Stefanie S. Jeffrey, MD

All Publications

• Investigating circulating tumor cells and distant metastases in patient-derived orthotopic xenograft models of triple-negative breast cancer. Breast cancer research : BCR Ramani, V. C., Lemaire, C. A., Triboulet, M., Casey, K. M., Heirich, K., Renier, C., Vilches-Moure, J. G., Gupta, R., Razmara, A. M., Zhang, H., Sledge, G. W., Sollier, E., Jeffrey, S. S. 2019; 21 (1): 98

  Abstract

  BACKGROUND: Circulating tumor cells (CTCs) represent a temporal "snapshot" of a patient's cancer and changes that occur during disease evolution. There is an extensive literature studying CTCs in breast cancer patients, and particularly in those with metastatic disease. In parallel, there is an increasing use of patient-derived models in preclinical investigations of human cancers. Yet studies are still limited demonstrating CTC shedding and metastasis formation in patient-derived models of breast cancer.METHODS: We used seven patient-derived orthotopic xenograft (PDOX) models generated from triple-negative breast cancer (TNBC) patients to study CTCs and distant metastases. Tumor fragments from PDOX tissue from each of the seven models were implanted into 57 NOD scid gamma (NSG) mice, and tumor growth and volume were monitored. Human CTC capture from mouse blood was first optimized on the marker-agnostic Vortex CTC isolation platform, and whole blood was processed from 37 PDOX tumor-bearing mice.RESULTS: Staining and imaging revealed the presence of CTCs in 32/37 (86%). The total number of CTCs varied between different PDOX tumor models and between individual mice bearing the same PDOX tumors. CTCs were heterogeneous and showed cytokeratin (CK) positive, vimentin (VIM) positive, and mixed CK/VIM phenotypes. Metastases were detected in the lung (20/57, 35%), liver (7/57, 12%), and brain (1/57, less than 2%). The seven different PDOX tumor models displayed varying degrees of metastatic potential, including one TNBC PDOX tumor model that failed to generate any detectable metastases (0/8 mice) despite having CTCs present in the blood of 5/5 tested, suggesting that CTCs from this particular PDOX tumor model may typify metastatic inefficiency.CONCLUSION: PDOX tumor models that shed CTCs and develop distant metastases represent an important tool for investigating TNBC.

  View details for DOI 10.1186/s13058-019-1182-4

  View details for PubMedID 31462307

• Anomalous hysteresis and current fluctuations in cyclic voltammograms at microelectrodes due to Ag leaching from Ag/AgCl reference electrodes ELECTROCHEMISTRY COMMUNICATIONS Chia, C., Jeffrey, S. S., Howe, R. T. 2019; 105

  View details for DOI 10.1016/j.elecom.2019.106499

  View details for Web of Science ID 000484833800013

• ALD HfO2 Films for Defining Microelectrodes for Electrochemical Sensing and Other Applications ACS APPLIED MATERIALS & INTERFACES Chia, C., Shulaker, M. M., Provine, J., Jeffrey, S. S., Howe, R. T. 2019; 11 (29): 26082–92

  Abstract

  Microelectrodes are used in a wide range of applications from analytical electrochemistry and biomolecular sensing to in vivo implants. While a variety of insulating materials have been used to define the microelectrode active area, most are not suitable for nanoscale electrodes (<1 μm2) due to the limited robustness of these films when the film thickness is on the order of the nanoelectrode dimension. In this study, we investigate atomic layer deposited hafnium dioxide (ALD HfO2) as an insulating film to coat planar platinum microelectrodes, with the active areas being defined where the HfO2 is etched. Thermally grown films with thicknesses between 10 and 60 nm were deposited by 100 to 550 ALD cycles and were initially characterized by measuring their standard electrical properties and imaging incipient texture development. Electrochemical measurements on the structures were made, including linear sweep voltammetry and electrochemical impedance spectroscopy, which identified the presence of pinholes in films deposited over the range of 100 to 350 cycles, resulting in leakage. These measurements also suggest a lower limit to the size of microelectrodes below which the electrochemical current detected is no longer dominated by that through the exposed active area. A bilayer insulator comprising ALD HfO2 coated with parylene-C was investigated to minimize the pinhole leakage. Steady-state currents were measured for different electrode areas, qualitatively agreeing with the theory for areas down to ∼1 μm2. For sub-square micrometer electrode areas, bilayer-insulated devices with parylene-C apertures that exposed the smallest microelectrode area showed measured currents that were consistent with extrapolations, indicating that it reduces leakage through HfO2.

  View details for DOI 10.1021/acsami.9b06891

  View details for Web of Science ID 000477787200048

  View details for PubMedID 31305057

• Liquid biopsy in pancreatic ductal adenocarcinoma: current status of circulating tumor cells and circulating tumor DNA. Molecular oncology Lee, J., Park, S. S., Lee, Y. K., Norton, J. A., Jeffrey, S. S. 2019

  Abstract

  Reliable biomarkers are required to evaluate and manage pancreatic ductal adenocarcinoma. Circulating tumor cells and circulating tumor DNA are shed into blood and can be relatively easily obtained from minimally invasive liquid biopsies for serial assays and characterization, thereby providing a unique potential for early diagnosis, forecast of disease prognosis, and monitoring of therapeutic response. In this review, we provide an overview of current technologies used to detect circulating tumor cells and circulating tumor DNA and describe recent advances regarding the multiple clinical applications of liquid biopsy in pancreatic ductal adenocarcinoma.

  View details for DOI 10.1002/1878-0261.12537

  View details for PubMedID 31243883

• Liquid biopsy: a perspective for probing blood for cancer. Lab on a chip Jeffrey, S. S., Toner, M. 2019

  View details for PubMedID 30688954

• Gold Nanobipyramids as Second Near Infrared Optical Coherence Tomography Contrast Agents for in Vivo Multiplexing Studies. Nano letters Si, P., Shevidi, S., Yuan, E., Yuan, K., Lautman, Z., Jeffrey, S. S., Sledge, G. W., de la Zerda, A. 2019

  Abstract

  Developing contrast-enhanced optical coherence tomography (OCT) techniques is important for specific imaging of tissue lesions, molecular imaging, cell-tracking, and highly sensitive microangiography and lymphangiography. Multiplexed OCT imaging in the second near-infrared (NIR-II) window is highly desirable since it allows simultaneous imaging and tracking of multiple biological events in high resolution with deeper tissue penetration in vivo. Here we demonstrate that gold nanobipyramids can function as OCT multiplexing contrast agents, allowing high-resolution imaging of two separate lymphatic flows occurring simultaneously from different drainage basins into the same lymph node in a live mouse. Contrast-enhanced multiplexed lymphangiography of a melanoma tumor in vivo shows that the peritumoral lymph flow upstream of the tumor is unidirectional, and tumor is accessible to such flow. Whereas the lymphatic drainage coming out from the tumor is multidirectional. We also demonstrate real-time tracking of the contrast agents draining from a melanoma tumor specifically to the sentinel lymph node of the tumor and the three-dimensional distribution of the contrast agents in the lymph node.

  View details for DOI 10.1021/acs.nanolett.9b03344

  View details for PubMedID 31585502

• Rapid identification of pathogenic bacteria using Raman spectroscopy and deep learning. Nature communications Ho, C. S., Jean, N., Hogan, C. A., Blackmon, L., Jeffrey, S. S., Holodniy, M., Banaei, N., Saleh, A. A., Ermon, S., Dionne, J. 2019; 10 (1): 4927

  Abstract

  Raman optical spectroscopy promises label-free bacterial detection, identification, and antibiotic susceptibility testing in a single step. However, achieving clinically relevant speeds and accuracies remains challenging due to weak Raman signal from bacterial cells and numerous bacterial species and phenotypes. Here we generate an extensive dataset of bacterial Raman spectra and apply deep learning approaches to accurately identify 30 common bacterial pathogens. Even on low signal-to-noise spectra, we achieve average isolate-level accuracies exceeding 82% and antibiotic treatment identification accuracies of 97.0±0.3%. We also show that this approach distinguishes between methicillin-resistant and -susceptible isolates of Staphylococcus aureus (MRSA and MSSA) with 89±0.1% accuracy. We validate our results on clinical isolates from 50 patients. Using just 10 bacterial spectra from each patient isolate, we achieve treatment identification accuracies of 99.7%. Our approach has potential for culture-free pathogen identification and antibiotic susceptibility testing, and could be readily extended for diagnostics on blood, urine, and sputum.

  View details for DOI 10.1038/s41467-019-12898-9

  View details for PubMedID 31666527

• Real-Time Detection of Circulating Tumor Cells in Living Animals Using Functionalized Large Gold Nanorods. Nano letters Dutta, R., Liba, O., SoRelle, E. D., Winetraub, Y., Ramani, V. C., Jeffrey, S. S., Sledge, G. W., de la Zerda, A. 2019; 19 (4): 2334–42

  Abstract

  Optical coherence tomography (OCT) can be utilized with significant speckle reduction techniques and highly scattering contrast agents for non-invasive, contrast-enhanced imaging of living tissues at the cellular scale. The advantages of reduced speckle noise and improved targeted contrast can be harnessed to track objects as small as 2 μm in vivo, which enables applications for cell tracking and quantification in living subjects. Here we demonstrate the use of large gold nanorods as contrast agents for detecting individual micron-sized polystyrene beads and single myeloma cells in blood circulation using speckle-modulating OCT. This report marks the first time that OCT has been used to detect individual cells within blood in vivo. This technical capability unlocks exciting opportunities for dynamic detection and quantification of tumor cells circulating in living subjects.

  View details for PubMedID 30895796

• Future of Liquid Biopsies With Growing Technological and Bioinformatics Studies: Opportunities and Challenges in Discovering Tumor Heterogeneity With Single-Cell Level Analysis CANCER JOURNAL Ramalingam, N., Jeffrey, S. S. 2018; 24 (2): 104–8

  Abstract

  Liquid biopsy provides minimally invasive and readily obtainable access to tumor-associated biological material in blood or other body fluids. These samples provide important insights into cancer biology, such as primary tumor heterogeneity; real-time tumor evolution; response to therapy, including immunotherapy; and mechanisms of cancer metastasis. Initial biological materials studied were circulating tumor cells and circulating nucleic acids, including circulating tumor DNA and microRNAs; more recently, studies have expanded to investigate extracellular vesicles, such as exosomes, microvesicles, and large oncosomes; tumor-derived circulating endothelial cells; and tumor-educated platelets. Even with an ongoing ambitious investment effort to develop liquid biopsy as an early cancer detection test in asymptomatic individuals, current challenges remain regarding how to access and analyze rare cells and tumor-derived nucleic acids in cancer patients. Technologies and associated bioinformatics tools are continuously evolving to capture these rare materials in an unbiased manner and to analyze them with high confidence. After first presenting recent applications of liquid biopsy, this review discusses aspects affecting the field, including tumor heterogeneity, single-cell analyses, and associated computational tools that will shape the future of liquid biopsy, with resultant opportunities and challenges.

