning the suitability of such lines for drug discovery efforts for late stage cancer therapy.For the first time, we directly measured high dimensional gene expression in individual CTCs without the common practice of pooling such cells. Elevated transcript levels of genes associated with metastasis NPTN, S100A4, S100A9, and with epithelial mesenchymal transition: VIM, TGFß1, ZEB2, FOXC1, CXCR4, were striking compared to cell lines. Our findings demonstrate that profiling CTCs on a cell-by-cell basis is possible and may facilitate the application of 'liquid biopsies' to better model drug discovery.

View details for DOI 10.1371/journal.pone.0033788

View details for Web of Science ID 000305335000005

View details for PubMedID 22586443

Abstract

Beyond enumeration, CTC characterization is expected to help guide therapeutic selection for personalized care of cancer patients. Different approaches may be used to simultaneously identify multiple CTC-specific markers for biological characterization; yet awareness of associated pitfalls is also important. We have focused this chapter on molecular profiling of CTCs following enrichment. We describe the MagSweeper technology that was specifically developed to isolate live and highly purified CTCs for pooled or single cell or pooled cell molecular analyses or for CTC growth in vitro or in vivo. However, most of what is discussed will apply to any multiplex analysis of CTCs, irrespective of the enrichment method.

View details for DOI 10.1007/978-3-642-28160-0_11

View details for PubMedID 22527500

Abstract

We conducted a case-control study to evaluate the risk of breast cancer associated with adipose concentrations of polybrominated diphenyl ethers (PBDEs) among women undergoing surgical breast biopsies in the San Francisco Bay Area of California (n=78 cases; 56 controls). Adipose tissue was analyzed for the five major congeners of PBDEs. Unconditional logistic regression was used to estimate age- and race-adjusted exposure-specific odds ratios (ORs) and 95% confidence intervals (95% CI). Adipose levels of PBDEs were among the highest ever reported. Adjusted ORs for the highest compared with lowest levels of exposures were as follows: 0.56 (95% CI 0.19-1.68) for BDE-47; 1.19 (95% CI 0.35-4.10) for BDE-99; 0.91 (95% CI 0.33-2.53) for BDE-100; 0.52 (95% CI 0.19-1.39) for BDE-153; 1.67 (95% CI 0.44-6.29) for BDE-154; 2.04 (95% CI 0.45-9.20) for total BDEs. These results provide no evidence of an association between PBDE adipose concentrations measured at or near the time of diagnosis and breast cancer risk. Our study was limited by a small sample size. Given the high levels of PBDEs found in this population of California women, future studies are warranted. Such studies would benefit from a larger sample size, a more representative control series, and/or a prospective design.

View details for DOI 10.1007/s10549-011-1481-7

View details for Web of Science ID 000293634000019

View details for PubMedID 21468638

Abstract

Identifying the best drug for each cancer patient requires an efficient individualized strategy. We present MATCH (Merging genomic and pharmacologic Analyses for Therapy CHoice), an approach using public genomic resources and drug testing of fresh tumor samples to link drugs to patients. Valproic acid (VPA) is highlighted as a proof-of-principle. In order to predict specific tumor types with high probability of drug sensitivity, we create drug response signatures using publically available gene expression data and assess sensitivity in a data set of >40 cancer types. Next, we evaluate drug sensitivity in matched tumor and normal tissue and exclude cancer types that are no more sensitive than normal tissue. From these analyses, breast tumors are predicted to be sensitive to VPA. A meta-analysis across breast cancer data sets shows that aggressive subtypes are most likely to be sensitive to VPA, but all subtypes have sensitive tumors. MATCH predictions correlate significantly with growth inhibition in cancer cell lines and three-dimensional cultures of fresh tumor samples. MATCH accurately predicts reduction in tumor growth rate following VPA treatment in patient tumor xenografts. MATCH uses genomic analysis with in vitro testing of patient tumors to select optimal drug regimens before clinical trial initiation.

View details for DOI 10.1038/msb.2011.47

View details for Web of Science ID 000293351900012

View details for PubMedID 21772261

Abstract

Whether stromal components facilitate growth, invasion, and dissemination of cancer cells or suppress neoplastic lesions from further malignant progression is a continuing conundrum in tumor biology. Conceptualizing a dynamic picture of tumorigenesis is complicated by inter-individual heterogeneity. In the post genomic era, unraveling such complexity remains a challenge for the cancer biologist. Towards establishing a functional association between cellular crosstalk and differential cancer aggressiveness, we identified a signature of malignant breast epithelial response to stromal signaling. Proximity to fibroblasts resulted in gene transcript alterations of >2-fold for 107 probes, collectively designated as Fibroblast Triggered Gene Expression in Tumor (FTExT). The hazard ratio predicted by the FTExT classifier for distant relapse in patients with intermediate and high grade breast tumors was significant compared to routine clinical variables (dataset 1, n?=?258, HR--2.11, 95% CI 1.17-3.80, p-value 0.01; dataset 2, n?=?171, HR--3.07, 95% CI 1.21-7.83, p-value 0.01). Biofunctions represented by FTExT included inflammatory signaling, free radical scavenging, cell death, and cell proliferation. Unlike genes of the 'proliferation cluster', which are overexpressed in aggressive primary tumors, FTExT genes were uniquely repressed in such cases. As proof of concept for our correlative findings, which link stromal-epithelial crosstalk and tumor behavior, we show a distinctive differential in stromal impact on prognosis-defining functional endpoints of cell cycle progression, and resistance to therapy-induced growth arrest and apoptosis in low vs. high grade cancer cells. Our experimental data thus reveal aspects of 'paracrine cooperativity' that are exclusively contingent upon the histopathologically defined grade of interacting tumor epithelium, and demonstrate that epithelial responsiveness to the tumor microenvironment is a deterministic factor underlying clinical outcome. In this light, early attenuation of epithelial-stromal crosstalk could improve the management of cases prone to be clinically challenging.

View details for DOI 10.1371/journal.pone.0020016

View details for Web of Science ID 000290771200040

View details for PubMedID 21625507

Abstract

We aimed to investigate the molecular characteristics of Korean breast cancer. A cDNA microarray study (>42k clones) was performed on 69 breast cancers and three normal breast tissues. The subjects had a high percentage of HER-2 expression, hormone receptor negativity, and young onset. Molecular subtypes according to gene expression profiles were determined and their correlations to the clinicopathologic characteristics and patients outcome were analyzed. The tumors were subdivided into luminal-, normal breast-like, ERBB2+, and basal-like subtypes according to the correlations to the previously described intrinsic genes and five centroids. Only a few tumors were highly correlated to the luminal B and normal-like centroids. The high grade tumors with high p53 and Ki-67 were found more commonly in non-luminal tumors. Distant recurrence-free survival was worse in ERBB2+ and basal-like subgroups than luminal tumors. In an unsupervised clustering with 864 genes, many interesting gene clusters were observed, some of which had not been previously described. Although the Korean breast cancers showed generally similar molecular phenotypes as Western studies, some distinct gene expression patterns and their association to clinical outcomes were observed.

View details for DOI 10.3892/ijo_00000652

View details for Web of Science ID 000279135000007

View details for PubMedID 20514396

Abstract

Increasing data support cancer as a stem cell-based disease. Cancer stem cells (CSCs) have been found in different human cancers, and recent evidence indicates that breast cancer originates from and is maintained by its own CSCs, as well as the normal mammary gland. Mammary stem cells and breast CSCs have been identified and purified in in vitro culture systems, transplantation assays and/or by cell surface antigen identification. Cell surface markers enable the functional isolation of stem cells that can initiate and propagate tumorigenesis in mammary gland. These observations have dramatic biological and clinical significance due to increasing evidence suggesting that the recurrence of human cancer and treatment failure may reflect the intrinsic quiescence and drug resistance of CSCs. Thus, the CSC hypothesis provides fundamental implications for understanding breast carcinogenesis and for developing new strategies for breast cancer prevention and therapy for advanced disease. Further strategies to isolate breast CSCs, to find additional trustworthy surface markers, and to compare gene expression pathways profiles with their normal stem cells counterparts are necessary to more accurately define putative breast cell-lineage markers for the different cell types present in the mature mammary gland and to identify potential therapeutical targets in breast cancer. This review discusses the current knowledge about stem cells and CSCs, focusing on mammary stem cells and breast CSCs, and their consequences for breast tumorigenesis and implications for breast cancer susceptibility, prognosis, and treatment.

View details for Web of Science ID 000273387200010

View details for PubMedID 20054808

Abstract

DNA amplifications in breast cancer are frequent on chromosome 11q, in which multiple driver oncogenes likely reside in addition to cyclin D1 (CCND1). One such candidate, the scaffolding adapter protein, GRB2-associated binding protein 2 (GAB2), functions in ErbB signaling and was recently shown to enhance mammary epithelial cell proliferation, and metastasis of ERBB2 (HER2/neu)-driven murine breast cancer. However, the amplification status and function of GAB2 in the context of amplification remain undefined. In this study, by genomic profiling of 172 breast tumors, and fluorescence in situ hybridization validation in an independent set of 210 scorable cases, we observed focal amplification spanning GAB2 (11q14.1) independent of CCND1 (11q13.2) amplification, consistent with a driver role. Further, small interfering RNA (siRNA)-mediated knockdown of GAB2 in breast cancer lines (SUM52, SUM44PE and MDA468) with GAB2 amplification revealed a dependency on GAB2 for cell proliferation, cell-cycle progression, survival and invasion, likely mediated through altered phosphatidylinositol 3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) signaling. GAB2 knockdown also reduced proliferation and survival in a cell line (BT474) with ERBB2 amplification, consistent with the possibility that GAB2 can function downstream of ERBB2. Our studies implicate focal amplification of GAB2 in breast carcinogenesis, and underscore an oncogenic role of scaffolding adapter proteins, and a potential new point of therapeutic intervention.

