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Stefanie S Jeffrey

Publications and source records attributed to Stefanie S Jeffrey.

At least 19 recordsLinked to original sources
PubMed2014

Single cell mutational analysis of PIK3CA in circulating tumor cells and metastases in breast cancer reveals heterogeneity, discordance, and mutation persistence in cultured disseminated tumor cells from bone marrow.

BACKGROUND: 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. METHODS: 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 mutations in exons 9 and 20 of the PIK3CA gene. Captured DTCs grown in cell culture were also sequenced for PIK3CA mutations. RESULTS: 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. CONCLUSIONS: 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.

Bone Marrow↗
PubMed2006

Discovery and validation of breast cancer subtypes.

BACKGROUND: 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+. RESULTS: 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. CONCLUSION: 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.

Algorithms↗
PubMed2006

Radiation-induced effects on gene expression: an in vivo study on breast cancer.

BACKGROUND AND PURPOSE: 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. MATERIAL AND METHODS: 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. RESULTS AND CONCLUSION: 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.

Breast Neoplasms↗
PubMed2006

Lysyl oxidase is essential for hypoxia-induced metastasis.

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.

Animals↗
PubMed2005

Adipose levels of dioxins and risk of breast cancer.

OBJECTIVE: Our objective was to evaluate the breast cancer risk associated with body burden levels of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs). METHODS: 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). RESULTS: 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). CONCLUSION: 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.

Adipose Tissue↗
PubMed2005

Rates of reexcision for breast cancer after magnetic resonance imaging-guided bracket wire localization.

BACKGROUND: 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. STUDY DESIGN: 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. RESULTS: 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. CONCLUSIONS: 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.

Adult↗
PubMed2005

A streamlined platform for high-content functional proteomics of primary human specimens.

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.

Biomarkers, Tumor↗
PubMed2005

Genomics-based prognosis and therapeutic prediction in breast cancer.

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.

Antineoplastic Agents↗
PubMed2004

A molecular 'signature' of primary breast cancer cultures; patterns resembling tumor tissue.

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.

Breast↗
PubMed2004

Different gene expression patterns in invasive lobular and ductal carcinomas of the breast.

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.

Breast Neoplasms↗
PubMed2004

The evolution of accelerated, partial breast irradiation as a potential treatment option for women with newly diagnosed breast cancer considering breast conservation.

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.

Brachytherapy↗
PubMed2004

Distribution of persistent, lipid-soluble chemicals in breast and abdominal adipose tissues: lessons learned from a breast cancer study.

OBJECTIVES: 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. METHODS: 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. RESULTS: 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. CONCLUSIONS: 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.

Adipose Tissue↗
PubMed2003

Predictors of reexcision findings and recurrence after breast conservation.

PURPOSE: To identify predictors of reexcision findings and local recurrence in the setting of breast-conserving therapy with radiation. METHODS: 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 (<or=2 mm), positive, or indeterminate. RESULTS: The pathologic margin status was the most important predictor of local recurrence. The freedom from local relapse (FFLR) at 6 years was 97% for patients with negative pathologic margins and 86% for all others (p < 0.0001). There was no significant difference in recurrence rates among patients with close, positive, or indeterminate margins. However, the use and sequencing of systemic therapy affected recurrence rates among these patients. For patients with close, positive, or indeterminate margins, the crude risk of local recurrence was 4% among patients who received tamoxifen or received chemotherapy integrated with or after radiation. The risk of local recurrence was 16-29% among the patients with close, positive, or indeterminate margins who did not receive systemic therapy or who received radiation after completion of chemotherapy. Local recurrence rates were low in patients with negative margins (2-8%) regardless of the use of systemic therapy or its timing. The presence or absence of residual disease at reexcision did not predict recurrence as long as the final margins were negative. Among patients who underwent reexcision before radiation, extensive intraductal component (EIC) (p = 0.0001) and young patient age (p = 0.03) were predictive of residual disease in the specimen. Patients with initially close margins and no EIC had a low risk of residual disease at the time of reexcision, as did patients older than age 65 without EIC. CONCLUSION: Pathologic margin status is the most important predictor of local recurrence after breast conservation with radiation. Patient age and EIC were significant predictors of residual disease at reexcision. The use and timing of systemic therapy appear to influence the risk of local recurrence in patients who do not have negative lumpectomy margins.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed2003

The diagnosis and management of pre-invasive breast disease: promise of new technologies in understanding pre-invasive breast lesions.

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.

Breast↗
PubMed2002

Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis.

BACKGROUND: 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. RESULTS: 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. CONCLUSION: T7 based linear amplification reproducibly generates amplified RNA that closely approximates original sample for gene expression profiling using cDNA microarrays.

Journal Article↗
PubMed2002

Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors.

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.

Breast Neoplasms↗
PubMed2002

Expression array technology in the diagnosis and treatment of breast cancer.

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.

Breast Neoplasms↗