  View details for DOI 10.1097/PPO.0000000000000308

  View details for Web of Science ID 000431182100008

  View details for PubMedID 29601337

  View details for PubMedCentralID PMC5880298

• Anti-HER2 scFv-directed extracellular vesicle-mediated mRNA-based gene delivery inhibits growth of HER2-positive human breast tumor xenografts by prodrug activation. Molecular cancer therapeutics Wang, J., Forterre, A. V., Zhao, J., Frimannsson, D. O., Delcayre, A., Antes, T. J., Efron, B., Jeffrey, S. S., Pegram, M. D., Matin, A. C. 2018

  Abstract

  This paper deals with specific targeting of the prodrug/enzyme regimen, CNOB/HChrR6, to treat a serious disease namely HER2+ve human breast cancer with minimal off-target toxicity. HChrR6 is an improved bacterial enzyme that converts CNOB into the cytotoxic drug MCHB. Extracellular vesicles (EVs) were used for mRNA-based HchrR6 gene delivery: EVs may cause minimal immune rejection, and mRNA may be superior to DNA for gene delivery. To confine HChrR6 generation and CNOB activation to the cancer, the EVHB chimeric protein was constructed. It contains high affinity anti-HER2 scFv antibody (ML39) and is capable of latching on to EV surface. Cells transfected with EVHB-encoding plasmid generated EVs displaying this protein ("directed EVs"). Transfection of a separate batch of cells with the new plasmid, XPort/HChrR6, generated EVs containing HChrR6 mRNA; incubation with pure EVHB enabled these to target the HER2 receptor, generating "EXO-DEPT" EVs. EXO-DEPT treatment specifically enabled HER2-overexpressing BT474 cells to convert CNOB into MCHB in actinomycin D independent manner, showing successful and specific delivery of HCHrR6 mRNA. EXO-DEPTs --but not undirected EVs-- plus CNOB caused near-complete growth-arrest of orthotopic BT474 xenografts in vivo, demonstrating for the first time EV-mediated delivery of functional exogenous mRNA to tumors. EXO-DEPTs may be generated from patient's own dendritic cells to evade immune rejection, and without plasmids and their potentially harmful genetic material, raising the prospect of clinical use of this regimen. This approach can be employed to treat any disease overexpressing a specific marker.

  View details for PubMedID 29483213

• Fast and Label-Free Isolation of Circulating Tumor Cells from Blood: From a Research Microfluidic Platform to an Automated Fluidic Instrument, VTX-1 Liquid Biopsy System SLAS TECHNOLOGY Lemaire, C. A., Liu, S. Z., Wilkerson, C. L., Ramani, V. C., Barzanian, N. A., Huang, K., Che, J., Chiu, M. W., Vuppalapaty, M., Dimmick, A. M., Di Carlo, D., Kochersperger, M. L., Crouse, S. C., Jeffrey, S. S., Englert, R. F., Hengstler, S., Renier, C., Sollier-Christen, E. 2018; 23 (1): 16–29

  View details for DOI 10.1177/2472630317738698

  View details for Web of Science ID 000423049500003

• Fast and Label-Free Isolation of Circulating Tumor Cells from Blood: From a Research Microfluidic Platform to an Automated Fluidic Instrument, VTX-1 Liquid Biopsy System. SLAS technology Lemaire, C. A., Liu, S. Z., Wilkerson, C. L., Ramani, V. C., Barzanian, N. A., Huang, K. W., Che, J., Chiu, M. W., Vuppalapaty, M., Dimmick, A. M., Carlo, D. D., Kochersperger, M. L., Crouse, S. C., Jeffrey, S. S., Englert, R. F., Hengstler, S., Renier, C., Sollier-Christen, E. 2018; 23 (1): 16–29

  Abstract

  Tumor tissue biopsies are invasive, costly, and collect a limited cell population not completely reflective of patient cancer cell diversity. Circulating tumor cells (CTCs) can be isolated from a simple blood draw and may be representative of the diverse biology from multiple tumor sites. The VTX-1 Liquid Biopsy System was designed to automate the isolation of clinically relevant CTC populations, making the CTCs available for easy analysis. We present here the transition from a cutting-edge microfluidic innovation in the lab to a commercial, automated system for isolating CTCs directly from whole blood. As the technology evolved into a commercial system, flexible polydimethylsiloxane microfluidic chips were replaced by rigid poly(methyl methacrylate) chips for a 2.2-fold increase in cell recovery. Automating the fluidic processing with the VTX-1 further improved cancer cell recovery by nearly 1.4-fold, with a 2.8-fold decrease in contaminating white blood cells and overall improved reproducibility. Two isolation protocols were optimized that favor either the cancer cell recovery (up to 71.6% recovery) or sample purity (≤100 white blood cells/mL). The VTX-1's performance was further tested with three different spiked breast or lung cancer cell lines, with 69.0% to 79.5% cell recovery. Finally, several cancer research applications are presented using the commercial VTX-1 system.

  View details for PubMedID 29355087

• T cell receptor sequencing of early-stage breast cancer tumors identifies altered clonal structure of the T cell repertoire. Proceedings of the National Academy of Sciences of the United States of America Beausang, J. F., Wheeler, A. J., Chan, N. H., Hanft, V. R., Dirbas, F. M., Jeffrey, S. S., Quake, S. R. 2017

  Abstract

  Tumor-infiltrating T cells play an important role in many cancers, and can improve prognosis and yield therapeutic targets. We characterized T cells infiltrating both breast cancer tumors and the surrounding normal breast tissue to identify T cells specific to each, as well as their abundance in peripheral blood. Using immune profiling of the T cell beta-chain repertoire in 16 patients with early-stage breast cancer, we show that the clonal structure of the tumor is significantly different from adjacent breast tissue, with the tumor containing 2.5-fold greater density of T cells and higher clonality compared with normal breast. The clonal structure of T cells in blood and normal breast is more similar than between blood and tumor, and could be used to distinguish tumor from normal breast tissue in 14 of 16 patients. Many T cell sequences overlap between tissue and blood from the same patient, including 50% of T cells between tumor and normal breast. Both tumor and normal breast contain high-abundance "enriched" sequences that are absent or of low abundance in the other tissue. Many of these T cells are either not detected or detected with very low frequency in the blood, suggesting the existence of separate compartments of T cells in both tumor and normal breast. Enriched T cell sequences are typically unique to each patient, but a subset is shared between many different patients. We show that many of these are commonly generated sequences, and thus unlikely to play an important role in the tumor microenvironment.

  View details for PubMedID 29138313

• Workflow optimization of whole genome amplification and targeted panel sequencing for CTC mutation detection NPJ GENOMIC MEDICINE Liu, H. E., Triboulet, M., Zia, A., Vuppalapaty, M., Kidess-Sigal, E., Coller, J., Natu, V. S., Shokoohi, V., Che, J., Renier, C., Chan, N. H., Hanft, V. R., Jeffrey, S. S., Sollier-Christen, E. 2017; 2

  View details for DOI 10.1038/s41525-017-0034-3

  View details for Web of Science ID 000416211000001

• Label-free isolation of prostate circulating tumor cells using Vortex microfluidic technology NPJ PRECISION ONCOLOGY Renier, C., Pao, E., Che, J., Liu, H. E., Lemaire, C. A., Matsumoto, M., Triboulet, M., Srivinas, S., Jeffrey, S. S., Rettig, M., Kulkarni, R. P., Di Carlo, D., Sollier-Christen, E. 2017; 1

  View details for DOI 10.1038/s41698-017-0015-0

  View details for Web of Science ID 000413625900001

• Profiling protein expression in circulating tumour cells using microfluidic western blotting NATURE COMMUNICATIONS Sinkala, E., Sollier-Christen, E., Renier, C., Rosas-Canyelles, E., Che, J., Heirich, K., Duncombe, T. A., Vlassakis, J., Yamauchi, K. A., Huang, H., Jeffrey, S. S., Herr, A. E. 2017; 8

  Abstract

  Circulating tumour cells (CTCs) are rare tumour cells found in the circulatory system of certain cancer patients. The clinical and functional significance of CTCs is still under investigation. Protein profiling of CTCs would complement the recent advances in enumeration, transcriptomic and genomic characterization of these rare cells and help define their characteristics. Here we describe a microfluidic western blot for an eight-plex protein panel for individual CTCs derived from estrogen receptor-positive (ER+) breast cancer patients. The precision handling and analysis reveals a capacity to assay sparingly available patient-derived CTCs, a biophysical CTC phenotype more lysis-resistant than breast cancer cell lines, a capacity to report protein expression on a per CTC basis and two statistically distinct GAPDH subpopulations within the patient-derived CTCs. Targeted single-CTC proteomics with the capacity for archivable, multiplexed protein analysis offers a unique, complementary taxonomy for understanding CTC biology and ascertaining clinical impact.

  View details for DOI 10.1038/ncomms14622

  View details for Web of Science ID 000397109800001

  View details for PubMedID 28332571

• 5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages. Cell research Song, C. X., Yin, S., Ma, L., Wheeler, A., Chen, Y., Zhang, Y., Liu, B., Xiong, J., Zhang, W., Hu, J., Zhou, Z., Dong, B., Tian, Z., Jeffrey, S. S., Chua, M. S., So, S., Li, W., Wei, Y., Diao, J., Xie, D., Quake, S. R. 2017

  Abstract

  5-Hydroxymethylcytosine (5hmC) is an important mammalian DNA epigenetic modification that has been linked to gene regulation and cancer pathogenesis. Here we explored the diagnostic potential of 5hmC in circulating cell-free DNA (cfDNA) using a sensitive chemical labeling-based low-input shotgun sequencing approach. We sequenced cell-free 5hmC from 49 patients of seven different cancer types and found distinct features that could be used to predict cancer types and stages with high accuracy. Specifically, we discovered that lung cancer leads to a progressive global loss of 5hmC in cfDNA, whereas hepatocellular carcinoma and pancreatic cancer lead to disease-specific changes in the cell-free hydroxymethylome. Our proof-of-principle results suggest that cell-free 5hmC signatures may potentially be used not only to identify cancer types but also to track tumor stage in some cancers.Cell Research advance online publication 18 August 2017; doi:10.1038/cr.2017.106.