View details for DOI 10.1038/onc.2009.364

View details for Web of Science ID 000274223700013

View details for PubMedID 19881546

Abstract

Tumours contain hypoxic regions that select for an aggressive cell phenotype; tumour hypoxia induces metastasis-associated genes. Treatment refractory patients with metastatic cancer show increased numbers of circulating tumour cells (CTCs), which are also associated with disease progression. The aim of this study was to examine the as yet unknown relationship between hypoxia and CTCs.We generated human MDA-MB-231 orthotopic xenografts and, using a new technology, isolated viable human CTCs from murine blood. The CTCs and parental MDA-MB-231 cells were incubated at 21 and 0.2% (hypoxia) oxygen, respectively. Colony formation was assayed and levels of hypoxia- and anoxia-inducible factors were measured. Xenografts generated from CTCs and parental cells were compared.MDA-MB-231 xenografts used to generate CTCs were hypoxic, expressing hypoxia factors: hypoxia-inducible factor1 alpha (HIF1alpha) and glucose transporter protein type 1 (GLUT1), and anoxia-induced factors: activating transcription factor 3 and 4 (ATF3 and ATF4). Parental MDA-MB-231 cells induced ATF3 in hypoxia, whereas CTCs expressed it constitutively. Asparagine synthetase (ASNS) expression was also higher in CTCs. Hypoxia induced ATF4 and the HIF1alpha target gene apelin in CTCs, but not in parental cells. Hypoxia induced lower levels of carbonic anhydrase IX (CAIX), GLUT1 and BCL2/adenovirus E1B 19-KD protein-interacting protein 3 (BNIP3) proteins in CTCs than in parental cells, supporting an altered hypoxia response. In chronic hypoxia, CTCs demonstrated greater colony formation than parental cells. Xenografts generated from CTCs were larger and heavier, and metastasised faster than MDA-MB-231 xenografts.CTCs show an altered hypoxia response and an enhanced aggressive phenotype in vitro and in vivo.

View details for DOI 10.1038/sj.bjc.6605491

View details for Web of Science ID 000274194700015

View details for PubMedID 20051957

Abstract

The enumeration of rare circulating epithelial cells (CEpCs) in the peripheral blood of metastatic cancer patients has shown promise for improved cancer prognosis. Moving beyond enumeration, molecular analysis of CEpCs may provide candidate surrogate endpoints to diagnose, treat, and monitor malignancy directly from the blood samples. Thorough molecular analysis of CEpCs requires the development of new sample preparation methods that yield easily accessible and purified CEpCs for downstream biochemical assays. Here, we describe a new immunomagnetic cell separator, the MagSweeper, which gently enriches target cells and eliminates cells that are not bound to magnetic particles. The isolated cells are easily accessible and can be extracted individually based on their physical characteristics to deplete any cells nonspecifically bound to beads. We have shown that our device can process 9 mL of blood per hour and captures >50% of CEpCs as measured in spiking experiments. We have shown that the separation process does not perturb the gene expression of rare cells. To determine the efficiency of our platform in isolating CEpCs from patients, we have isolated CEpCs from all 47 tubes of 9-mL blood samples collected from 17 women with metastatic breast cancer. In contrast, we could not find any circulating epithelial cells in samples from 5 healthy donors. The isolated CEpCs are all stored individually for further molecular analysis.

View details for DOI 10.1073/pnas.0813188106

View details for Web of Science ID 000264036900059

View details for PubMedID 19234122

Abstract

Breast cancer exhibits clinical and molecular heterogeneity, where expression profiling studies have identified five major molecular subtypes. The basal-like subtype, expressing basal epithelial markers and negative for estrogen receptor (ER), progesterone receptor (PR) and HER2, is associated with higher overall levels of DNA copy number alteration (CNA), specific CNAs (like gain on chromosome 10p), and poor prognosis. Discovering the molecular genetic basis of tumor subtypes may provide new opportunities for therapy. To identify the driver oncogene on 10p associated with basal-like tumors, we analyzed genomic profiles of 172 breast carcinomas. The smallest shared region of gain spanned just seven genes at 10p13, including calcium/calmodulin-dependent protein kinase ID (CAMK1D), functioning in intracellular signaling but not previously linked to cancer. By microarray, CAMK1D was overexpressed when amplified, and by immunohistochemistry exhibited elevated expression in invasive carcinomas compared to carcinoma in situ. Engineered overexpression of CAMK1D in non-tumorigenic breast epithelial cells led to increased cell proliferation, and molecular and phenotypic alterations indicative of epithelial-mesenchymal transition (EMT), including loss of cell-cell adhesions and increased cell migration and invasion. Our findings identify CAMK1D as a novel amplified oncogene linked to EMT in breast cancer, and as a potential therapeutic target with particular relevance to clinically unfavorable basal-like tumors.

View details for DOI 10.1016/j.molonc.2008.09.004

View details for Web of Science ID 000264062400005

View details for PubMedID 19383354

Abstract

Triple-negative breast cancer (TNBC) is defined by a lack of expression of estrogen, progesterone, and HER2 receptors, and genetically most of them fall into the basal subgroup of breast cancer. The important issue of TNBC is poorer clinical outcome and absence of effective targeted therapy. In this study, we sought to identify DNA copy number alterations and expression of relevant genes characteristic of TNBC to discover potential therapeutic targets. Frozen tissues from 114 breast cancers were analyzed using high-resolution array comparative genomic hybridization. The classification into subtype was determined by estrogen and progesterone receptor expression, and by the presence or absence of gain on the ERBB2 containing clone. The ACE algorithm was used for calling gain and loss of clones. Twenty-eight cases (25%) were classified as TNBC. Recurrent gains (> or =25%) unique to TNBC were 9p24-p21, 10p15-p13, 12p13, 13q31-q34, 18q12, 18q21-q23, and 21q22. Two published gene expression array data sets comparing basal subtype versus other subtype breast cancers were used for searching candidate genes. Of the genes upregulated in the basal subtype, 45 of 686 genes in one data set and 59 of 1,428 in the second data set were found to be located in the gained regions. Of these candidate genes, gain of NFIB (9p24.1) was specific for TNBC in a validation set by real-time PCR. In conclusion, we have identified recurrently gained regions characteristic of TNBC, and found that NFIB copy number and expression is increased in TNBC across the data sets. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.

View details for DOI 10.1002/gcc.20550

View details for Web of Science ID 000255386700005

View details for PubMedID 18314908

Abstract

The introduction of global gene expression analysis in breast cancer research has focused attention onto a repeatedly described subgroup of invasive breast cancer, the basal-like carcinomas. This subgroup is characterised by the expression of high-molecular weight cytokeratins 5, 14 and 17; using immunohistochemical diagnosis, it represents approximately 7-20% of invasive breast cancers. Some of these tumours fulfil the criteria of grade 3 invasive ductal carcinoma, the so-called triple negative carcinomas. However, other rare subgroups of metaplastic, medullary and myoepithelial carcinomas also belong to this entity. Even though the initial clinical prognostic relevance of basal-like breast cancers may have been overestimated, its distinctive biology generates many questions regarding the pathogenesis, chemosensitivity and optimal clinical management of this subgroup. Physiological progenitor cells within the normal female breast share essential immunohistochemical features with basal-like breast cancers. Although the exact relationship between subgroups of normal breast cells and their respective malignant counterparts is still under investigation, the major hallmarks of physiological progenitor cells are either maintained or reactivated by distinct genetic changes in basal breast cancer cells. This review will discuss the impact of these findings on our global understanding of breast cancer pathogenesis, especially from the perspective of its potential histogenesis. Clinical consequences and potential future research directions driven by the definition of basal breast cancers will also be discussed.

View details for DOI 10.1136/jcp.2008.055475

View details for Web of Science ID 000255326200003

View details for PubMedID 18326009

View details for DOI 10.1038/nbt0408-400

View details for Web of Science ID 000254782500020

View details for PubMedID 18392022

Abstract

Current practice is to perform a completion axillary lymph node dissection (ALND) for breast cancer patients with tumor-involved sentinel lymph nodes (SLNs), although fewer than half will have non-sentinel node (NSLN) metastasis. Our goal was to develop new models to quantify the risk of NSLN metastasis in SLN-positive patients and to compare predictive capabilities to another widely used model.We constructed three models to predict NSLN status: recursive partitioning with receiver operating characteristic curves (RP-ROC), boosted Classification and Regression Trees (CART), and multivariate logistic regression (MLR) informed by CART. Data were compiled from a multicenter Northern California and Oregon database of 784 patients who prospectively underwent SLN biopsy and completion ALND. We compared the predictive abilities of our best model and the Memorial Sloan-Kettering Breast Cancer Nomogram (Nomogram) in our dataset and an independent dataset from Northwestern University.285 patients had positive SLNs, of which 213 had known angiolymphatic invasion status and 171 had complete pathologic data including hormone receptor status. 264 (93%) patients had limited SLN disease (micrometastasis, 70%, or isolated tumor cells, 23%). 101 (35%) of all SLN-positive patients had tumor-involved NSLNs. Three variables (tumor size, angiolymphatic invasion, and SLN metastasis size) predicted risk in all our models. RP-ROC and boosted CART stratified patients into four risk levels. MLR informed by CART was most accurate. Using two composite predictors calculated from three variables, MLR informed by CART was more accurate than the Nomogram computed using eight predictors. In our dataset, area under ROC curve (AUC) was 0.83/0.85 for MLR (n = 213/n = 171) and 0.77 for Nomogram (n = 171). When applied to an independent dataset (n = 77), AUC was 0.74 for our model and 0.62 for Nomogram. The composite predictors in our model were the product of angiolymphatic invasion and size of SLN metastasis, and the product of tumor size and square of SLN metastasis size.We present a new model developed from a community-based SLN database that uses only three rather than eight variables to achieve higher accuracy than the Nomogram for predicting NSLN status in two different datasets.

