Detection of EGFR Mutations in cfDNA and CTCs, and Comparison to Tumor Tissue in Non-Small-Cell-Lung-Cancer (NSCLC) Patients

Lung cancer is the leading cause of cancer-related mortality worldwide. Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) therapies, based on the evaluation of EGFR mutations, have shown dramatic clinical benefits. EGFR mutation assays are mainly performed on tumor biopsies, which carry risks, are not always successful and give results relevant to the timepoint of the assay. To detect secondary EGFR mutations, which cause resistance to 1st and 2nd generation TKIs and lead to the administration of a 3rd generation drug, effective and non-invasive monitoring of EGFR mutation status is needed. Liquid biopsy analytes, such as circulating tumor cells (CTCs) and circulating tumor DNA (cfDNA), allow such monitoring over the course of the therapy. The aim of this study was to develop and optimize a workflow for the evaluation of cfDNA and CTCs in NSCLC patients all from one blood sample. Using Vortex technology and EntroGen ctEGFR assay, EGFR mutations were identified at 0.5 ng of DNA (∼83 cells), with a sensitivity ranging from 0.1 to 2.0% for a total DNA varying from 25 ng (∼4 CTCs among 4000 white blood cells, WBCs) to 1 ng (∼4 CTCs among 200 WBCs). The processing of plasma-depleted-blood provided comparable capture recovery as whole blood, confirming the possibility of a multimodality liquid biopsy analysis (cfDNA and CTC DNA) from a single tube of blood. Different anticoagulants were evaluated and compared in terms of respective performance. Blood samples from 24 NSCLC patients and 6 age-matched healthy donors were analyzed with this combined workflow to minimize blood volume needed and sample-to-sample bias, and the EGFR mutation profile detected from CTCs and cfDNA was compared to matched tumor tissues. Despite the limited size of the patient cohort, results from this non-invasive EGFR mutation analysis are encouraging and this combined workflow represents a valuable means for informing therapy selection and for monitoring treatment of patients with NSCLC.

Abstract B31: Detection of viable tumor cells from cryopreserved buffy coat using the VTX-1 Liquid Biopsy Platform

Introduction: Several circulating tumor cell (CTC) technologies have been developed amidst growing interests in the “liquid biopsy” field. The fully automated VTX-1 platform is developed to gently isolate intact CTCs from whole blood with high recovery and viability, compatible with many applications (1-3). However, many CTC technologies require processing of fresh patient samples at off-site facilities. Here we present encouraging preliminary results showing viable cell isolation by VTX-1 from cryopreserved buffy coat, using a telomerase-selective replicating adenovirus (TelomeScan). This widens potential applications of viable CTC detection for retrospective clinical studies and drug development.

Methods: Buffy coat preparation: Buffy coat was prepared by centrifugation of healthy donor blood collected in EDTA, heparin, or heparin CPT vacutainers. Cell spiking and processing: 1) Cancer cells were spiked into freshly prepared buffy coat and processed with the Vortex chip at different dilutions. 2) Cancer cells were labeled and spiked into healthy donor blood, and buffy coat was prepared and processed by VTX-1 either immediately or following cryopreservation up to 1 week. Imaging was evaluated for cell recovery. Viable, telomerase-activated tumor cell detection: VTX-1 enriched cells were directly collected in chamber slides and infected with the TelomeScan adenovirus (OBP-401) for 24 h (4). The percentage of GFP (+), viable, telomerase-expressing cells was evaluated alongside cell recovery.

Results: MCF7 cells were spiked into freshly prepared buffy coat, resuspended in 8mL, and processed at 5X, 10X, and 20X dilutions. The best compromise between recovery, WBC count, and processing time was obtained for the 10X dilution with 46% recovery. The majority of spiked cells (MCF7 and H1299) collected from buffy coat were shown to be viable, as demonstrated by infection with the telomerase-selective replicating adenovirus (TelomeScan, OBP-401). Cryopreservation of the buffy coat samples showed a slight reduction following cryopreservation.

Discussion: The optimal performance of the Vortex chip on buffy coat samples has previously been shown at 10X dilution. This capability of the VTX-1 was further demonstrated through infection with a telomerase-selective replicating adenovirus. This combined workflow has shown seamless integration from whole blood. Noteworthy recovery and sensitivity were also observed with cryopreserved buffy coat. Patient biobanked samples are currently being pursued. The overall advantages are: a) viable cell detection, b) direct collection of cells into culture media ready for in vitro testing, c) no requirements for fixation, labeling, backflushing, d) a very low WBC background eliminating false positives, and e) the potential to retrospectively analyze clinical biobanked samples at a centralized laboratory.

References: 1. Sollier E et al. Lab Chip 2014. 2. C. Renier et al. Nature Precision Oncology 2017. 3. H. Liu et al. Nature Genomic Medicine 2017. 4. Kojima T et al. J Clin Invest 2009.

Citation Format: Corinne Renier, Jamin Steffen, Azadeh Timnak, Clementine Lemaire, Elodie Sollier, Haiyan E. Liu. Detection of viable tumor cells from cryopreserved buffy coat using the VTX-1 Liquid Biopsy Platform [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B31.

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

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.