  View details for PubMedID 28820176

• Workflow optimization of whole genome amplification and targeted panel sequencing for CTC mutation detection. NPJ genomic medicine Liu, H. E., Triboulet, M., Zia, A., Vuppalapaty, M., Kidess-Sigal, E., Coller, J., Natu, V. S., Shokoohi, V., Che, J., Renier, C., Chan, N. H., Hanft, V. R., Jeffrey, S. S., Sollier-Christen, E. 2017; 2: 34

  Abstract

  Genomic characterization of circulating tumor cells (CTCs) may prove useful as a surrogate for conventional tissue biopsies. This is particularly important as studies have shown different mutational profiles between CTCs and ctDNA in some tumor subtypes. However, isolating rare CTCs from whole blood has significant hurdles. Very limited DNA quantities often can't meet NGS requirements without whole genome amplification (WGA). Moreover, white blood cells (WBC) germline contamination may confound CTC somatic mutation analyses. Thus, a good CTC enrichment platform with an efficient WGA and NGS workflow are needed. Here, Vortex label-free CTC enrichment platform was used to capture CTCs. DNA extraction was optimized, WGA evaluated and targeted NGS tested. We used metastatic colorectal cancer (CRC) as the clinical target, HCT116 as the corresponding cell line, GenomePlex® and REPLI-g as the WGA methods, GeneRead DNAseq Human CRC Panel as the 38 gene panel. The workflow was further validated on metastatic CRC patient samples, assaying both tumor and CTCs. WBCs from the same patients were included to eliminate germline contaminations. The described workflow performed well on samples with sufficient DNA, but showed bias for rare cells with limited DNA input. REPLI-g provided an unbiased amplification on fresh rare cells, enabling an accurate variant calling using the targeted NGS. Somatic variants were detected in patient CTCs and not found in age matched healthy donors. This demonstrates the feasibility of a simple workflow for clinically relevant monitoring of tumor genetics in real time and over the course of a patient's therapy using CTCs.

  View details for PubMedID 29263843

• Label-free isolation of prostate circulating tumor cells using Vortex microfluidic technology. NPJ precision oncology Renier, C., Pao, E., Che, J., Liu, H. E., Lemaire, C. A., Matsumoto, M., Triboulet, M., Srivinas, S., Jeffrey, S. S., Rettig, M., Kulkarni, R. P., Di Carlo, D., Sollier-Christen, E. 2017; 1 (1): 15

  Abstract

  There has been increased interest in utilizing non-invasive "liquid biopsies" to identify biomarkers for cancer prognosis and monitoring, and to isolate genetic material that can predict response to targeted therapies. Circulating tumor cells (CTCs) have emerged as such a biomarker providing both genetic and phenotypic information about tumor evolution, potentially from both primary and metastatic sites. Currently, available CTC isolation approaches, including immunoaffinity and size-based filtration, have focused on high capture efficiency but with lower purity and often long and manual sample preparation, which limits the use of captured CTCs for downstream analyses. Here, we describe the use of the microfluidic Vortex Chip for size-based isolation of CTCs from 22 patients with advanced prostate cancer and, from an enumeration study on 18 of these patients, find that we can capture CTCs with high purity (from 1.74 to 37.59%) and efficiency (from 1.88 to 93.75 CTCs/7.5 mL) in less than 1 h. Interestingly, more atypical large circulating cells were identified in five age-matched healthy donors (46-77 years old; 1.25-2.50 CTCs/7.5 mL) than in five healthy donors <30 years old (21-27 years old; 0.00 CTC/7.5 mL). Using a threshold calculated from the five age-matched healthy donors (3.37 CTCs/mL), we identified CTCs in 80% of the prostate cancer patients. We also found that a fraction of the cells collected (11.5%) did not express epithelial prostate markers (cytokeratin and/or prostate-specific antigen) and that some instead expressed markers of epithelial-mesenchymal transition, i.e., vimentin and N-cadherin. We also show that the purity and DNA yield of isolated cells is amenable to targeted amplification and next-generation sequencing, without whole genome amplification, identifying unique mutations in 10 of 15 samples and 0 of 4 healthy samples.

  View details for PubMedID 29872702

• Enumeration and targeted analysis of KRAS, BRAF and PIK3CA mutations in CTCs captured by a label-free platform: Comparison to ctDNA and tissue in metastatic colorectal cancer ONCOTARGET Kidess-Sigal, E., Liu, H. E., Triboulet, M. M., Che, J., Ramani, V. C., Visser, B. C., Poultsides, G. A., Longacre, T. A., Marziali, A., Vysotskaia, V., Wiggin, M., Heirich, K., Hanft, V., Keilholz, U., Tinhofer, I., Norton, J. A., Lee, M., Sollier-Christen, E., Jeffrey, S. S. 2016; 7 (51): 85349-85364

  Abstract

  Treatment of advanced colorectal cancer (CRC) requires multimodal therapeutic approaches and need for monitoring tumor plasticity. Liquid biopsy biomarkers, including CTCs and ctDNA, hold promise for evaluating treatment response in real-time and guiding therapeutic modifications. From 15 patients with advanced CRC undergoing liver metastasectomy with curative intent, we collected 41 blood samples at different time points before and after surgery for CTC isolation and quantification using label-free Vortex technology. For mutational profiling, KRAS, BRAF, and PIK3CA hotspot mutations were analyzed in CTCs and ctDNA from 23 samples, nine matched liver metastases and three primary tumor samples. Mutational patterns were compared. 80% of patient blood samples were positive for CTCs, using a healthy baseline value as threshold (0.4 CTCs/mL), and 81.4% of captured cells were EpCAM+ CTCs. At least one mutation was detected in 78% of our blood samples. Among 23 matched CTC and ctDNA samples, we found a concordance of 78.2% for KRAS, 73.9% for BRAF and 91.3% for PIK3CA mutations. In several cases, CTCs exhibited a mutation that was not detected in ctDNA, and vice versa. Complementary assessment of both CTCs and ctDNA appears advantageous to assess dynamic tumor profiles.

  View details for DOI 10.18632/oncotarget.13350

  View details for PubMedID 27863403

• Label-free enumeration, collection and downstream cytological and cytogenetic analysis of circulating tumor cells SCIENTIFIC REPORTS Dhar, M., Pao, E., Renier, C., Go, D. E., Che, J., Montoya, R., Conrad, R., Matsumoto, M., Heirich, K., Triboulet, M., Rao, J., Jeffrey, S. S., Garon, E. B., Goldman, J., Rao, N. P., Kulkarni, R., Sollier-Christen, E., Di Carlo, D. 2016; 6

  Abstract

  Circulating tumor cells (CTCs) have a great potential as indicators of metastatic disease that may help physicians improve cancer prognostication, treatment and patient outcomes. Heterogeneous marker expression as well as the complexity of current antibody-based isolation and analysis systems highlights the need for alternative methods. In this work, we use a microfluidic Vortex device that can selectively isolate potential tumor cells from blood independent of cell surface expression. This system was adapted to interface with three protein-marker-free analysis techniques: (i) an in-flow automated image processing system to enumerate cells released, (ii) cytological analysis using Papanicolaou (Pap) staining and (iii) fluorescence in situ hybridization (FISH) targeting the ALK rearrangement. In-flow counting enables a rapid assessment of the cancer-associated large circulating cells in a sample within minutes to determine whether standard downstream assays such as cytological and cytogenetic analyses that are more time consuming and costly are warranted. Using our platform integrated with these workflows, we analyzed 32 non-small cell lung cancer (NSCLC) and 22 breast cancer patient samples, yielding 60 to 100% of the cancer patients with a cell count over the healthy threshold, depending on the detection method used: respectively 77.8% for automated, 60-100% for cytology, and 80% for immunostaining based enumeration.

  View details for DOI 10.1038/srep35474

  View details for Web of Science ID 000385311800001

  View details for PubMedID 27739521

  View details for PubMedCentralID PMC5064381

• Regression of experimental NIS-expressing breast cancer brain metastases in response to radioiodide/gemcitabine dual therapy ONCOTARGET Renier, C., Do, J., Reyna-Neyra, A., Foster, D., De, A., Vogel, H., Jeffrey, S. S., Tse, V., Carrasco, N., Wapnir, I. 2016; 7 (34): 54811-54824

  Abstract

  Treating breast cancer brain metastases (BCBMs) is challenging. Na+/I- symporter (NIS) expression in BCBMs would permit their selective targeting with radioiodide (131I-). We show impressive enhancement of tumor response by combining131I- with gemcitabine (GEM), a cytotoxic radiosensitizer. Nude mice mammary fat-pad (MFP) tumors and BCBMs were generated with braintropic MDA-MB-231Br cells transduced with bicistronically-linked NIS and firefly luciferase cDNAs. Response was monitored in vivo via bioluminescent imaging and NIS tumor expression.131I-/GEM therapy inhibited MFP tumor growth more effectively than either agent alone. BCBMs were treated with: high or low-dose GEM (58 or 14.5 mg/Kg×4); 131I- (1mCi or 2×0.5 mCi 7 days apart); and 131I-/GEM therapy. By post-injection day (PID) 25, 82-86% of controls and 78-83% of 131I--treated BCBM grew, whereas 17% low-dose and 36% high-dose GEM regressed. The latter tumors were smaller than the controls with comparable NIS expression (~20% of cells). High and low-dose 131I-/ GEM combinations caused 89% and 57% tumor regression, respectively. High-dose GEM/131I- delayed tumor growth: tumors increased 5-fold in size by PID45 (controls by PID18). Although fewer than 25% of cells expressed NIS, GEM/131I- caused dramatic tumor regression in NIS-transduced BCBMs. This effect was synergistic, and supports the hypothesis that GEM radiosensitizes cells to 131I-.

  View details for DOI 10.18632/oncotarget.10238

  View details for Web of Science ID 000385435000059

• Electropermanent magnet actuation for droplet ferromicrofluidics. Technology Padovani, J. I., Jeffrey, S. S., Howe, R. T. 2016; 4 (2): 110-119

  Abstract

  Droplet actuation is an essential mechanism for droplet-based microfluidic systems. On-demand electromagnetic actuation is used in a ferrofluid-based microfluidic system for water droplet displacement. Electropermanent magnets (EPMs) are used to induce 50 mT magnetic fields in a ferrofluid filled microchannel with gradients up to 6.4 × 10(4) kA/m(2). Short 50 µs current pulses activate the electropermanent magnets and generate negative magnetophoretic forces that range from 10 to 70 nN on 40 to 80 µm water-in-ferrofluid droplets. Maximum droplet displacement velocities of up to 300 µm/s are obtained under flow and no-flow conditions. Electropermanent magnet-activated droplet sorting under continuous flow is demonstrated using a split-junction microfluidic design.