View details for DOI 10.1186/1471-2407-8-66

View details for Web of Science ID 000255935500001

View details for PubMedID 18315887

Abstract

To prospectively determine if estrogen receptor (ER)-negative human epidermal growth factor receptor type 2 (HER2)-positive and ER-negative HER2-negative breast cancers have distinguishing clinical and imaging features with use of retrospectively identified patients and tissue samples.This HIPAA-compliant study was institutional review board approved. Informed consent was obtained from living patients and waived for deceased patients. Mean patient age at diagnosis was 53 years (range, 31-84 years). Clinical history; histopathologic, mammographic, and breast sonographic findings; and HER2 status as determined with immunohistochemistry or fluorescent in situ hybridization were evaluated in 56 women with ER-negative breast cancer. Imaging appearances and clinicopathologic characteristics were correlated with tumor HER2 status. P < .05 indicated a significant difference.Lesion margins on mammograms (P = .028) and sonograms (P = .023), calcifications on mammograms (P = .003), and clinical cancer stage at diagnosis (P = .029) were significantly associated with HER2 status. In contrast to ER-negative HER2-negative tumors, ER-negative HER2-positive tumors were more likely to have spiculated margins (56% vs 15%), be associated with calcifications (65% vs 21%), and be detected at a higher cancer stage (74% vs 57%).Biologic diversity of cancers may manifest in imaging characteristics, and, conversely, studying the range of imaging features of cancers may help refine current molecular phenotypes.

View details for DOI 10.1148/radio1.2462070169

View details for Web of Science ID 000252796300005

View details for PubMedID 18180338

Abstract

This study was designed to demonstrate the feasibility of MRI-guided radiofrequency ablation (RFA) of breast cancer. A total of three women diagnosed with invasive ductal breast cancer were treated with percutaneous MRI-guided RFA, according to a treat and resect protocol, in our hospital. RFA procedures were performed in an open 0.5T Signa-SP imager allowing direct patient access and real-time monitoring of the procedure. In all patients ablation was performed with a 15-gauge insulated MRI-compatible multiple needle probe. MRI thermometry and contrast-enhanced postablation MRI were used to evaluate the ablation process. Patients underwent lumpectomy within a week of the RFA procedure. Histopathology confirmed successful (100%) tumor ablation in one patient, and partial tumor destruction (33% and 50%, respectively) in two patients. Challenges of MRI-guided breast RFA that need to be solved to facilitate progress of the technique toward clinical practice are discussed.

View details for DOI 10.1002/jmri.21190

View details for Web of Science ID 000252104100029

View details for PubMedID 18050333

Abstract

The development of protocols for RNA extraction from paraffin-embedded samples facilitates gene expression studies on archival samples with known clinical outcome. Older samples are particularly valuable because they are associated with longer clinical follow up. RNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue is problematic due to chemical modifications and continued degradation over time. We compared quantity and quality of RNA extracted by four different protocols from 14 ten year old and 14 recently archived (three to ten months old) FFPE breast cancer tissues. Using three spin column purification-based protocols and one magnetic bead-based protocol, total RNA was extracted in triplicate, generating 336 RNA extraction experiments. RNA fragment size was assayed by reverse transcription-polymerase chain reaction (RT-PCR) for the housekeeping gene glucose-6-phosphate dehydrogenase (G6PD), testing primer sets designed to target RNA fragment sizes of 67 bp, 151 bp, and 242 bp.Biologically useful RNA (minimum RNA integrity number, RIN, 1.4) was extracted in at least one of three attempts of each protocol in 86-100% of older and 100% of recently archived ("months old") samples. Short RNA fragments up to 151 bp were assayable by RT-PCR for G6PD in all ten year old and months old tissues tested, but none of the ten year old and only 43% of months old samples showed amplification if the targeted fragment was 242 bp.All protocols extracted RNA from ten year old FFPE samples with a minimum RIN of 1.4. Gene expression of G6PD could be measured in all samples, old and recent, using RT-PCR primers designed for RNA fragments up to 151 bp. RNA quality from ten year old FFPE samples was similar to that extracted from months old samples, but quantity and success rate were generally higher for the months old group. We preferred the magnetic bead-based protocol because of its speed and higher quantity of extracted RNA, although it produced similar quality RNA to other protocols. If a chosen protocol fails to extract biologically useful RNA from a given sample in a first attempt, another attempt and then another protocol should be tried before excluding the case from molecular analysis.

View details for DOI 10.1186/1471-2199-8-118

View details for Web of Science ID 000253110900001

View details for PubMedID 18154675

Abstract

An improved understanding of cell immortalization and its manifestation in clinical tumors could facilitate novel therapeutic approaches. However, only rare tumor cells, which maintain telomerase expression in vitro, immortalize spontaneously. By expression-profiling analyses of limited-life primary breast tumor cultures pre- and post-hTERT transduction, and spontaneously immortalized breast cancer cell lines, we identified a common signature characteristic of tumor cell immortalization. A predominant feature of this immortalization signature (ImmSig) was the significant overexpression of oxidoreductase genes. In contrast to epithelial cells derived from low histologic grade primary tumors, which required hTERT transduction for the acquisition of ImmSig, spontaneously immortalizing high-grade tumor cultures displayed similar molecular changes independent of exogenous hTERT. Silencing the hTERT gene reversed ImmSig expression, increased cellular reactive oxygen species levels, altered mitochondrial membrane potential and induced apoptotic and proliferation changes in immortalized cells. In clinical breast cancer samples, cell-proliferation-pathway genes were significantly associated with ImmSig. In these cases, ImmSig expression itself was inversely correlated with patient survival (P=0), and was particularly relevant to the outcome of estrogen receptor-positive tumors. Our data support the notion that ImmSig assists in surmounting normal barriers related to oxidative and replicative stress response. Targeting a subset of aggressive breast cancers by reversing ImmSig components could be a practical therapeutic strategy.

View details for DOI 10.1038/sj.1210452

View details for Web of Science ID 000249583300003

View details for PubMedID 17471242

Abstract

Genomic high-throughput technology generates massive data, providing opportunities to understand countless facets of the functioning genome. It also raises profound issues in identifying data relevant to the biology being studied.We introduce a method for the analysis of pathologic biology that unravels the disease characteristics of high dimensional data. The method, disease-specific genomic analysis (DSGA), is intended to precede standard techniques like clustering or class prediction, and enhance their performance and ability to detect disease. DSGA measures the extent to which the disease deviates from a continuous range of normal phenotypes, and isolates the aberrant component of data. In several microarray cancer datasets, we show that DSGA outperforms standard methods. We then use DSGA to highlight a novel subdivision of an important class of genes in breast cancer, the estrogen receptor (ER) cluster. We also identify new markers distinguishing ductal and lobular breast cancers. Although our examples focus on microarrays, DSGA generalizes to any high dimensional genomic/proteomic data.

View details for DOI 10.1093/bioinformatics/btm033

View details for Web of Science ID 000246293000006

View details for PubMedID 17277331

Abstract

Gene expression profiling of breast carcinomas has increased our understanding of the heterogeneous biology of this disease and promises to impact clinical care. The aim of this study was to evaluate the prognostic value of gene expression-based classification along with established prognostic markers and mutation status of the TP53 gene (tumour protein p53) in a group of breast cancer patients with long-term (12 to 16 years) follow-up.The clinical and histopathological parameters of 200 breast cancer patients were studied for their effects on clinical outcome using univariate/multivariate Cox regression. The prognostic impact of mutations in the TP53 gene, identified using temporal temperature gradient gel electrophoresis and sequencing, was also evaluated. Eighty of the samples were analyzed for gene expression using 42 K cDNA microarrays and the patients were assigned to five previously defined molecular expression groups. The strength of the gene expression based classification versus standard markers was evaluated by adding this variable to the Cox regression model used to analyze all samples.Both univariate and multivariate analysis showed that TP53 mutation status, tumor size and lymph node status were the strongest predictors of breast cancer survival for the whole group of patients. Analyses of the patients with gene expression data showed that TP53 mutation status, gene expression based classification, tumor size and lymph node status were significant predictors of survival. Breast cancer cases in the 'basal-like' and 'ERBB2+' gene expression subgroups had a very high mortality the first two years, while the 'highly proliferating luminal' cases developed the disease more slowly, showing highest mortality after 5 to 8 years. The TP53 mutation status showed strong association with the 'basal-like' and 'ERBB2+' subgroups, and tumors with mutation had a characteristic gene expression pattern.TP53 mutation status and gene-expression based groups are important survival markers of breast cancer, and these molecular markers may provide prognostic information that complements clinical variables. The study adds experience and knowledge to an ongoing characterization and classification of the disease.

View details for DOI 10.1186/bcr1675

View details for Web of Science ID 000248673800010

View details for PubMedID 17504517

Abstract

High throughput DNA microarray technology has been broadly applied to the study of breast cancer to classify molecular subtypes, to predict outcome, survival, response to treatment, and for the identification of novel therapeutic targets. Although results are promising, this technology will not have a full impact on routine clinical practice until there is further standardization of techniques and optimal clinical trial design. Due to substantial disease heterogeneity and the number of genes being analyzed, collaborative, multi-institutional studies are required to accrue enough patients for sufficient statistical power. Newer bioinformatic approaches are being developed to assist with the analysis of this important data.

View details for DOI 10.1039/b618163e

View details for Web of Science ID 000247397700003

View details for PubMedID 17579771

Abstract

Previous studies demonstrated breast cancer tumor tissue samples could be classified into different subtypes based upon DNA microarray profiles. The most recent study presented evidence for the existence of five different subtypes: normal breast-like, basal, luminal A, luminal B, and ERBB2+.Based upon the analysis of 599 microarrays (five separate cDNA microarray datasets) using a novel approach, we present evidence in support of the most consistently identifiable subtypes of breast cancer tumor tissue microarrays being: ESR1+/ERBB2-, ESR1-/ERBB2-, and ERBB2+ (collectively called the ESR1/ERBB2 subtypes). We validate all three subtypes statistically and show the subtype to which a sample belongs is a significant predictor of overall survival and distant-metastasis free probability.As a consequence of the statistical validation procedure we have a set of centroids which can be applied to any microarray (indexed by UniGene Cluster ID) to classify it to one of the ESR1/ERBB2 subtypes. Moreover, the method used to define the ESR1/ERBB2 subtypes is not specific to the disease. The method can be used to identify subtypes in any disease for which there are at least two independent microarray datasets of disease samples.

View details for DOI 10.1186/1471-2164-7-231

View details for Web of Science ID 000240732900001

View details for PubMedID 16965636

Abstract

Breast cancer is diagnosed worldwide in approximately one million women annually and radiation therapy is an integral part of treatment. The purpose of this study was to investigate the molecular basis underlying response to radiotherapy in breast cancer tissue.Tumour biopsies were sampled before radiation and after 10 treatments (of 2 Gray (Gy) each) from 19 patients with breast cancer receiving radiation therapy. Gene expression microarray analyses were performed to identify in vivo radiation-responsive genes in tumours from patients diagnosed with breast cancer. The mutation status of the TP53 gene was determined by using direct sequencing.Several genes involved in cell cycle regulation and DNA repair were found to be significantly induced by radiation treatment. Mutations were found in the TP53 gene in 39% of the tumours and the gene expression profiles observed seemed to be influenced by the TP53 mutation status.

View details for DOI 10.1016/j.radonc.2006.07.007

View details for Web of Science ID 000240882300018

View details for PubMedID 16890317

Abstract

Magnetic resonance imaging (MRI) can detect clinically and mammographically occult breast lesions. In this study we report the results of MRI-guided needle localization of suspicious breast lesions by using a freehand technique. Preoperative MRI-guided single-needle localization was performed in 220 patients with 304 MRI-only breast lesions at our hospital between January 1997 and July 2004. Procedures were performed in an open 0.5-T Signa-SP imager allowing real-time monitoring, with patient in prone position, by using a dedicated breast coil. MRI-compatible hookwires were placed in a noncompressed breast by using a freehand technique. MRI findings were correlated with pathology and follow-up. MRI-guided needle localization was performed for a single lesion in 150 patients, for two lesions in 56 patients, and for three lesions in 14 patients. Histopathologic analysis of these 304 lesions showed 104 (34%) malignant lesions, 51 (17%) high-risk lesions, and 149 (49%) benign lesions. The overall lesion size ranged from 2.0-65.0 mm (mean 11.2 mm). No direct complications occurred. Follow-up MRI in 54 patients showed that two (3.7%) lesions were missed by surgical biopsy. MRI-guided freehand needle localization is accurate and allows localization of lesions anterior in the breast, the axillary region, and near the chest wall.

View details for DOI 10.1007/s00330-006-0214-5

View details for Web of Science ID 000238860700022

View details for PubMedID 16683117

Abstract

Metastasis is a multistep process responsible for most cancer deaths, and it can be influenced by both the immediate microenvironment (cell-cell or cell-matrix interactions) and the extended tumour microenvironment (for example vascularization). Hypoxia (low oxygen) is clinically associated with metastasis and poor patient outcome, although the underlying processes remain unclear. Microarray studies have shown the expression of lysyl oxidase (LOX) to be elevated in hypoxic human tumour cells. Paradoxically, LOX expression is associated with both tumour suppression and tumour progression, and its role in tumorigenesis seems dependent on cellular location, cell type and transformation status. Here we show that LOX expression is regulated by hypoxia-inducible factor (HIF) and is associated with hypoxia in human breast and head and neck tumours. Patients with high LOX-expressing tumours have poor distant metastasis-free and overall survivals. Inhibition of LOX eliminates metastasis in mice with orthotopically grown breast cancer tumours. Mechanistically, secreted LOX is responsible for the invasive properties of hypoxic human cancer cells through focal adhesion kinase activity and cell to matrix adhesion. Furthermore, LOX may be required to create a niche permissive for metastatic growth. Our findings indicate that LOX is essential for hypoxia-induced metastasis and is a good therapeutic target for preventing and treating metastases.

View details for DOI 10.1038/nature04695

View details for Web of Science ID 000237080000052

View details for PubMedID 16642001

Abstract

This paper presents a novel device which provides the opportunity to perform high-throughput biochemical assays on different individual cells. In particular, the proposed device is suited to screen the rare cells in biological samples for early stage cancer diagnosis and explore their biochemical functionality. In the process, single cells are precisely positioned and captured in activated micropores. To show the performance of the proposed device, cultured yeast cells and human epithelial circulating tumor cells are successfully captured.

View details for PubMedID 17945673

View details for Web of Science ID 000247284701134

Abstract

Achieving information content of satisfactory breadth and depth remains a formidable challenge for proteomics. This problem is particularly relevant to the study of primary human specimens, such as tumor biopsies, which are heterogeneous and of finite quantity. Here we present a functional proteomics strategy that unites the activity-based protein profiling and multidimensional protein identification technologies (ABPP-MudPIT) for the streamlined analysis of human samples. This convergent platform involves a rapid initial phase, in which enzyme activity signatures are generated for functional classification of samples, followed by in-depth analysis of representative members from each class. Using this two-tiered approach, we identified more than 50 enzyme activities in human breast tumors, nearly a third of which represent previously uncharacterized proteins. Comparison with cDNA microarrays revealed enzymes whose activity, but not mRNA expression, depicted tumor class, underscoring the power of ABPP-MudPIT for the discovery of new markers of human disease that may evade detection by other molecular profiling methods.

View details for DOI 10.1038/NMETH778

View details for Web of Science ID 000235261900022

View details for PubMedID 16118640

View details for Web of Science ID 000229951900035

View details for PubMedID 15972423

Abstract

Our objective was to evaluate the breast cancer risk associated with body burden levels of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs).We conducted a hospital-based case-control study among 79 women diagnosed with invasive breast cancer and 52 controls diagnosed with benign breast conditions. We collected breast adipose tissue and analyzed it for all 17 2,3,7,8-substitituted PCDD/PCDFs. We used unconditional logistic regression to calculate age- and race-adjusted exposure-specific odds ratios (ORs) and 95% confidence intervals (CI) for each individual PCDD/PCDF congener as well as for the summary measures (I-TEQ, Adj-TEQ).Dioxin levels were consistent with reports from other small, contemporary studies of body burdens in the U.S. None of the odds ratios for any of the congeners or summary measures differed significantly from one. Especially for the PCDF congeners, point estimates tended to be below one. One notable exception was octachlorodibenzo-p-dioxin (OCDD), for which the odds ratio for the second and third tertiles appeared modestly elevated (OR = 1.22, 95% CI: 0.47:3.16 and OR = 1.62, 95% CI: 0.64:4.12, respectively), though the test for trend was not significant (p = 0.36).Breast cancer risk was not associated with adipose levels of PCDD/PCDFs. More study is suggested among women of color who may have higher body burden levels of these compounds.

View details for DOI 10.1007/s10552-004-7840-5

View details for Web of Science ID 000230174900006

View details for PubMedID 15986107

Abstract

Breast cancer is a heterogeneous disease. DNA microarray technology is being applied to breast cancer to identify new prognostic biomarkers, to predict response to therapy, and to discover targets for the development of novel therapies. New diagnostic assays based on global gene expression are being introduced into clinical practice or tested in large-scale clinical trials. This review focuses on translational studies using microarray analyses and discusses best practice features and pitfalls. We note that factors that predict metastatic disease are not necessarily the same factors that predict therapeutic response. We believe that the characterization and discernment of different systems among breast cancers is crucial for understanding drug sensitivity and resistance mechanisms and for guiding therapy.

View details for PubMedID 16002001

Abstract

We performed this study to determine rates of close or transected cancer margins after magnetic resonance imaging-guided bracket wire localization for nonpalpable breast lesions.Of 243 women undergoing MRI-guided wire localizations, 26 had MRI bracket wire localization to excise either a known cancer (n = 19) or a suspicious MRI-detected lesion (n = 7). We reviewed patient age, preoperative diagnosis, operative intent, mammographic breast density, MRI lesion size, MRI enhancement curve and morphology, MRI Breast Imaging Reporting and Data System (BI-RADS) assessment code, number of bracket wires, and pathology size. We analyzed these findings for their relationship to obtaining clear margins at first operative excision.Twenty-one of 26 (81%) patients had cancer. Of 21 patients with cancer, 12 (57%) had negative margins at first excision and 9 (43%) had close/transected margins. MRI size > or = 4 cm was associated with a higher reexcision rate (7 of 9, 78%) than those < 4 cm (2 of 12, 17%) (p = 0.009). MRI BI-RADS score, enhancement curve, morphology, and preoperative core biopsy demonstrating ductal carcinoma in situ (DCIS) were not predictive of reexcision. The average number of wires used for bracketing increased with lesion size, but was not associated with improved outcomes. On pathology, cancer size was smaller in patients with negative margins (12 patients, 1.2 cm) than in those with close/transected margins (9 patients, 4.6 cm) (p < 0.001). Reexcision was based on close/transected margins involving DCIS alone (6, 67%), infiltrating ductal carcinoma and DCIS (2, 22%), or infiltrating ductal carcinoma alone (1, 11%). Reexcision pathology demonstrated DCIS (3, 33%), no residual cancer (5, 55%), and 1 patient was lost to followup (1, 11%). Interestingly, cancer patients who required reexcision were younger (p = 0.022), but breast density was not associated with reexcision.To our knowledge, this is the first report of MRI-guided bracket wire localization. Patients with MRI-detected lesions less than 4 cm had clear margins at first excision; larger MRI-detected lesions were more likely to have close/transected margins. Reexcision was often because of DCIS and was the only pathology found at reexcision, perhaps because MRI is more sensitive for detecting invasive carcinoma than DCIS.