  View details for PubMedID 27583301

• Classification of large circulating tumor cells isolated with ultra-high throughput microfluidic Vortex technology ONCOTARGET Che, J., Yu, V., Dhar, M., Renier, C., Matsumoto, M., Heirich, K., Garon, E. B., Goldman, J., Rao, J., Sledge, G. W., Pegram, M. D., Sheth, S., Jeffrey, S. S., Kulkarni, R. P., Sollier, E., Di Carlo, D. 2016; 7 (11): 12748-12760

  Abstract

  Circulating tumor cells (CTCs) are emerging as rare but clinically significant non-invasive cellular biomarkers for cancer patient prognosis, treatment selection, and treatment monitoring. Current CTC isolation approaches, such as immunoaffinity, filtration, or size-based techniques, are often limited by throughput, purity, large output volumes, or inability to obtain viable cells for downstream analysis. For all technologies, traditional immunofluorescent staining alone has been employed to distinguish and confirm the presence of isolated CTCs among contaminating blood cells, although cells isolated by size may express vastly different phenotypes. Consequently, CTC definitions have been non-trivial, researcher-dependent, and evolving. Here we describe a complete set of objective criteria, leveraging well-established cytomorphological features of malignancy, by which we identify large CTCs. We apply the criteria to CTCs enriched from stage IV lung and breast cancer patient blood samples using the High Throughput Vortex Chip (Vortex HT), an improved microfluidic technology for the label-free, size-based enrichment and concentration of rare cells. We achieve improved capture efficiency (up to 83%), high speed of processing (8 mL/min of 10x diluted blood, or 800 μL/min of whole blood), and high purity (avg. background of 28.8±23.6 white blood cells per mL of whole blood). We show markedly improved performance of CTC capture (84% positive test rate) in comparison to previous Vortex designs and the current FDA-approved gold standard CellSearch assay. The results demonstrate the ability to quickly collect viable and pure populations of abnormal large circulating cells unbiased by molecular characteristics, which helps uncover further heterogeneity in these cells.

  View details for PubMedID 26863573

• Circulating tumor cell technologies MOLECULAR ONCOLOGY Ferreira, M. M., Romani, V. C., Jeffrey, S. S. 2016; 10 (3): 374-394

  View details for DOI 10.1016/j.molonc.2016.01.007

  View details for Web of Science ID 000372379800002

• Label-Free Enumeration, Collection and Downstream Cytological and Cytogenetic Analysis of Circulating Tumor Cells Rao, J., Dhar, M., Pao, E., Renier, C., Go, D. E., Che, J., Montoya, R., Conrad, R., Matsumoto, M., Heirich, K., Triboulet, M., Jeffrey, S. S., Garon, E., Goldman, J., Rao, N. P., Kulkarni, R., Sollier, E. NATURE PUBLISHING GROUP. 2016: 117A

  View details for Web of Science ID 000369270700457

• Perspectives on Clinical Applications of CTCs CIRCULATING TUMOR CELLS: ADVANCES IN BASIC SCIENCE AND CLINICAL APPLICATIONS Kulkarni, R. P., Jeffrey, S. S., Cote, R. J., Datar, R. H. 2016: 315–23

  View details for DOI 10.1007/978-1-4939-3363-1_16

  View details for Web of Science ID 000371329000018

• Regression of experimental NIS-expressing breast cancer brain metastases in response to radioiodide/gemcitabine dual therapy. Oncotarget Renier, C., Do, J., Reyna-Neyra, A., Foster, D., De, A., Vogel, H., Jeffrey, S. S., Tse, V., Carrasco, N., Wapnir, I. 2016

  Abstract

  Treating breast cancer brain metastases (BCBMs) is challenging. Na+/I- symporter (NIS) expression in BCBMs would permit their selective targeting with radioiodide (131I-). We show impressive enhancement of tumor response by combining131I- with gemcitabine (GEM), a cytotoxic radiosensitizer. Nude mice mammary fat-pad (MFP) tumors and BCBMs were generated with braintropic MDA-MB-231Br cells transduced with bicistronically-linked NIS and firefly luciferase cDNAs. Response was monitored in vivo via bioluminescent imaging and NIS tumor expression.131I-/GEM therapy inhibited MFP tumor growth more effectively than either agent alone. BCBMs were treated with: high or low-dose GEM (58 or 14.5 mg/Kg×4); 131I- (1mCi or 2×0.5 mCi 7 days apart); and 131I-/GEM therapy. By post-injection day (PID) 25, 82-86% of controls and 78-83% of 131I--treated BCBM grew, whereas 17% low-dose and 36% high-dose GEM regressed. The latter tumors were smaller than the controls with comparable NIS expression (~20% of cells). High and low-dose 131I-/ GEM combinations caused 89% and 57% tumor regression, respectively. High-dose GEM/131I- delayed tumor growth: tumors increased 5-fold in size by PID45 (controls by PID18). Although fewer than 25% of cells expressed NIS, GEM/131I- caused dramatic tumor regression in NIS-transduced BCBMs. This effect was synergistic, and supports the hypothesis that GEM radiosensitizes cells to 131I-.

  View details for PubMedID 27363025

• Circulating Tumor Cells and Circulating Tumor DNA: Challenges and Opportunities on the Path to Clinical Utility CLINICAL CANCER RESEARCH Ignatiadis, M., Lee, M., Jeffrey, S. S. 2015; 21 (21): 4786-4800

  Abstract

  Recent technological advances have enabled the detection and detailed characterization of circulating tumor cells (CTC) and circulating tumor DNA (ctDNA) in blood samples from patients with cancer. Often referred to as a "liquid biopsy," CTCs and ctDNA are expected to provide real-time monitoring of tumor evolution and therapeutic efficacy, with the potential for improved cancer diagnosis and treatment. In this review, we focus on these opportunities as well as the challenges that should be addressed so that these tools may eventually be implemented into routine clinical care. Clin Cancer Res; 21(21); 4786-800. ©2015 AACR.

  View details for DOI 10.1158/1078-0432.CCR-14-1190

  View details for PubMedID 26527805

• High efficiency vortex trapping of circulating tumor cells BIOMICROFLUIDICS Dhar, M., Wong, J., Karimi, A., Che, J., Renier, C., Matsumoto, M., Triboulet, M., Garon, E. B., Goldman, J. W., Rettig, M. B., Jeffrey, S. S., Kulkarni, R. P., Sollier, E., Di Carlo, D. 2015; 9 (6)

  Abstract

  Circulating tumor cells (CTCs) are important biomarkers for monitoring tumor dynamics and efficacy of cancer therapy. Several technologies have been demonstrated to isolate CTCs with high efficiency but achieve a low purity from a large background of blood cells. We have previously shown the ability to enrich CTCs with high purity from large volumes of blood through selective capture in microvortices using the Vortex Chip. The device consists of a narrow channel followed by a series of expansion regions called reservoirs. Fast flow in the narrow entry channel gives rise to inertial forces, which direct larger cells into trapping vortices in the reservoirs where they remain circulating in orbits. By studying the entry and stability of particles following entry into reservoirs, we discover that channel cross sectional area plays an important role in controlling the size of trapped particles, not just the orbital trajectories. Using these design modifications, we demonstrate a new device that is able to capture a wider size range of CTCs from clinical samples, uncovering further heterogeneity. This simple biophysical method opens doors for a range of downstream interventions, including genetic analysis, cell culture, and ultimately personalized cancer therapy.

  View details for DOI 10.1063/1.4937895

  View details for Web of Science ID 000367821100020

  View details for PubMedCentralID PMC4684572

• Cancer Core 125 Panel for quantitative expression and mutation profiling Chenchik, A., Makhanov, M., Dolganov, G., Jeffrey, S. AMER ASSOC CANCER RESEARCH. 2015

  View details for DOI 10.1158/1538-7445.AM2015-3384

  View details for Web of Science ID 000371597101412

• Label-free concentration of viable breast cancer CTCs for single cell Western blotting Sinkala, E., Sollier, E., Renier, C., Che, J., Jeffrey, S. S., Herr, A. E. AMER ASSOC CANCER RESEARCH. 2015

  View details for DOI 10.1158/1538-7445.AM2015-1997

  View details for Web of Science ID 000371578504104

• Label-free isolation of circulating tumor cells for cytomorphological analysis Renier, C., Pao, E., Go, D. E., Che, J., Ra, J., Rao, N., Garon, E., Goldman, J., Kulkarni, R. P., Jeffrey, S. S., Sollier, E., Di Carlo, D. AMER ASSOC CANCER RESEARCH. 2015

  View details for DOI 10.1158/1538-7445.AM2015-629

  View details for Web of Science ID 000371578501085

• Impact of navigation on knowledge and attitudes about clinical trials among chinese patients undergoing treatment for breast and gynecologic cancers. Journal of immigrant and minority health Clair McClung, E., Davis, S. W., Jeffrey, S. S., Kuo, M., Lee, M. M., Teng, N. N. 2015; 17 (3): 976-979

  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

• HIGD1A Regulates Oxygen Consumption, ROS Production, and AMPK Activity during Glucose Deprivation to Modulate Cell Survival and Tumor Growth CELL REPORTS Ameri, K., Jahangiri, A., Rajah, A. M., Tormos, K. V., Nagarajan, R., Pekmezci, M., Vien Nguyen, V., Wheeler, M. L., Murphy, M. P., Sanders, T. A., Jeffrey, S. S., Yeghiazarians, Y., Rinaudo, P. F., Costello, J. F., Aghi, M. K., Maltepe, E. 2015; 10 (6): 891-899

  View details for DOI 10.1016/j.celrep.2015.01.020

  View details for Web of Science ID 000349440200006

• Mutation profiling of tumor DNA from plasma and tumor tissue of colorectal cancer patients with a novel, high-sensitivity multiplexed mutation detection platform ONCOTARGET Kidess, E., Heirich, K., Wiggin, M., Vysotskaia, V., Visser, B. C., Marziali, A., Wiedenmann, B., Norton, J. A., Lee, M., Jeffrey, S. S., Poultsides, G. A. 2015; 6 (4): 2549-2561

  Abstract

  Circulating tumor DNA (ctDNA) holds promise as a non-invasive means for tumor monitoring in solid malignancies. Assays with high sensitivity and multiplexed analysis of mutations are needed to enable broad application.We developed a new assay based on sequence-specific synchronous coefficient of drag alteration (SCODA) technology, which enriches for mutant DNA to achieve high sensitivity and specificity. This assay was applied to plasma and tumor tissue from non-metastatic and metastatic colorectal cancer (CRC) patients, including patients undergoing surgical resection for CRC liver metastases.Across multiple characterization experiments, the assay demonstrated a limit of detection of 0.001% (1 molecule in 100,000) for the majority of the 46 mutations in the panel. In CRC patient samples (n=38), detected mutations were concordant in tissue and plasma for 93% of metastatic patients versus 54% of non-metastatic patients. For three patients, ctDNA identified additional mutations not detected in tumor tissue. In patients undergoing liver metastatectomy, ctDNA anticipated tumor recurrence earlier than carcinoembryonic antigen (CEA) value or imaging.The multiplexed SCODA mutation enrichment and detection method can be applied to mutation profiling and quantitation of ctDNA, and is likely to have particular utility in the metastatic setting, including patients undergoing metastatectomy.