View details for DOI 10.1016/j.jamcollsurg.2004.12.013

View details for Web of Science ID 000228085200005

View details for PubMedID 15804466

Abstract

Breast conservation therapy (BCT) is a safe, effective alternative to mastectomy for many women with newly diagnosed breast cancer. This approach involves local excision of the malignancy with tumor-free margins, followed by 5-7 weeks of external beam whole breast (WB) radiotherapy (XRT) to minimize the risk of an in-breast tumor recurrence (IBTR). Though clearly beneficial, the extended course of almost daily postoperative radiotherapy interrupts normal activities and lengthens care. Additional options are now available that shorten the radiotherapy treatment time to 1-5 days (accelerated) and focus an increased dose of radiation on just the breast tissue around the excision cavity (partial breast). Recent trials with accelerated, partial breast irradiation (APBI) have shown promise as a potential replacement to the longer, whole breast treatments for select women with early-stage breast cancer. Current APBI approaches include interstitial brachytherapy, intracavitary (balloon) brachytherapy, and accelerated external beam (3-D conformal) radiotherapy, all of which normally complete treatment over 5 days, while intraoperative radiotherapy (IORT) condenses the entire treatment into a single dose delivered immediately after tumor excision. Each approach has benefits and limitations. This study covers over 2 decades of clinical trials exploring APBI, discusses treatment variables that appear necessary for successful implementation of this new form of radiotherapy, compares and contrasts the various APBI approaches, and summarizes current and planned randomized trials that will shape if and how APBI is introduced into routine clinical care. Some of the more important outcome variables from these trials will be local toxicity, local and regional recurrence, and overall survival. If APBI options are ultimately demonstrated to be as safe and effective as current whole breast radiotherapy approaches, breast conservation may become an even more appealing choice, and the overall impact of treatment may be further reduced for certain women with newly diagnosed breast cancer.

View details for Web of Science ID 000226744200003

View details for PubMedID 15665616

Abstract

The purpose of this study was to assess the utility of contrast-enhanced breast magnetic resonance imaging (MRI) in identifying lesions unidentified on the craniocaudal projection. The authors reviewed five patients with suspicious mammographic lesions not imaged on the craniocaudal mammogram who were referred for contrast-enhanced MRI and underwent subsequent preoperative needle localization in four of the five cases. Five patients, ages 56 to 69 years, had suspicious lesions identified on mediolateral oblique (MLO) or mediolateral (ML) projections only. Ultrasound did not identify the lesion in any of these cases. MRI identified suspicious breast lesions measuring 5 to 12 mm in size. These were located high on the chest wall or in the upper inner quadrant. Suspicious lesions seen only on the MLO or ML projections may reside high on the chest wall or in the upper inner quadrant. Lesions in these locations may be typically excluded on the craniocaudal projection during mammography. Breast MRI has the advantage of imaging the entire breast and is particularly useful for these lesions. In this series, MRI prevented delay in breast cancer diagnosis.

View details for PubMedID 15327495

Abstract

To identify the spectrum of malignant attributes maintained outside the host environment, we have compared global gene expression in primary breast tumors and matched short-term epithelial cultures.In contrast to immortal cell lines, a characteristic 'limited proliferation' phenotype was observed, which included over expressed genes associated with the TGFbeta signal transduction pathway, such as SPARC, LOXL1, RUNX1, and DAPK1. Underlying this profile was the conspicuous absence of hTERT expression and telomerase activity, a significant increase in TbetaRII, its cognate ligand, and the CDK inhibitor, p21CIP1/WAF1. Concurrently, tumor tissue and primary cultures displayed low transcript levels of proliferation-related genes, such as, TOP2A, ANKT, RAD51, UBE2C, CENPA, RRM2, and PLK.Our data demonstrate that commonly used immortal cell lines do not reflect some aspects of tumor biology as closely as primary tumor cell cultures. The gene expression profile of malignant tissue, which is uniquely retained by cells cultured on solid substrates, could facilitate the development and testing of novel molecular targets for breast cancer.

View details for DOI 10.1186/1471-2164-5-47

View details for Web of Science ID 000223187800001

View details for PubMedID 15260889

Abstract

Invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) are the two major histological types of breast cancer worldwide. Whereas IDC incidence has remained stable, ILC is the most rapidly increasing breast cancer phenotype in the United States and Western Europe. It is not clear whether IDC and ILC represent molecularly distinct entities and what genes might be involved in the development of these two phenotypes. We conducted comprehensive gene expression profiling studies to address these questions. Total RNA from 21 ILCs, 38 IDCs, two lymph node metastases, and three normal tissues were amplified and hybridized to approximately 42,000 clone cDNA microarrays. Data were analyzed using hierarchical clustering algorithms and statistical analyses that identify differentially expressed genes (significance analysis of microarrays) and minimal subsets of genes (prediction analysis for microarrays) that succinctly distinguish ILCs and IDCs. Eleven of 21 (52%) of the ILCs ("typical" ILCs) clustered together and displayed different gene expression profiles from IDCs, whereas the other ILCs ("ductal-like" ILCs) were distributed between different IDC subtypes. Many of the differentially expressed genes between ILCs and IDCs code for proteins involved in cell adhesion/motility, lipid/fatty acid transport and metabolism, immune/defense response, and electron transport. Many genes that distinguish typical and ductal-like ILCs are involved in regulation of cell growth and immune response. Our data strongly suggest that over half the ILCs differ from IDCs not only in histological and clinical features but also in global transcription programs. The remaining ILCs closely resemble IDCs in their transcription patterns. Further studies are needed to explore the differences between ILC molecular subtypes and to determine whether they require different therapeutic strategies.

View details for DOI 10.1091/mbc.E03-11-0786

View details for Web of Science ID 000221778300001

View details for PubMedID 15034139

Abstract

We sought to determine differences between concentrations of persistent, lipid-soluble chemical contaminants in breast and abdominal adipose tissues and to explore whether concentrations measured in one tissue could predict concentrations in the other tissue.We analyzed surgical specimens and measured concentrations of prevalent dioxins, furans, polychlorinated biphenyls, organochlorine pesticides, and brominated diphenyl ethers to determine their partitioning between breast and abdominal adipose tissues of 21 women. The women constituted a subgroup, undergoing mastectomies with simultaneous breast reconstruction, of a case-control study evaluating links between breast cancer and body burdens of organohalogen contaminants.For every contaminant, differences between concentrations in breast and abdominal adipose tissues did not exceed the analytical error. Results indicated that, with some notable exceptions, measurements in breast and abdominal adipose tissues were correlated and that concentrations of target chemicals in one tissue could be derived from measurements in the other tissue.This information will allow comparison of results from body burden studies that used different tissues. It may also facilitate future breast cancer studies by allowing selection of controls among patients undergoing surgical procedures other than breast surgery, minimizing concerns about overmatching. We also observed large differences in the lipid content of surgical specimens. These differences underscore the need for lipid adjustment of concentrations to avoid misclassification.

View details for Web of Science ID 000220081000014

View details for PubMedID 15006918

Abstract

To identify predictors of reexcision findings and local recurrence in the setting of breast-conserving therapy with radiation.The records of 535 patients who underwent breast-conserving surgery followed by radiation for Stage I or II cancer between 1972 and 1996 were reviewed. The mean follow-up period for surviving patients without evidence of recurrence is 6 years. Various clinical and pathologic prognostic factors were examined for significance with regard to reexcision findings and recurrence rates. Pathologic margin status was classified as negative, close (

View details for DOI 10.1016/S0360-3016(03)00740-5

View details for Web of Science ID 000186293800010

View details for PubMedID 14575828

Abstract

Array-based comparative genomic hybridization, RNA expression profiling, and proteomic analyses are new molecular technologies used to study breast cancer. Invasive breast cancers were originally evaluated because they provided ample quantities of DNA, RNA, and protein. The application of these technologies to pre-invasive breast lesions is discussed, including methods that facilitate their implementation. Data indicate that atypical ductal hyperplasia and ductal carcinoma in situ are precursor lesions molecularly similar to adjacent invasive breast cancer. It is expected that molecular technologies will identify breast tissue at risk for the development of unfavorable subtypes of invasive breast cancer and reveal strategies for targeted chemoprevention or eradication.

View details for DOI 10.1186/bcr655

View details for Web of Science ID 000185946100009

View details for PubMedID 14580250

Abstract

Genomic DNA copy number alterations are key genetic events in the development and progression of human cancers. Here we report a genome-wide microarray comparative genomic hybridization (array CGH) analysis of DNA copy number variation in a series of primary human breast tumors. We have profiled DNA copy number alteration across 6,691 mapped human genes, in 44 predominantly advanced, primary breast tumors and 10 breast cancer cell lines. While the overall patterns of DNA amplification and deletion corroborate previous cytogenetic studies, the high-resolution (gene-by-gene) mapping of amplicon boundaries and the quantitative analysis of amplicon shape provide significant improvement in the localization of candidate oncogenes. Parallel microarray measurements of mRNA levels reveal the remarkable degree to which variation in gene copy number contributes to variation in gene expression in tumor cells. Specifically, we find that 62% of highly amplified genes show moderately or highly elevated expression, that DNA copy number influences gene expression across a wide range of DNA copy number alterations (deletion, low-, mid- and high-level amplification), that on average, a 2-fold change in DNA copy number is associated with a corresponding 1.5-fold change in mRNA levels, and that overall, at least 12% of all the variation in gene expression among the breast tumors is directly attributable to underlying variation in gene copy number. These findings provide evidence that widespread DNA copy number alteration can lead directly to global deregulation of gene expression, which may contribute to the development or progression of cancer.