  View details for PubMedID 25575824

• Molecular profiling of heterogeneous tumor cells Chenchik, A., Deng, D., Bonneau, K., Makhanov, M., Coram, M., Dolganov, G., Jeffrey, S. S. ELSEVIER SCI LTD. 2014: 60

  View details for DOI 10.1016/S0959-8049(14)70310-7

  View details for Web of Science ID 000347755700185

• Genotype discordance between circulating tumor cells in blood and disseminated tumor cells in bone marrow at single cell level in breast cancer patients Deng, G., Krishnakumar, S., Coram, M. A., Powell, A. A., Zhang, H., Mindrinos, M. N., Telli, M. L., Effenberger, K. E., Herrler, M., Pantel, K., Davis, R. W., Jeffrey, S. S. AMER ASSOC CANCER RESEARCH. 2014

  View details for DOI 10.1158/1538-7445.AM2014-3528

  View details for Web of Science ID 000349910201024

• High-Throughput Time-Resolved FRET Reveals Akt/PKB Activation as a Poor Prognostic Marker in Breast Cancer CANCER RESEARCH Veeriah, S., Leboucher, P., de Naurois, J., Jethwa, N., Nye, E., Bunting, T., Stone, R., Stamp, G., Calleja, V., Jeffrey, S. S., Parker, P. J., Larijani, B. 2014; 74 (18): 4983-4995

  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 Web of Science ID 000342358300004

  View details for PubMedID 24970478

• Patient-derived xenografts of triple-negative breast cancer reproduce molecular features of patient tumors and respond to mTOR inhibition. Breast cancer research Zhang, H., Cohen, A. L., Krishnakumar, S., Wapnir, I. L., Veeriah, S., Deng, G., Coram, M. A., Piskun, C. M., Longacre, T. A., Herrler, M., Frimannsson, D. O., Telli, M. L., Dirbas, F. M., Matin, A. C., Dairkee, S. H., Larijani, B., Glinsky, G. V., Bild, A. H., Jeffrey, S. S. 2014; 16 (2): R36-?

  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

• Isolation and mutational analysis of circulating tumor cells from lung cancer patients with magnetic sifters and biochips LAB ON A CHIP Earhart, C. M., Hughes, C. E., Gaster, R. S., Ooi, C. C., Wilson, R. J., Zhou, L. Y., Humke, E. W., Xu, L., Wong, D. J., Willingham, S. B., Schwartz, E. J., Weissman, I. L., Jeffrey, S. S., Neal, J. W., Rohatgi, R., Wakeleebe, H. A., Wang, S. X. 2014; 14 (1): 78-88

  View details for DOI 10.1039/c3lc50580d

  View details for Web of Science ID 000327669000008

• 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. BMC cancer Deng, G., Krishnakumar, S., Powell, A. A., Zhang, H., Mindrinos, M. N., Telli, M. L., Davis, R. W., Jeffrey, S. S. 2014; 14: 456-?

  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

• Circulating tumor cells (CTCs) and circulating DNA to monitor tumor heterogeneity in clinical trials Jeffrey, S. ELSEVIER SCI LTD. 2013: S5

  View details for Web of Science ID 000209470700017

• Circulating tumor cells versus tumor-derived cell-free DNA: rivals or partners in cancer care in the era of single-cell analysis? GENOME MEDICINE Kidess, E., Jeffrey, S. S. 2013; 5

  View details for DOI 10.1186/gm474

  View details for Web of Science ID 000323065600001

• Colorectal cancer diagnostics: biomarkers, cell-free DNA, circulating tumor cells and defining heterogeneous populations by single-cell analysis. Expert review of molecular diagnostics Kin, C., Kidess, E., Poultsides, G. A., Visser, B. C., Jeffrey, S. S. 2013; 13 (6): 581-599

  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 PubMedID 23895128

• Nuclear Localization of the Mitochondrial Factor HIGD1A during Metabolic Stress PLOS ONE Ameri, K., Rajah, A. M., Vien Nguyen, V., Sanders, T. A., Jahangiri, A., DeLay, M., Donne, M., Choi, H. J., Tormos, K. V., Yeghiazarians, Y., Jeffrey, S. S., Rinaudo, P. F., Rowitch, D. H., Aghi, M., Maltepe, E. 2013; 8 (4)

  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

  View details for PubMedCentralID PMC3639984

• Circulating tumor cells versus tumor-derived cell-free DNA: rivals or partners in cancer care in the era of single-cell analysis? Genome medicine Kidess, E., Jeffrey, S. S. 2013; 5 (8): 70-?

  View details for DOI 10.1186/gm474

  View details for PubMedID 23953663

• Overcoming obstacles to clinical trials' enrollment: A lay navigator pilot program focused on Chinese women with cancer McClung, E., Davis, S., Kuo, M., Lee, M., Jeffrey, S., Teng, N. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2012: S26

  View details for DOI 10.1016/j.ygyno.2012.07.071

  View details for Web of Science ID 000308783800120

• Single Cell Profiling of Circulating Tumor Cells: Transcriptional Heterogeneity and Diversity from Breast Cancer Cell Lines PLOS ONE Powell, A. A., Talasaz, A. H., Zhang, H., Coram, M. A., Reddy, A., Deng, G., Telli, M. L., Advani, R. H., Carlson, R. W., Mollick, J. A., Sheth, S., Kurian, A. W., Ford, J. M., Stockdale, F. E., Quake, S. R., Pease, R. F., Mindrinos, M. N., Bhanot, G., Dairkee, S. H., Davis, R. W., Jeffrey, S. S. 2012; 7 (5)

  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 PubMedID 22586443

• Multiplex molecular analysis of CTCs. Recent results in cancer research. Fortschritte der Krebsforschung. Progrès dans les recherches sur le cancer Sieuwerts, A. M., Jeffrey, S. S. 2012; 195: 125-140

  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

• Breast Cancer Heterogeneity and Treatment Resistance: Clues from Metaplastic Tumors Felding-Habermann, B., O'Sullivan, D. M., Lorger, M., MacDermed, D., Fernandez-Santidrian, A., Steele, J. B., Telli, M. L., Jeffrey, S. S., Murray, S., Torkamani, A., Cunliffe, H., Vaughn, S. V. AMER ASSOC CANCER RESEARCH. 2011

  View details for DOI 10.1158/0008-5472.SABCS11-PD03-07

  View details for Web of Science ID 000209699800076

• Adipose levels of polybrominated diphenyl ethers and risk of breast cancer BREAST CANCER RESEARCH AND TREATMENT Hurley, S., Reynolds, P., Goldberg, D., Nelson, D. O., Jeffrey, S. S., Petreas, M. 2011; 129 (2): 505-511

  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

• A pharmacogenomic method for individualized prediction of drug sensitivity MOLECULAR SYSTEMS BIOLOGY Cohen, A. L., Soldi, R., Zhang, H., Gustafson, A. M., Wilcox, R., Welm, B. E., Chang, J. T., Johnson, E., Spira, A., Jeffrey, S. S., Bild, A. H. 2011; 7

  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

  View details for PubMedCentralID PMC3159972

• Distinctive Responsiveness to Stromal Signaling Accompanies Histologic Grade Programming of Cancer Cells PLOS ONE Luciani, M. g., Seok, J., Sayeed, A., Champion, S., Goodson, W. H., Jeffrey, S. S., Xiao, W., Mindrinos, M., Davis, R. W., Dairkee, S. H. 2011; 6 (5)

  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

  View details for PubMedCentralID PMC3098270

• Characterization of molecular subtypes of Korean breast cancer: An ethnically and clinically distinct population INTERNATIONAL JOURNAL OF ONCOLOGY Han, W., Nicolau, M., Noh, D., Jeffrey, S. S. 2010; 37 (1): 51-59

  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

• Stem cells in human breast cancer HISTOLOGY AND HISTOPATHOLOGY Oliveira, L. R., Jeffrey, S. S., Ribeiro-Silva, A. 2010; 25 (3): 371-385

  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

• Focal amplification and oncogene dependency of GAB2 in breast cancer ONCOGENE Bocanegra, M., Bergamaschi, A., Kim, Y. H., Miller, M. A., Rajput, A. B., Kao, J., Langerod, A., Han, W., Noh, D., Jeffrey, S. S., Huntsman, D. G., Borresen-Dale, A., Pollack, J. R. 2010; 29 (5): 774-779

  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

• Circulating tumour cells demonstrate an altered response to hypoxia and an aggressive phenotype BRITISH JOURNAL OF CANCER Ameri, K., Luong, R., Zhang, H., Powell, A. A., Montgomery, K. D., Espinosa, I., Bouley, D. M., Harris, A. L., Jeffrey, S. S. 2010; 102 (3): 561-569

  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

  View details for PubMedCentralID PMC2805847

• A Phenotype-Based Model for Rational Selection of Novel Targeted Therapies in Treating Aggressive Breast Cancer 32nd Annual San Antonio Breast Cancer Symposium Soldi, R., Gustafson, A., Zhu, H., Wilcox, R., Welm, B., Spira, A., JEFFREY, S., Bild, A. H. AMER ASSOC CANCER RESEARCH. 2009: 594S–594S

  View details for Web of Science ID 000272920701042

• Y Quantification of multiple biomarker expression in circulating tumor cells Hsieh, H., Bethel, K., Curry, D., Jeffrey, S., Krivacic, R., Kuhn, P., Lazarus, N., Marrinucci, D., Nieva, J., Schwartz, E., Somlo, G., Wakelee, H., Bruce, R. AMER ASSOC CANCER RESEARCH. 2009

  View details for Web of Science ID 000209701805127

• Isolating highly enriched populations of circulating epithelial cells and other rare cells from blood using a magnetic sweeper device PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Talasaz, A. H., Powell, A. A., Huber, D. E., Berbee, J. G., Roh, K., Yu, W., Xiao, W., Davis, M. M., Pease, R. F., Mindrinos, M. N., Jeffrey, S. S., Davis, R. W. 2009; 106 (10): 3970-3975

  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

  View details for PubMedCentralID PMC2645911

• CAMK1D amplification implicated in epithelial-mesenchymal transition in basal-like breast cancer MOLECULAR ONCOLOGY Bergamaschi, A., Kim, Y. H., Kwei, K. A., Choi, Y. L., Bocanegra, M., Langerod, A., Han, W., Noh, D., Huntsman, D. G., Jeffrey, S. S., Borresen-Dale, A., Pollack, J. R. 2008; 2 (4): 327-339

  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

  View details for PubMedCentralID PMC2653212

• DNA copy number alterations and expression of relevant genes in triple-negative breast cancer GENES CHROMOSOMES & CANCER Han, W., Jung, E., Cho, J., Lee, J. W., Hwang, K., Yang, S., Kang, J. J., Bae, J., Jeon, Y. K., Park, I., Nicolau, M., Jeffrey, S. S., Noh, D. 2008; 47 (6): 490-499

  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

• New models and online calculator for predicting non-sentinel lymph node status in sentinel lymph node positive breast cancer patients 30th Annual San Antonio Breast Cancer Symposium Kohrt, H., Olshen, R., Bermas, H., GOODSON, W., Henry, S., Rouse, R., Bailey, L., Philben, V., Dirbas, F., Dunn, J., Johnson, D., Wapnir, I., Carlson, R., STOCKDALE, F., Hansen, N., JEFFREY, S. SPRINGER. 2008: 588–88

  View details for Web of Science ID 000255851900029

• Basal carcinoma of the breast revisited: an old entity with new interpretations JOURNAL OF CLINICAL PATHOLOGY Korsching, E., Jeffrey, S. S., MEINERZ, W., Decker, T., Boecker, W., Buerger, H. 2008; 61 (5): 553-560

  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

• Cancer biomarker profiling with microRNAs NATURE BIOTECHNOLOGY Jeffrey, S. S. 2008; 26 (4): 400-401

  View details for DOI 10.1038/nbt0408-400

  View details for Web of Science ID 000254782500020

  View details for PubMedID 18392022

• New models and online calculator for predicting non-sentinel lymph node status in sentinel lymph node positive breast cancer patients BMC CANCER Kohrt, H. E., Olshen, R. A., Bermas, H. R., Goodson, W. H., Wood, D. J., Henry, S., Rouse, R. V., Bailey, L., Philben, V. J., Dirbas, F. M., Dunn, J. J., Johnson, D. L., Wapnir, I. L., Carlson, R. W., Stockdale, F. E., Hansen, N. M., Jeffrey, S. S. 2008; 8

  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 PubMedID 18315887

• Estrogen receptor-negative invasive breast cancer: Imaging features of tumors with and without human epidermal growth factor receptor type 2 overexpression RADIOLOGY Wang, Y., Ikeda, D. M., Narasimhan, B., Longacre, T. A., Bleicher, R. J., Pal, S., Jackman, R. J., Jeffrey, S. S. 2008; 246 (2): 367-375

  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

• MRI-guided radiofrequency ablation of breast cancer: Preliminary clinical experience JOURNAL OF MAGNETIC RESONANCE IMAGING van den Bosch, M., Daniel, B., Rieke, V., Butts-Pauly, K., Kermit, E., Jeffrey, S. 2008; 27 (1): 204-208

  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 PubMedID 18050333

• RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies BMC MOLECULAR BIOLOGY Ribeiro-Silva, A., Zhang, H., Jeffrey, S. S. 2007; 8

  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

  View details for PubMedCentralID PMC2233637

• MagSweeper: an automated system for high efficiency and specificity capture of live circulating tumor cells 30th Annual San Antonio Breast Cancer Symposium Powell, A. A., Talasaz, A. A., Mindrinos, M., Carlson, R., Pease, F. W., Davis, R. W., Jeffrey, S. S. SPRINGER. 2007: S24–S24

  View details for Web of Science ID 000251398500063

• Oxidative stress pathways highlighted in tumor cell immortalization: association with breast cancer outcome ONCOGENE Dairkee, S. H., Nicolau, M., Sayeed, A., Champion, S., Ji, Y., Moore, D. H., Yong, B., Meng, Z., Jeffrey, S. S. 2007; 26 (43): 6269-6279

  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

• Disease-specific genomic analysis: identifying the signature of pathologic biology BIOINFORMATICS Nicolau, M., Tibshirani, R., Borresen-Dale, A., Jeffrey, S. S. 2007; 23 (8): 957-965

  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

• Transcriptomic signatures in breast cancer MOLECULAR BIOSYSTEMS Fu, J., Jeffrey, S. S. 2007; 3 (7): 466-472

  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

• TP53 mutation status and gene expression profiles are powerful prognostic markers of breast cancer BREAST CANCER RESEARCH Langerod, A., Zhao, H., Borgan, O., Nesland, J. M., Bukholm, I. R., Ikdahl, T., Karesen, R., Borresen-Dale, A., Jeffrey, S. S. 2007; 9 (3)

  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

  View details for PubMedCentralID PMC1929092

• Discovery and validation of breast cancer subtypes BMC GENOMICS Kapp, A. V., Jeffrey, S. S., Langerod, A., Borresen-Dale, A., Han, W., Noh, D., Bukholm, I. R., Nicolau, M., Brown, P. O., Tibshirani, R. 2006; 7

  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

  View details for PubMedCentralID PMC1574316

• Radiation-induced effects on gene expression: An in vivo study on breast cancer 3rd International Conference on Translational Research and Pre-Clinical Strategies in Radiation Oncology Helland, A., Johnsen, H., Froyland, C., Landmark, H. B., Saetersdal, A. B., Holmen, M. M., Gjertsen, T., Nesland, J. M., Ottestad, W., Jeffrey, S. S., Ottestad, L. O., Rodningen, O. K., Sherlock, G., Borresen-Dale, A. ELSEVIER IRELAND LTD. 2006: 230–35

  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

• MRI-guided needle localization of suspicious breast lesions: results of a freehand technique EUROPEAN RADIOLOGY van den Bosch, M. A., Daniel, B. L., Pal, S., Nowels, K. W., Birdwell, R. L., Jeffrey, S. S., Ikeda, D. M. 2006; 16 (8): 1811-1817

  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

• Predicting non-sentinel lymph node involvement in breast cancer patients. 42nd Annual Meeting of the American-Society-of-Clinical-Oncology Kohrt, H. E., Olshen, R. A., Goodson, W. H., Rouse, R. V., Bailey, L., Philben, V., Dirbas, F. M., Stockdale, F. E., Carlson, R. W., Jeffrey, S. S. AMER SOC CLINICAL ONCOLOGY. 2006: 10S–10S

  View details for Web of Science ID 000239009400039

• Lysyl oxidase is essential for hypoxia-induced metastasis NATURE Erler, J. T., Bennewith, K. L., Nicolau, M., Dornhofer, N., Kong, C., Le, Q. T., Chi, J. T., Jeffrey, S. S., Giaccia, A. J. 2006; 440 (7088): 1222-1226

  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 PubMedID 16642001

• LOX is essential for hypoxia-induced metastasis 3rd International Conference on Translational Research and Pre-Clinical Strategies in Radiation Oncology Erler, J. T., Dornhoefer, N., Le, Q. T., Kong, C., Chi, J. T., Nicolau, M., Jeffrey, S. S., Giaccia, A. J. ELSEVIER IRELAND LTD. 2006: S5–S5

  View details for Web of Science ID 000237599000013

• Cell trapping in activated micropores for functional analysis. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference Talasaz, A. H., Powell, A. A., Stahl, P., Ronaghi, M., Jeffrey, S. S., Mindrinos, M., Davis, R. W. 2006; 1: 1838-1841

  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

• Development of a new device for high throughput isolation of live circulating tumor cells. 29th Annual San Antonio Breast Cancer Symposium Talasaz, A. A., Powell, A. A., Mindrinos, M., Carlson, R. W., Pease, F. W., Davis, R. W., Jeffrey, S. S. SPRINGER. 2006: S213–S213

  View details for Web of Science ID 000242047101189

• A streamlined platform for high-content functional proteomics of primary human specimens NATURE METHODS Jessani, N., Niessen, S., Wei, B. Q., Nicolau, M., Humphrey, M., Ji, Y. R., Han, W. S., Noh, D. Y., Yates, J. R., Jeffrey, S. S., Cravatt, B. F. 2005; 2 (9): 691-697

  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

• MRI features of mucosa-associated lymphoid tissue lymphoma in the breast AMERICAN JOURNAL OF ROENTGENOLOGY Espinosa, L. A., Daniel, B. L., Jeffrey, S. S., Nowels, K. W., Ikeda, D. M. 2005; 185 (1): 199-202

  View details for Web of Science ID 000229951900035

  View details for PubMedID 15972423

• Adipose levels of dioxins and risk of breast cancer CANCER CAUSES & CONTROL Reynolds, P., Hurley, S. E., Petreas, M., Goldberg, D. E., Smith, D., Gilliss, D., Mahoney, M. E., Jeffrey, S. S. 2005; 16 (5): 525-535

  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

• Genomics-based prognosis and therapeutic prediction in breast cancer. Journal of the National Comprehensive Cancer Network Jeffrey, S. S., Lønning, P. E., Hillner, B. E. 2005; 3 (3): 291-300

  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

• Rates of reexcision for breast cancer after magnetic resonance imaging-guided bracket wire localization JOURNAL OF THE AMERICAN COLLEGE OF SURGEONS Wallace, A. M., Daniel, B. L., Jeffrey, S. S., Birdwell, R. L., Nowels, K. W., Dirbas, F. M., Schraedley-Desmond, P., Ikeda, D. M. 2005; 200 (4): 527-537

  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

• Gene expression profiles and the TP53 mutation status are powerful prognostic markers of breast cancer 3rd International Symposium on the Molecular Biology of Breast Cancer Langerod, A., Zhao, H., Borgan, O., Nesland, J. M., Hernandez-Boussard, T., Bukholm, I. K., Karesen, R., Borresen-Dale, A. L., Jeffrey, S. S. BIOMED CENTRAL LTD. 2005: S52–S52

  View details for DOI 10.1186/bcr1174

  View details for Web of Science ID 000232330500127

• Hypoxia promotes invasion and metastasis of breast cancer cells by increasing lysyl oxidase expression Erler, J. T., Jeffrey, S. S., Giaccia, A. J. BIOMED CENTRAL LTD. 2005: S57

  View details for DOI 10.1186/bcr1186

  View details for Web of Science ID 000232330500139

• Molecular distinctions among ERBB2-overexpressing breast cancers Jeffrey, S. S. BIOMED CENTRAL LTD. 2005: S8

  View details for DOI 10.1186/bcr1065

  View details for Web of Science ID 000232330500020

• TP53 mutations among molecular subtypes of HER2-positive tumors 3rd International Symposium on the Molecular Biology of Breast Cancer Helland, A., Nicolau, M., Ji, Y., Langerod, A., Sommervoll, D. E., Bergamaschi, A., Pollack, J. R., Borresen-Dale, A. L., Jeffrey, S. S. BIOMED CENTRAL LTD. 2005: S53–S53

  View details for DOI 10.1186/bcr1175

  View details for Web of Science ID 000232330500128

• Immortalization-associated gene signature in breast cancer 3rd International Symposium on the Molecular Biology of Breast Cancer Dairkee, S. H., Nicolau, M., Champion, S., Ji, Y., Sayeed, A., Meng, Z., Demeter, J., Jeffrey, S. S. BIOMED CENTRAL LTD. 2005: S34–S34