View details for DOI 10.1073/pnas.162471999

View details for Web of Science ID 000178391700085

View details for PubMedID 12297621

Abstract

Our study aimed to correlate the dynamic contrast-enhanced MR appearance of infiltrating lobular carcinoma of the breast with histopathologic findings.We retrospectively reviewed the high-resolution, fat-suppressed and dynamic contrast-enhanced MR images of 13 of 20 women diagnosed with pathologically proven infiltrating lobular carcinoma of the breast. Twelve of the 13 women presented with breast symptoms and underwent mammography. Five of the women also had breast sonography. MR imaging was performed for evaluation of disease extent before the patients underwent modified radical mastectomy (n = 11) or lumpectomy (n = 2). Three experienced radiologists reviewed the MR scans. The tumor pattern types described on imaging were correlated with a detailed analysis of the pathology.We found three patterns of infiltrating lobular carcinoma on MR imaging. The tumor pattern on imaging correlated with pathologic tumor morphology. We found the following patterns of infiltrating lobular carcinoma: a solitary mass with irregular margins (n = 4) that corresponded to the same appearance at pathology; multiple lesions, either connected by enhancing strands (n = 6) or separated by nonenhancing intervening tissue (n = 2), that correlated with the pathologic appearance of noncontiguous tumor foci, with malignant cells streaming in single-file fashion in the breast stroma or small tumor aggregates separated by normal tissue; and enhancing septa only, which were correlated with the histopathologic appearance of tumor cells streaming in the breast stroma (n = 1).Infiltrating lobular carcinoma may be detected on MR imaging as solitary or multiple lesions that correspond to tumor morphology on pathologic examination. The appearance of multiple lesions or of enhancing fibroglandular breast elements on MR imaging is suggestive of infiltrating lobular carcinoma.

View details for Web of Science ID 000175077200034

View details for PubMedID 11959737

Abstract

The most common group of cancers among American women involves malignancies of the breast. Breast cancer is a complex disease, involving several different types of tissues and specific cells with various functions, that is categorized into many distinct subtypes. Microarray analysis has recently revealed that different biological subtypes of breast cancer are accompanied by differences in their specific gene expression profile. Because breast tissue (and breast cancer) is heterogeneous, microarray analysis may provide clinicians with a better understanding of how to treat each specific case. Thus, microarray analysis may translate basic research data into more confident diagnoses, specifically designed treatment regimens geared to each patient's needs, and better clinical prognoses.

View details for PubMedID 14993355

Abstract

T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays.Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified samples is 0.82 (0.85 when a virtual array was created using repeatedly amplified samples to minimize experimental variation). Less than 4% of genes show changes in expression level by 2-fold or greater after amplification compared to unamplified samples. Most changes due to amplification are not systematic both within one tumor sample and between different tumors. Amplification appears to dampen the variation of gene expression for some genes when compared to unamplified poly(A)+ RNA. The reproducibility between repeatedly amplified samples is 0.97 when performed on the same day, but drops to 0.90 when performed weeks apart. The fidelity and reproducibility of amplification is not affected by decreasing the amount of input total RNA in the 0.3-3 micrograms range. Adding template-switching primer, DNA ligase, or column purification of double-stranded cDNA does not improve the fidelity of amplification. The correlation coefficient between amplified and unamplified samples is higher when total RNA is used as template for both experimental and reference RNA amplification.T7 based linear amplification reproducibly generates amplified RNA that closely approximates original sample for gene expression profiling using cDNA microarrays.

View details for Web of Science ID 000181477100031

View details for PubMedID 12445333

Abstract

The purpose of this study was to classify breast carcinomas based on variations in gene expression patterns derived from cDNA microarrays and to correlate tumor characteristics to clinical outcome. A total of 85 cDNA microarray experiments representing 78 cancers, three fibroadenomas, and four normal breast tissues were analyzed by hierarchical clustering. As reported previously, the cancers could be classified into a basal epithelial-like group, an ERBB2-overexpressing group and a normal breast-like group based on variations in gene expression. A novel finding was that the previously characterized luminal epithelial/estrogen receptor-positive group could be divided into at least two subgroups, each with a distinctive expression profile. These subtypes proved to be reasonably robust by clustering using two different gene sets: first, a set of 456 cDNA clones previously selected to reflect intrinsic properties of the tumors and, second, a gene set that highly correlated with patient outcome. Survival analyses on a subcohort of patients with locally advanced breast cancer uniformly treated in a prospective study showed significantly different outcomes for the patients belonging to the various groups, including a poor prognosis for the basal-like subtype and a significant difference in outcome for the two estrogen receptor-positive groups.

View details for Web of Science ID 000170966800067

View details for PubMedID 11553815

Abstract

To compare patients with visualized sentinel lymph nodes (SLNs) and patients with nonvisualized SLNs, with a focus on variables affecting SLN visualization at preoperative lymphoscintigraphy and on nodal drainage basins as related to tumor location.One hundred thirty-six patients who had breast cancer underwent preoperative lymphoscintigraphy before SLN biopsy. Patients with visualized and nonvisualized SLNs were compared for age; tumor site, size, and histologic findings; injection guidance method; diagnostic biopsy type; interval between biopsy and lymphoscintigraphy; intraoperative identification method; and surgical identification rate. Visualized SLN drainage basins were noted.Ninety-nine patients had visualized and 37 had nonvisualized SLNs, without statistically significant differences in tumor site, size, and histologic findings; injection guidance method; diagnostic biopsy type; and interval between biopsy and lymphoscintigraphy. Ninety-nine (73%) of the 136 SLNs were visualized at lymphoscintigraphy; 30 (81%) of the 37 nonvisualized SLNS were identified at surgery. Of the seven SLNs not identified at surgery, five were mapped with radiocolloid only. Patients with nonvisualized SLNs were older than those with visualized SLNs. Eleven (46%) of 24 tumors with internal mammary drainage were in the outer part of the breast.Patients with and those without visualization differed in age, SLN identification at surgery, and surgical identification method. Nonvisualized status does not preclude axillary metastasis. In older patients with nonvisualized SLNs, blue dye may aid in SLN detection, as compared with isotope-only localization.

View details for Web of Science ID 000169468400007

View details for PubMedID 11425971

Abstract

A retrospective analysis of the treatment of locally advanced breast cancer (LABC) was undertaken at Stanford Medical Center to assess the outcome of patients who did not undergo surgical removal of their tumors. Between 1981 and 1998, 64 patients with locally advanced breast cancer were treated with induction chemotherapy, radiation with or without breast surgery, and additional chemotherapy. Sixty-two (97%) patients received cyclophosphamide, doxorubicin, and 5-fluorouracil (CAF) induction chemotherapy. Induction chemotherapy was followed by local radiotherapy in 59 (92%) patients. Based on the clinical response to chemotherapy and patient preference, 44 (69%) patients received no local breast surgery. Radiotherapy was followed by an additional, non-doxorubicin-containing chemotherapy in all patients. The mean age of patients was 49 years. Of the 65 locally advanced breast cancers in 64 patients, 26 (41%) were stage IIIA, 35 (55%) were stage IIIB, and 4 (6%) were stage IV (supraclavicular lymph nodes only). Response to induction chemotherapy was seen in 59 patients (92%), with 29 (45%) achieving a complete clinical response and 30 (47%) a partial clinical response. With a mean follow-up of 51 months (range 7-187 months), 43 patients (67.2%) have no evidence of recurrent disease. Eight (12.5%) have recurred locally, and 21 (32.8%) have recurred with distant metastasis. Actuarial 5-year survival is 75%, disease-free survival is 58%, and local control rate is 87.5%. These data indicate that the routine inclusion of breast surgery in a combined modality treatment program for LABC does not appear necessary for the majority of patients who experience a response to induction chemotherapy.

View details for PubMedID 11328324

View details for Web of Science ID 000172448200006

View details for PubMedID 11804185

Abstract

Certain vital dyes are known to cause pulse oximetry (Spo2) desaturation. The authors studied the effect of isosulfan blue (IB) on Spo2.Thirty-three women, aged 34-81 yr, who were undergoing surgery for breast cancer were studied. IB, 5 ml (50 mg), was injected intraparenchymally around the tumor area by the surgeon. A pulse oximeter was used to continuously record Spo2 values up to 130 min after IB injection. Friedman repeated-measures analysis of ranks was used to analyze the baseline Spo2 and values at 5, 10, 20, 30, 40, 50, and 60 min.Spo2 values were significantly different from baseline values at 5, 10, 20, 30, 40, 50, and 60 min (P < 0.05). In a typical patient, a maximum Spo2 decrease of 3% can be anticipated 25 min after injection of IB.After peritumoral administration of IB, 50 mg, a significant interference with Spo2 will occur.

View details for Web of Science ID 000089671900017

View details for PubMedID 11020754

Abstract

Human breast tumours are diverse in their natural history and in their responsiveness to treatments. Variation in transcriptional programs accounts for much of the biological diversity of human cells and tumours. In each cell, signal transduction and regulatory systems transduce information from the cell's identity to its environmental status, thereby controlling the level of expression of every gene in the genome. Here we have characterized variation in gene expression patterns in a set of 65 surgical specimens of human breast tumours from 42 different individuals, using complementary DNA microarrays representing 8,102 human genes. These patterns provided a distinctive molecular portrait of each tumour. Twenty of the tumours were sampled twice, before and after a 16-week course of doxorubicin chemotherapy, and two tumours were paired with a lymph node metastasis from the same patient. Gene expression patterns in two tumour samples from the same individual were almost always more similar to each other than either was to any other sample. Sets of co-expressed genes were identified for which variation in messenger RNA levels could be related to specific features of physiological variation. The tumours could be classified into subtypes distinguished by pervasive differences in their gene expression patterns.

View details for Web of Science ID 000088767700049

View details for PubMedID 10963602

Abstract

Sentinel lymph node biopsy, validated in melanoma staging, is currently under investigation for breast cancer staging. Reports suggest that the sentinel lymph node has a high predictive value in determining the presence of axillary metastases. Identification of a sentinel lymph node that is free of metastatic tumor cells may eliminate the necessity of performing a standard axillary lymph node dissection with its attendant morbidity. Numerous techniques are utilized to identify the sentinel node with approximately the same success rate. This paper will address some of the controversial areas of sentinel lymph node biopsy and offer an option for physicians who want to develop a sentinel lymph node program in their hospital.