  View details for DOI 10.1186/bcr1130

  View details for Web of Science ID 000232330500083

• The evolution of accelerated, partial breast irradiation as a potential treatment option for women with newly diagnosed breast cancer considering breast conservation CANCER BIOTHERAPY AND RADIOPHARMACEUTICALS Dirbas, F. M., Jeffrey, S. S., Goffinet, D. R. 2004; 19 (6): 673-705

  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

• Magnetic resonance imaging of suspicious breast masses seen on one mammographic view. breast journal Offodile, R. S., Daniel, B. L., Jeffrey, S. S., Wapnir, I., Dirbas, F. M., Ikeda, D. M. 2004; 10 (5): 416-422

  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

• A molecular 'signature' of primary breast cancer cultures; patterns resembling tumor tissue BMC GENOMICS Dairkee, S. H., Ji, Y. R., Ben, Y., Moore, D. H., Meng, Z. H., Jeffrey, S. S. 2004; 5

  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

  View details for PubMedCentralID PMC509241

• Different gene expression patterns in invasive lobular and ductal carcinomas of the breast MOLECULAR BIOLOGY OF THE CELL Zhao, H. J., Langerod, A., Ji, Y., Nowels, K. W., Nesland, J. M., Tibshirani, R., Bukholm, I. K., Karesen, R., Botstein, D., Borresen-Dale, A. L., Jeffrey, S. S. 2004; 15 (6): 2523-2536

  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

  View details for PubMedCentralID PMC420079

• Distribution of persistent, lipid-soluble chemicals in breast and abdominal adipose tissues: Lessons learned from a breast cancer study CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Petreas, M., Smith, D., Hurley, S., Jeffrey, S. S., Gilliss, D., Reynolds, P. 2004; 13 (3): 416-424

  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

• Central carbon metabolism genes that predict disease-free survival in hormone receptor negative tumors. 27th Annual San Antonio Breast Cancer Symposium Funari, V. A., Tibshirani, R., Ji, Y., Nicolau, M., Carlson, R. W., Brown, P. O., Noh, D. Y., Jeffrey, S. S. SPRINGER. 2004: S115–S115

  View details for Web of Science ID 000225589600326

• Predictors of reexcision findings and recurrence after breast conservation 44th Annual Meeting of the American-Society-for-Therapeutic-Radiology-and-Oncology Smitt, M. C., Nowels, K., Carlson, R. W., Jeffrey, S. S. ELSEVIER SCIENCE INC. 2003: 979–85

  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

• The diagnosis and management of pre-invasive breast disease - Promise of new technologies in understanding pre-invasive breast lesions BREAST CANCER RESEARCH Jeffrey, S. S., Pollack, J. R. 2003; 5 (6): 320-328

  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

  View details for PubMedCentralID PMC314415

• Gene expression profiling of breast carcinomas. 25th San Antonio Breast Cancer Symposium Langerod, A., Zhao, H., Ji, Y., Bukholm, I. R., BROWN, P., Botstein, D., Borresen-Dale, A. L., JEFFREY, S. SPRINGER. 2002: S101–S101

  View details for Web of Science ID 000179770100290

• Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Pollack, J. R., Sorlie, T., Perou, C. M., Rees, C. A., Jeffrey, S. S., Lonning, P. E., Tibshirani, R., Botstein, D., Borresen-Dale, A. L., Brown, P. O. 2002; 99 (20): 12963-12968

  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

  View details for PubMedCentralID PMC130569

• MR imaging features of infiltrating lobular carcinoma of the breast: Histopathologic correlation AMERICAN JOURNAL OF ROENTGENOLOGY Qayyum, A., Birdwell, R. L., Daniel, B. L., Nowels, K. W., Jeffrey, S. S., Agoston, T. A., Herfkens, R. J. 2002; 178 (5): 1227-1232

  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

• Expression array technology in the diagnosis and treatment of breast cancer. Molecular interventions Jeffrey, S. S., Fero, M. J., Børresen-Dale, A., Botstein, D. 2002; 2 (2): 101-109

  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

• Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis BMC GENOMICS Zhao, H. J., Hastie, T., Whitfield, M. L., Borresen-Dale, A. L., Jeffrey, S. S. 2002; 3

  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

• Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Sorlie, T., Perou, C. M., Tibshirani, R., Aas, T., Geisler, S., Johnsen, H., Hastie, T., Eisen, M. B., van de Rijn, M., Jeffrey, S. S., Thorsen, T., Quist, H., Matese, J. C., Brown, P. O., Botstein, D., Lonning, P. E., Borresen-Dale, A. L. 2001; 98 (19): 10869-10874

  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

  View details for PubMedCentralID PMC58566

• Breast cancer: Variables affecting sentinel lymph node visualization at preoperative lymphoscintigraphy RADIOLOGY Birdwell, R. L., Smith, K. L., Betts, B. J., Ikeda, D. M., Strauss, H. W., Jeffrey, S. S. 2001; 220 (1): 47-53

  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

• Freehand iMRI-guided large-gauge core needle biopsy: A new minimally invasive technique for diagnosis of enhancing breast lesions 7th Annual Meeting of the International-Society-for-Magnetic-Resonance-in-Medicine (ISMRM) Daniel, B. L., Birdwell, R. L., Butts, K., Nowels, K. W., Ikeda, D. M., Heiss, S. G., Cooper, C. R., Jeffrey, S. S., Dirbas, F. M., Herfkens, R. J. JOHN WILEY & SONS INC. 2001: 896–902

  Abstract

  The lack of reliable methods for minimally invasive biopsy of suspicious enhancing breast lesions has hindered the utilization of contrast-enhanced magnetic resonance imaging (MRI) for the detection and diagnosis of breast cancer. In this study, a freehand method was developed for large-gauge core needle biopsy (LCNB) guided by intraprocedural MRI (iMRI). Twenty-seven lesions in nineteen patients were biopsied using iMRI-guided LCNB without significant complications. Diagnostic tissue was obtained in all cases. Nineteen of the 27 lesions were subsequently surgically excised. Histopathologic analysis confirmed that iMRI-guided LCNB correctly distinguished benign lesions from malignancy in 18 of the 19 lesions. The histology revealed by core biopsy was partially discrepant with surgical biopsy in 2 of the other 19 lesions. Freehand iMRI-guided LCNB of enhancing breast lesions is promising. Larger studies are needed to determine the smallest lesion that can be sampled reliably and to precisely measure the accuracy of iMRI-guided LCNB as a minimally invasive tool to diagnose suspicious lesions found by breast MRI. J. Magn. Reson. Imaging 2001;13:896-902.

  View details for Web of Science ID 000171296500013

  View details for PubMedID 11382950

• Locally advanced breast cancer: is surgery necessary? breast journal Favret, A. M., Carlson, R. W., Goffinet, D. R., Jeffrey, S. S., Dirbas, F. M., Stockdale, F. E. 2001; 7 (2): 131-137

  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

• Expedition inspiration consensus 2001 BREAST CANCER RESEARCH AND TREATMENT Benz, C. C., Hilakivi-Clarke, L., Conzen, S., Dorn, R. V., Fleming, G. F., Grant, K., Greene, G., Hellman, S., Henderson, C., Hoover, R., Hryniuk, W., JEFFREY, S., Lippman, M., Lung, J., Mitchell, M., Pike, M. 2001; 70 (3): 213-219

  View details for Web of Science ID 000172448200006

  View details for PubMedID 11804185

• Isosulfan blue affects pulse oximetry ANESTHESIOLOGY Vokach-Brodsky, L., Jeffrey, S. S., Lemmens, H. J., Brock-Utne, J. G. 2000; 93 (4): 1002-1003

  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

• Molecular portraits of human breast tumours NATURE Perou, C. M., Sorlie, T., Eisen, M. B., van de Rijn, M., Jeffrey, S. S., Rees, C. A., Pollack, J. R., Ross, D. T., Johnsen, H., Akslen, L. A., Fluge, O., Pergamenschikov, A., Williams, C., Zhu, S. X., Lonning, P. E., Borresen-Dale, A. L., Brown, P. O., Botstein, D. 2000; 406 (6797): 747-752

  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 PubMedID 10963602

• Controversies in sentinel lymph node biopsy for breast cancer CANCER BIOTHERAPY AND RADIOPHARMACEUTICALS Jeffrey, S. S., Jones, S. B., Smith, K. L. 2000; 15 (3): 223-233

  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

• Systematic variation in gene expression patterns in human cancer cell lines NATURE GENETICS Ross, D. T., Scherf, U., Eisen, M. B., Perou, C. M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S. S., van de Rijn, M., Waltham, M., Pergamenschikov, A., Lee, J. C., Lashkari, D., Shalon, D., Myers, T. G., Weinstein, J. N., Botstein, D., Brown, P. O. 2000; 24 (3): 227-235

  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 PubMedID 10700174

• Characterization of breast lesion morphology with delayed 3DSSMT: An adjunct to dynamic breast MRI JOURNAL OF MAGNETIC RESONANCE IMAGING Leong, C. S., Daniel, B. L., Herfkens, R. J., Birdwell, R. L., Jeffrey, S. S., Ikeda, D. M., Sawyer-Glover, A. M., Glover, G. H. 2000; 11 (2): 87-96

  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

• Management of breast cancer after Hodgkin's disease 39th Annual Meeting of the American-Society-for-Therapeutic-Radiology-and-Oncology Wolden, S. L., Hancock, S. L., Carlson, R. W., Goffinet, D. R., Jeffrey, S. S., Hoppe, R. T. AMER SOC CLINICAL ONCOLOGY. 2000: 765–72

  Abstract

  To evaluate the incidence, detection, pathology, management, and prognosis of breast cancer occurring after Hodgkin's disease.Seventy-one cases of breast cancer in 65 survivors of Hodgkin's disease were analyzed.The median age at diagnosis was 24.6 years for Hodgkin's disease and 42.6 years for breast cancer. The relative risk for invasive breast cancer after Hodgkin's disease was 4.7 (95% confidence interval, 3.4 to 6. 0) compared with an age-matched cohort. Cancers were detected by self-examination (63%), mammography (30%), and physician exam (7%). The histologic distribution paralleled that reported in the general population (85% ductal histology) as did other features (27% positive axillary lymph nodes, 63% positive estrogen receptors, and 25% family history). Although 87% of tumors were less than 4 cm, 95% were managed with mastectomy because of prior radiation. Two women underwent lumpectomy with breast irradiation. One of these patients developed tissue necrosis in the region of overlap with the prior mantle field. The incidence of bilateral breast cancer was 10%. Adjuvant systemic therapy was well tolerated; doxorubicin was used infrequently. Ten-year disease-specific survival was as follows: in-situ disease, 100%; stage I, 88%; stage II, 55%; stage III, 60%; and stage IV, zero.The risk of breast cancer is increased after Hodgkin's disease. Screening has been successful in detecting early-stage cancers. Pathologic features and prognosis are similar to that reported in the general population. Repeat irradiation of the breast can lead to tissue necrosis, and thus, mastectomy remains the standard of care in most cases.