View details for Web of Science ID 000088471700002

View details for PubMedID 10941529

Abstract

We used cDNA microarrays to explore the variation in expression of approximately 8,000 unique genes among the 60 cell lines used in the National Cancer Institute's screen for anti-cancer drugs. Classification of the cell lines based solely on the observed patterns of gene expression revealed a correspondence to the ostensible origins of the tumours from which the cell lines were derived. The consistent relationship between the gene expression patterns and the tissue of origin allowed us to recognize outliers whose previous classification appeared incorrect. Specific features of the gene expression patterns appeared to be related to physiological properties of the cell lines, such as their doubling time in culture, drug metabolism or the interferon response. Comparison of gene expression patterns in the cell lines to those observed in normal breast tissue or in breast tumour specimens revealed features of the expression patterns in the tumours that had recognizable counterparts in specific cell lines, reflecting the tumour, stromal and inflammatory components of the tumour tissue. These results provided a novel molecular characterization of this important group of human cell lines and their relationships to tumours in vivo.

View details for Web of Science ID 000085590600011

View details for PubMedID 10700174

Abstract

The purpose of the study was to determine the sensitivity and specificity of various morphologic criteria in distinguishing malignant from benign breast lesions using a new sequence (3DSSMT) performed immediately after dynamic breast MRI. 3DSSMT combines a water-selective spectral-spatial excitation and an on-resonance magnetization transfer pulse with three-dimensional spoiled gradient-echo imaging. Morphologic features of 87 pathologically confirmed lesions were analyzed. The presence of either skin thickening, or a combination of a spiculated or microlobulated border, with a rim, ductal, linear, or clumped enhancement pattern was 94% specific and 54% sensitive for malignancy. Conversely, the presence of either a perfectly smooth border, a well-defined margin, non-enhancing internal septations, or a macrolobulated border was 97% specific and 35% sensitive for a benign diagnosis. In conclusion, delayed 3DSSMT discriminates a significant number of benign and malignant breast lesions; it has the potential to improve the diagnostic accuracy of dynamic breast MRI.

View details for Web of Science ID 000086078100003

View details for PubMedID 10713939

Abstract

Radiofrequency (RF) energy applied to breast cancers will result in cancer cell death.Prospective nonrandomized interventional trial.A university hospital tertiary care center.Five women with locally advanced invasive breast cancer, aged 38 to 66 years, who were undergoing surgical resection of their tumor. One patient underwent preoperative chemotherapy and radiation therapy, 3 patients received preoperative chemotherapy, and 1 had no preoperative therapy. All patients completed the study.While patients were under general anesthesia and just before surgical resection, a 15-gauge insulated multiple-needle electrode was inserted into the tumor under sonographic guidance. Radiofrequency energy was applied at a low power by a preset protocol for a period of up to 30 minutes. Only a portion of the tumor was treated to evaluate the zone of RF ablation and the margin between ablated and nonablated tissue. Immediately after RF ablation, the tumor was surgically resected (4 mastectomies, 1 lumpectomy). Pathologic analysis included hematoxylin-eosin staining and enzyme histochemical analysis of cell viability with nicotinamide adenine dinucleotide-diaphorase (NADH-diaphorase) staining of snap-frozen tissue to assess immediate cell death.Cancer cell death as visualized on hematoxylin-eosin-stained paraffin section and NADH-diaphorase cell viability stains.There was evidence of cell death in all patients. Hematoxylin-eosin staining showed complete cell death in 2 patients. In 3 patients there was a heterogeneous pattern of necrotic and normal-appearing cells within the ablated tissue. The ablated zone extended around the RF electrode for a diameter of 0.8 to 1.8 cm. NADH-diaphorase cell viability stains of the ablated tissue showed complete cell death in 4 patients. The fifth patient had a single focus of viable cells (<1 mm) partially lining a cyst. There were no perioperative complications related to RF ablation.Intraoperative RF ablation results in invasive breast cancer cell death. Based on this initial report of the use of RF ablation in breast cancer, this technique merits further investigation as a percutaneous minimally invasive modality for the local treatment of breast cancer.

View details for Web of Science ID 000083020900010

View details for PubMedID 10522847

Abstract

Gene amplifications and deletions frequently contribute to tumorigenesis. Characterization of these DNA copy-number changes is important for both the basic understanding of cancer and its diagnosis. Comparative genomic hybridization (CGH) was developed to survey DNA copy-number variations across a whole genome. With CGH, differentially labelled test and reference genomic DNAs are co-hybridized to normal metaphase chromosomes, and fluorescence ratios along the length of chromosomes provide a cytogenetic representation of DNA copy-number variation. CGH, however, has a limited ( approximately 20 Mb) mapping resolution, and higher-resolution techniques, such as fluorescence in situ hybridization (FISH), are prohibitively labour-intensive on a genomic scale. Array-based CGH, in which fluorescence ratios at arrayed DNA elements provide a locus-by-locus measure of DNA copy-number variation, represents another means of achieving increased mapping resolution. Published array CGH methods have relied on large genomic clone (for example BAC) array targets and have covered only a small fraction of the human genome. cDNAs representing over 30,000 radiation-hybrid (RH)-mapped human genes provide an alternative and readily available genomic resource for mapping DNA copy-number changes. Although cDNA microarrays have been used extensively to characterize variation in human gene expression, human genomic DNA is a far more complex mixture than the mRNA representation of human cells. Therefore, analysis of DNA copy-number variation using cDNA microarrays would require a sensitivity of detection an order of magnitude greater than has been routinely reported. We describe here a cDNA microarray-based CGH method, and its application to DNA copy-number variation analysis in breast cancer cell lines and tumours. Using this assay, we were able to identify gene amplifications and deletions genome-wide and with high resolution, and compare alterations in DNA copy number and gene expression.

View details for Web of Science ID 000082337300013

View details for PubMedID 10471496

Abstract

cDNA microarrays and a clustering algorithm were used to identify patterns of gene expression in human mammary epithelial cells growing in culture and in primary human breast tumors. Clusters of coexpressed genes identified through manipulations of mammary epithelial cells in vitro also showed consistent patterns of variation in expression among breast tumor samples. By using immunohistochemistry with antibodies against proteins encoded by a particular gene in a cluster, the identity of the cell type within the tumor specimen that contributed the observed gene expression pattern could be determined. Clusters of genes with coherent expression patterns in cultured cells and in the breast tumors samples could be related to specific features of biological variation among the samples. Two such clusters were found to have patterns that correlated with variation in cell proliferation rates and with activation of the IFN-regulated signal transduction pathway, respectively. Clusters of genes expressed by stromal cells and lymphocytes in the breast tumors also were identified in this analysis. These results support the feasibility and usefulness of this systematic approach to studying variation in gene expression patterns in human cancers as a means to dissect and classify solid tumors.

View details for Web of Science ID 000081835500080

View details for PubMedID 10430922

Abstract

To compare various subjective, empiric, and pharmacokinetic methods for interpreting findings at dynamic magnetic resonance (MR) imaging of the breast.Dynamic spiral breast MR imaging was performed in 52 women suspected of having or with known breast disease. Gadolinium-enhanced images were obtained at 12 locations through the whole breast every 7.8 seconds for 8.5 minutes after bolus injection of contrast material. Time-signal intensity curves from regions of interest corresponding to 57 pathologically proved lesions were analyzed by means of a two-compartment pharmacokinetic model, and the diagnostic performance of various parameters was analyzed.Findings included invasive carcinoma in 17 patients, isolated ductal carcinoma in situ (DCIS) in six, and benign lesions in 34. Although some overlap between carcinomas and benign diagnoses was noted for all parameters, receiver operating characteristic analysis indicated that the exchange rate constant had the greatest overall ability to discriminate benign and malignant disease. The elimination rate constant and washout were the most specific parameters. The exchange rate constant, wash-in, and extrapolation point were the most sensitive parameters. DCIS was not consistently distinguished from benign disease with any method.Dynamic spiral breast MR imaging proved an excellent method with which to collect contrast enhancement data rapidly enough that accurate comparisons can be made between many analytic methods.

View details for Web of Science ID 000076618000034

View details for PubMedID 9807580

Abstract

To evaluate interactive magnetic resonance (MR) imaging-guided preoperative needle localization and hookwire placement in the noncompressed breast in patients in the prone position.Nineteen MR imaging-guided breast lesion localization procedures were performed in 17 patients aged 38-70 years (mean age, 48 years) by using an open-platform breast coil in either a 1.5-T, closed-bore imager (n = 14) or a 0.5-T, open-bore imager (n = 5). Rapid imaging (fast spin-echo, water-selective fast spin-echo, or water-specific three-point Dixon gradient-echo) was alternated with freehand manipulation of an MR-compatible needle to achieve accurate needle placement.Up to three manipulations of the needle were required during an average of 9 minutes to reach the target lesion. MR imaging findings confirmed the final needle position within 9 mm of the target in all cases. The accuracy of 10 localizations was independently corroborated either at mammography or at ultrasonography. Nine lesions were visible on MR images only.Interactive MR imaging-guided, freehand needle localization is simple, accurate, and requires no special stereotactic equipment. Lesions throughout the breast, including those in the anterior part of the breast and those near the chest wall, which can be inaccessible with standard grid or compression-plate techniques, can be localized. A variety of needle trajectories in addition to the horizontal path are possible, including circumareolar approaches and tangential needle paths designed to avoid puncture of implants.

View details for Web of Science ID 000073204300031

View details for PubMedID 9577495

Abstract

Contrast material-enhanced magnetic resonance (MR) imaging is reported to be the most accurate modality for determining the extent of breast cancer before surgery. Three-dimensionally rendered MR images can be used as an adjunct in planning breast surgery. Semiautomated methods are used to isolate the breast tissue within high-resolution MR images and to render the skin with a shaded-surface method. Cut-away views reveal lesions in the interior of the breast. Cut-plane shaded-surface display provides the surgeon with information on the size, extent, and spatial relationships of a breast lesion in a simple, intuitive format. This technique can help the surgeon plan a breast biopsy, lumpectomy, or mastectomy that will maximize local control of breast cancer while minimizing cosmetic damage to the unaffected portions of the breast. In a review of 15 clinical cases, cut-plane shaded-surface rendering aided surgical planning in 10 cases.

View details for PubMedID 9536491

Abstract

Tissue classification by examining sets of ultrasound parameters is an elusive goal. We report analysis of measurements of ultrasound speed, attenuation and backscatter in the range 3 to 8 MHz in breast tissues at 37 C. Statistical discriminant analysis and neural net analysis were employed. Data were acquired from 24 biopsy and 7 mastectomy specimens. Best separation of the classes normal, benign, and malignant occurred in the 18 cases where two tissue classes were present in the same specimen and parameters were corrected for within-patient mean; then 85-90% of cases in test sets were correctly classified. Most errors comprised misclassified benign cases. The neural net was comparable to discriminant analysis and slightly superior in separating normal and malignant classes.

View details for Web of Science ID A1996WA72700004

View details for PubMedID 9123674

Abstract

The impact of the surgical margin status on long-term local control rates for breast cancer in women treated with lumpectomy and radiation therapy is unclear.The records of 289 women with 303 invasive breast cancers who were treated with lumpectomy and radiation therapy from 1972 to 1992 were reviewed. The surgical margin was classified as positive (transecting the inked margin), close (less than or equal to 2 mm from the margin), negative, or indeterminate, based on the initial biopsy findings and reexcision specimens, as appropriate. Various clinical and pathologic factors were analyzed as potential prognostic factors for local recurrence in addition to the margin status, including T classification, N classification, age, histologic features, and use of adjuvant therapy. The mean follow-up was 6.25 years.The actuarial probability of freedom from local recurrence for the entire group of patients at 5 and 10 years was 94% and 87%, respectively. The actuarial probability of local control at 10 years was 98% for those patients with negative surgical margins versus 82% for all others (P = 0.007). The local control rate at 10 years was 97% for patients who underwent reexcision and 84% for those who did not. Reexcision appears to convey a local control benefit for those patients with close, indeterminate, or positive initial margins, when negative final margins are attained (P = 0.0001). Final margin status was the most significant determinant of local recurrence rates in univariate analysis. By multivariate analysis, the final margin status and use of adjuvant chemotherapy were significant prognostic factors.The attainment of negative surgical margins, initially or at the time of reexcision, is the most significant predictor of local control after breast-conserving treatment with lumpectomy and radiation therapy.

View details for Web of Science ID A1995RH15100015

View details for PubMedID 8625101

Abstract

Exploratory laparotomy and a search for gastrinomas was performed in 52 patients with the Zollinger-Ellison syndrome (ZES). Gastrinoma tissue was resected in 11 patients (21%), 6 (12%) of whom appear to have been cured. After surgery, serum gastrin levels in these six patients have remained normal from 10 months to 10 years. In the 46 other patients, tumor was unresectable because of metastases or multiple primary tumors (21 patients; 40%) or inability to find the tumor at laparotomy (21 patients; 40%). Multiple pancreatic islet cell adenomata were found in six of seven patients with multiple endocrine neoplasia (MEN), indicating that patients with this condition usually have diffuse involvement of the pancreas. The results of CT scans correlated with findings at laparotomy in 13 of 16 patients. The smallest tumor detected by CT scans was 1 cm in diameter. CT technology is more accurate in finding gastrinomas now than in the past and has a useful role in preoperative evaluation. The possibility of resection should be seriously considered in every patient with Zollinger-Ellison syndrome. Abdominal CT scans, transhepatic portal venous sampling, and laparotomy should be used to find the tumor and to determine whether it is resectable. Using presently available methods, it should be possible to cure about 25% of patients with gastrinomas who do not have MEN and over 70% of those without MEN who appear to have a solitary tumor. Total pancreatectomy may be necessary to cure some patients with MEN, but that operation is rarely justified. The morbidity and mortality of surgical attempts at curing this disease have become minimal; we have had no deaths or serious complications following such operations in over 10 yrs. Total gastrectomy and indefinite use of H2-receptor blocking agents are the therapeutic options for patients with unresectable gastrinomas. Because H2-receptor blocking agents fail to control acid secretion in many patients after several yrs of therapy, total gastrectomy is indicated in a large proportion of patients whose tumors cannot be resected. Total gastrectomy in patients with ZES is also safe using current techniques; our last death following this operation for ZES occurred 15 yrs ago.

View details for Web of Science ID A1983RK44300015

View details for PubMedID 6138003

Abstract

From 1977 to 1983 we used cimetidine as primary therapy for 17 patients with the Zollinger-Ellison syndrome. All patients were treated with oral doses of cimetidine, 300 to 600 mg, four times a day, unless symptoms of hyperacidity developed or until evidence of a potentially resectable tumor became available, at which time they underwent definitive therapy. Eleven (65 percent) had no response to cimetidine therapy, 7 of whom had symptomatic recurrent ulcers, 3 of whom had esophagitis, and 2 of whom had severe diarrhea. Eight of these patients were treated with total gastrectomy, two with successful tumor resection, and one with parietal cell vagotomy (which facilitated the control of hyperacidity with cimetidine). All operations except one were performed electively and there was no operative mortality.

View details for Web of Science ID A1983QY54600022

View details for PubMedID 6869669

Abstract

To reassess the role of laparotomy and extraserosal drainage in the treatment of patients with abdominal abscess, we analyzed the course of 79 patients who underwent 97 operations to treat 120 abdominal abscesses during a five-year period. In 66 clinical episodes the abscess was drained by the most direct approach. Sepsis resolved with a single operation In 80% of these patients, five patients (8%) required a second operation for drainage for an abscess, and eight patients (12%) died. In 31 clinical episodes, the abscess was drained by a laparotomy. Sepsis resolved with a single operation in 61% of these patients, seven patients (21%) had a second abscess, six patients (19%) required a second operation to drain a metachronous abscess, and six patients (19%) died. When the location or number of abscesses was diagnosed incorrectly, the success rate of therapy fell substantially. Since most abdominal abscesses can now be accurately diagnosed preoperatively, most abscesses should be drained by a direct approach. Exploratory laparotomy is indicated when preoperative localization is unsuccessful, when sepsis has not resolved after other methods of drainage, or when the patient has a concomitant abdominal condition that must be treated surgically.

View details for Web of Science ID A1983QN39800021

View details for PubMedID 6838370

View details for PubMedID 7076936

Abstract

Normal cell deprived of amino acids or serum factors enter a resting state, whereas cells transformed by wild-type simian virus 40 do not. The ability to enter a resting state is temperature-sensitive (ts) in cells transformed by a tsA mutant of simian virus 40. We shown further: (i) that when complete medium is added to resting cells, the length of time until the onset of DNA synthesis often exceeds the length of G1 in growing cells; (ii) that the length of this interval depends upon the conditions used to arrest cell growth; but (iii) that transferring cultures from medium depleted for one factor to medium depleted in a second factor never leads to a round of DNA synthesis; and (iv) that DNA synthesis does not resume rapidly when a resting culture of cells transformed by the tsA mutant is transferred to the permissive temperature in suboptimal medium. A model proposing that in suboptimal conditions cells leave the cell cycle and traverse a branch pathway to enter the resting state is consistent with these findings.

View details for Web of Science ID A1976BS77400064

View details for PubMedID 179093

Abstract

Two nonerythropoietic tissues, brian and liver, contain an initiation factor that can overcome the block in initiation of protein synthesis seen in reticulocyte lysates when exogenous hemin is not present. Upon incubation of the brain factor with hemin and removal of free hemin by gel filtration, the factor activity is strongly stimulated. This stimulation shows a concentration dependence on hemin close to that seen for stimulation of protein synthesis in whole reticulocyte lysates. The data indicate that hemin mediates the formation of an active initiation factor complex from inactive, lower molecular weight components.

View details for Web of Science ID A1974U614000051

View details for PubMedID 4530282

Abstract

The metabolism of glucose was examined in several clinical isolates of Neisseria gonorrhoeae. Radiorespirometric studies revealed that growing cells metabolized glucose by a combination on the Entner-Doudoroff and pentose phosphate pathways. A portion of the glyceraldehyde-3-phosphate formed via the Entner-Doudoroff pathway was recycled by conversion to glucose-6-phosphate. Subsequent catabolism of this glucose-6-phosphate by either the Entner-Doudoroff or pentose phosphate pathways yielded CO(2) from the original C6 of glucose. Enzyme analyses confirmed the presence of all enzymes of the Entner-Doudoroff, pentose phosphate, and Embden-Meyerhof-Parnas pathways. There was always a high specific activity of glucose-6-phosphate dehydrogenase (EC 1.1.1.49) relative to that of 6-phosphogluconate dehydrogenase (EC 1.1.1.44). The glucose-6-phosphate dehydrogenase utilized either nicotinamide adenine dinucleotide phosphate or nicotinamide adenine dinucleotide as electron acceptor. Acetate was the only detectable nongaseous end product of glucose metabolism. Following the disappearance of glucose, acetate was metabolized by the tricarboxylic acid cycle as evidenced by the preferential oxidation of [1-(14)C]acetate over that of [2-(14)C]acetate. When an aerobically grown log-phase culture was subjected to anaerobic conditions, lactate and acetate were formed from glucose. Radiorespirometric studies showed that under these conditions, glucose was dissimilated entirely by the Entner-Doudoroff pathway. Further studies determined that this anaerobic dissimilation of glucose was not growth dependent.

View details for Web of Science ID A1974U770400018

View details for PubMedID 4156358