  View details for Web of Science ID 000085401800008

  View details for PubMedID 10673517

• Contrast-enhanced locally advanced breast cancer magnetic resonance: Comparison of sagittal thin slice and 2 maximum intensity projection displays. Minor, M. A., Ikeda, D. M., Daniel, B. L., Birdwell, R. L., Jeffrey, S. S., Herfkens, R. J. LIPPINCOTT WILLIAMS & WILKINS. 2000: 86A

  View details for Web of Science ID 000086346600472

• Radiofrequency ablation of breast cancer - First report of an emerging technology ARCHIVES OF SURGERY Jeffrey, S. S., Birdwell, R. L., Ikeda, D. M., Daniel, B. L., Nowels, K. W., Dirbas, F. M., Griffey, S. M. 1999; 134 (10): 1064-1068

  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

• Genome-wide analysis of DNA copy-number changes using cDNA microarrays NATURE GENETICS Pollack, J. R., Perou, C. M., Alizadeh, A. A., Eisen, M. B., Pergamenschikov, A., Williams, C. F., Jeffrey, S. S., Botstein, D., Brown, P. O. 1999; 23 (1): 41-46

  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

• Isosulfan blue affects pulse oximetry Vokach-Brodsky, L., JEFFREY, S., Lemmens, H. J., Brock-Utne, J. G. LIPPINCOTT WILLIAMS & WILKINS. 1999: U465–U465

  View details for Web of Science ID 000082480601170

• Distinctive gene expression patterns in human mammary epithelial cells and breast cancers PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Perou, C. M., Jeffrey, S. S., van de Rijn, M., Rees, C. A., Eisen, M. B., Ross, D. T., Pergamenschikov, A., Williams, C. F., Zhu, S. X., Lee, J. C., Lashkari, D., Shalon, D., Brown, P. O., Botstein, D. 1999; 96 (16): 9212-9217

  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 PubMedID 10430922

• Non-visualization of sentinel lymph node in patients with breast cancer. Krausz, Y., Jeffrey, S. S., Ikeda, D. M., Jadvar, H., Langleben, D., Strauss, H. W. SOC NUCLEAR MEDICINE INC. 1999: 253P

  View details for Web of Science ID 000080105801036

• Lymphatic mapping and sentinel node biopsy in breast cancer. Pace, W. M., Jeffrey, S. S., Strauss, H. W. SOC NUCLEAR MEDICINE INC. 1999: 139P

  View details for Web of Science ID 000080105800560

• Gene expression patterns in human breast cancer; correlation of microarray analysis with immunohistochemistry. van de Rijn, M., Perou, C. M., Jeffrey, S. S., Elsen, M. B., Brown, P. O., Botstein, D. LIPPINCOTT WILLIAMS & WILKINS. 1999: 32A

  View details for Web of Science ID 000078376600177

• Breast disease: Dynamic spiral MR imaging 82nd Scientific Assembly and Annual Meeting of the Radiological-Society-of-North-America Daniel, B. L., Yen, Y. F., Glover, G. H., Ikeda, D. M., Birdwell, R. L., Sawyer-Glover, A. M., Black, J. W., Plevritis, S. K., Jeffrey, S. S., Herfkens, R. J. RADIOLOGICAL SOC NORTH AMERICA. 1998: 499–509

  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 PubMedID 9807580

• Breast lesion localization: A freehand, interactive MR imaging-guided technique RADIOLOGY Daniel, B. L., Birdwell, R. L., Ikeda, D. M., Jeffrey, S. S., Black, J. W., Block, W. F., Sawyer-Glover, A. M., Glover, G. H., Herfkens, R. J. 1998; 207 (2): 455-463

  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

• Value of combined imaging and use of gamma probe in intraoperative localization of sentinel lymph node in breast cancer Jadvar, H., Jeffrey, S., Cua, D., Birdwell, R., Strauss, H. W. SOC NUCLEAR MEDICINE INC. 1998: 24P

  View details for Web of Science ID 000073560300087

• Three-dimensional shaded-surface rendering of MR images of the breast: technique, applications, and impact on surgical management of breast disease. Radiographics Daniel, B. L., Jeffrey, S. S., Birdwell, R. L., Ikeda, D. M., Sawyer-Glover, A. M., Herfkens, R. J. 1998; 18 (2): 483-496

  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

• Shaded-surface rendering of MR images of the breast: Technique, applications, and impact on surgical management of breast disease RADIOGRAPHICS Daniel, B. L., Jeffrey, S. S., Birdwell, R. L., Ikeda, D. M., Sawyer-Glover, A. M., Herfkens, R. J. 1998; 18 (2): 483-496

  View details for Web of Science ID 000072493100020

• Preliminary experience with power Doppler imaging of solid breast masses 1995 Annual Meeting of the Radiological-Society-of-North-America Birdwell, R. L., Ikeda, D. M., Jeffrey, S. S., Jeffrey, R. B. AMER ROENTGEN RAY SOC. 1997: 703–7

  Abstract

  The purpose of our study was to assess the potential of power Doppler imaging (PDI) to differentiate benign from malignant solid breast masses.Sixty-nine biopsy-proven solid breast masses were evaluated with PDI using 7- to 10-MHz transducers optimized for low-volume flow sensitivity. The extent of flow on PDI was estimated as a percentage of the lesion area on multiple longitudinal and transverse static sonographic images. Flow was categorized as avascular; less than 10%; 10-25%; 25.1-50%; and greater than 50%.Of the 69 lesions evaluated, 33 were malignant and 36 were benign. Of the avascular lesions, nine were malignant and eight were benign. Significant overlap was seen in the vascularity of the other 52 lesions: both malignant and benign lesions revealed a similar range of vascular patterns.Preliminary experience with PDI suggests that both malignant and benign lesions can be avascular and that the presence of color within a solid breast mass is a nonspecific finding. Assessing the extent of vascularity with PDI appears to be of limited value in the diagnostic evaluation of solid breast masses.

  View details for Web of Science ID A1997XR81100021

  View details for PubMedID 9275882

• Management of breast cancer following Hodgkin's disease Wolden, S. L., Carlson, R. W., Jeffrey, S. S., Hancock, S. L. PERGAMON-ELSEVIER SCIENCE LTD. 1997: 258

  View details for DOI 10.1016/S0360-3016(97)80805-X

  View details for Web of Science ID A1997XW28000328

• Ultrasound tissue characterization of breast biopsy specimens: Expanded study ULTRASONIC IMAGING MORTENSEN, C. L., Edmonds, P. D., Gorfu, Y., Hill, J. R., Jensen, J. F., Schattner, P., Shifrin, L. A., VALDES, A. D., Jeffrey, S. S., Esserman, L. J. 1996; 18 (3): 215-230

  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

• Value of sonographic identification of breast masses in excised specimens in the breast imaging department. Breast Disease Birdwell RL, Ikeda DM, Jeffrey SS 1996; 9: 93-99
• AXILLARY LYMPHADENECTOMY FOR BREAST-CANCER WITHOUT AXILLARY DRAINAGE 66th Annual Session of the Pacific-Coast-Surgical-Association Jeffrey, S. S., Goodson, W. H., Ikeda, D. M., Birdwell, R. L., Bogetz, M. S. AMER MEDICAL ASSOC. 1995: 909–13

  Abstract

  To evaluate axillary lymph node dissection done without closed drainage in conjunction with breast conservation cancer surgery.Prospective clinical study.Two university hospitals.Eighty-one women undergoing wide local excision of breast cancer with simultaneous or subsequent axillary lymph node dissection.No axillary drain was placed following axillary lymphadenectomy.The development and resorption of axillary seroma fluid as measured by clinical aspiration and serial sonographic examination.Thirty-four (42%) of the 81 women required axillary seroma aspiration even though axillary fluid was present in 92% (22/24) of those studied sonographically. The seromas accumulated over the first 2 weeks following axillary dissection and resorbed over the next 2 weeks, as assessed by both clinical and sonographic examination. The complication rate was 2% (2/81). The surgery was performed safely on an outpatient or short-stay basis in 99% (80/81) of patients. All patients except one were discharged within 23 hours of surgery, and 56 patients were discharged directly after anesthesia.Axillary lymph node dissection done in conjunction with breast conservation surgery can be performed in an ambulatory or short-stay setting without axillary drainage. Postoperative seromas will resolve within 1 month, and fewer than half will require aspiration. Lymphadenectomy without drainage reduces morbidity and allows the patient greater personal comfort.

  View details for Web of Science ID A1995RN02200018

  View details for PubMedID 7632155

• THE IMPORTANCE OF THE LUMPECTOMY SURGICAL MARGIN STATUS IN LONG-TERM RESULTS OF BREAST-CONSERVATION CANCER Smitt, M. C., Nowels, K. W., ZDEBLICK, M. J., JEFFREY, S., Carlson, R. W., Stockdale, F. E., Goffinet, D. R. 1995; 76 (2): 259-267

  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

• ABDOMINAL ABSCESS - A SURGICAL STRATEGY ARCHIVES OF SURGERY Glick, P. L., Pellegrini, C. A., Stein, S., Way, L. W. 1983; 118 (5): 646-650

  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

• RESECTION OF GASTRINOMAS ANNALS OF SURGERY Deveney, C. W., Deveney, K. E., Stark, D., Moss, A., Stein, S., Way, L. W. 1983; 198 (4): 546-553

  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

• CIMETIDINE IN THE TREATMENT OF ZOLLINGER-ELLISON SYNDROME AMERICAN JOURNAL OF SURGERY Deveney, C. W., Stein, S., Way, L. W. 1983; 146 (1): 116-123

  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

• INTRAMURAL HEMATOMA OF THE CECUM FOLLOWING BLUNT TRAUMA JOURNAL OF COMPUTER ASSISTED TOMOGRAPHY Jeffrey, R. B., Federle, M. P., Stein, S. M., Crass, R. A. 1982; 6 (2): 404-405

  View details for Web of Science ID A1982NG42900032

• RESTING STATE IN NORMAL AND SIMIAN VIRUS-40 TRANSFORMED CHINESE-HAMSTER LUNG-CELLS PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Martin, R. G., Stein, S. 1976; 73 (5): 1655-1659

  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

• ROLE FOR HEME IN MAMMALIAN PROTEIN-SYNTHESIS - ACTIVATION OF AN INITIATION-FACTOR PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Raffel, C., Stein, S., Kaempfer, R. 1974; 71 (10): 4020-4024

  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

• GLUCOSE-METABOLISM IN NEISSERIA-GONORRHOEAE JOURNAL OF BACTERIOLOGY Morse, S. A., Stein, S., Hines, J. 1974; 120 (2): 702-714

  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