VTX-1 Liquid Biopsy System for Fully-Automated and Label-Free Isolation of Circulating Tumor Cells with Automated Enumeration by BioView Platform

Clinicians continue to rely on invasive tissue biopsies as a mean to assess a patient's disease and prescribe appropriate treatment regimens. Biopsies not only are risky and expensive but also limit the understanding of disease. Circulating tumor cells (CTCs) can be isolated from a simple blood draw and offer a promising potential to both diagnose and monitor cancer progression. The VTX‐1 Liquid Biopsy System automates the isolation of clinically relevant CTC populations, while simplifying their collection for easy analysis, ultimately expanding the clinical possibilities for CTCs. We present here the key features and performance of this automated system for isolating CTCs directly from whole blood, both with cell spiking experiments and patient samples. As a first step toward the characterization of CTCs for research applications and transfer to clinical practice, we present workflows for both molecular analyses and automated cell enumeration and biomarker quantification with the BioView imaging platform. © 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.

Abstract 3664: A workflow to evaluate PD-L1 protein expression on circulating tumor cells (CTCs) from non-small cell lung cancer (NSCLC)

Introduction

Many tumors evade immune surveillance by deploying immunosuppressive mechanisms and co-opting immune checkpoint pathways, such as PD-1/PD-L1. PD-1/PD-L1 pathway blockade is a highly promising therapy and has elicited durable antitumor responses in a variety of cancers. Challenges in advancing immunotherapies lie in patient stratification and monitoring therapy. Evaluation of PD-L1 expression is generally regarded as an inclusion criterion for clinical trials. Current methods rely on the analysis of excisional biopsies, which are invasive and carry associated medical risks. Isolation and analysis of CTCs is a noninvasive alternative that may provide, in real-time, more representative information on tumor biomarkers, and allow the monitoring of treatment effectiveness over time. Here, we present an integrated workflow for the analysis of PD-L1 protein expression on CTCs from metastatic NSCLC patients isolated with the Vortex Biosciences VTX-1 liquid biopsy system.

Methods

Cell lines expressing various level of PD-L1 and white blood cells prepared from healthy donors were used to optimize the PD-L1 immunostaining assay. Several PD-L1 antibodies were titrated, and their specificity estimated with isotype controls. PD-L1 expression quantification was evaluated using two independent methods i) Zen 2 imaging (Zeiss) and ii) CellProfiler software. Clinical validation was performed on blood samples collected from a cohort of metastatic NSCLC patients (stage IV) with known PD-L1 tumor status. CTCs were isolated using the VTX-1 Liquid Biopsy System, stained (PD-L1, CK, CD45, CD11b, DAPI) and classified, then PD-L1 expression was quantified.

Results

We have developed a PD-L1 immunofluorescent assay that shows specificity, sensitivity, and very good intra-assay repeatability. The two methods evaluated for the quantification of PD-L1 expression provided equivalent data and could be used interchangeably. The PD-L1 assay was further validated on CTCs isolated from a small cohort of metastatic NSCLC patients. Preliminary data shows heterogeneity in PD-L1 expression levels across CTCs from the same patient. Interestingly, among PD-L1 positive CTCs, both traditional CK+/PD-L1+ and CK-/PD-L1+ cells were observed. To move toward a more automated workflow for immunostaining, imaging, and fluorescence signal analysis, methods to collect CTC on glass slides were evaluated, with cell recovery ranging from 33 to 98%.

Conclusion

We demonstrated the feasibility of evaluating PD-L1 protein expression on NSCLC's CTCs isolated with the VTX-1 Liquid Biopsy System. While further clinical validation is warranted, this test could represent a simple, non-invasive method to help identify patients most likely to respond to PD-1/PD-L1 immunotherapies. Future work will focus on compatibility of the assay with autostainers and fully automated imaging and analysis platforms.

Citation Format: Corinne Renier, Charles L. Wilkerson, SJ Claire Hur, Da Eun Rachel Park, Clementine A. Lemaire, Melissa Matsumoto, James Carroll, Steve Crouse, Jonathan W. Goldman, Edward B. Garon, Dino Di Carlo, Elodie Christen-Sollier. A workflow to evaluate PD-L1 protein expression on circulating tumor cells (CTCs) from non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3664.

Regression of experimental NIS-expressing breast cancer brain metastases in response to radioiodide/gemcitabine dual therapy

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⁻.

Classification of large circulating tumor cells isolated with ultra-high throughput microfluidic Vortex technology

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.

Workflow optimization of whole genome amplification and targeted panel sequencing for CTC mutation detection

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.

Abstract 1847: Evaluating the metastatic potential and the molecular heterogeneity of patient-derived orthotopic xenograft models of triple-negative breast cancer

We report an in-depth characterization of patient-derived orthotopic xenograft (PDOX) models of triple-negative breast cancer (TNBC) regarding their molecular profile at the single cell level, tumor heterogeneity, 3D organoid generation, and ability to generate circulating tumor cells (CTCs). A panel of seven TNBC PDOX tumors were grown orthotopically in Nod scid gamma mice and used in this study. Blood obtained via cardiac puncture from tumor bearing animals was processed on the Vortex microfluidic platform, for label-free, size-based enrichment of circulating tumor cells (CTCs). Enriched cell populations were stained for human-specific cytokeratin (CK) and Vimentin (Vim), mouse-specific CD45, and DAPI; CTCs were identified as cells that were CD45 negative and positive for CK or Vim. Bulk tumor growing in the mammary fat pads was dissociated to single cells and characterized using Fluidigm’s® PolarisTM platform for single cell biological experimentation and cDNA generation within an integrated fluidic circuit (IFC). From the cell suspension, Polaris identified single cells that were then processed for mRNA-seq. The resulting cDNA libraries were then multiplexed using Nextera XT® (Illumina®) and sequenced on Illumina systems. Data generated from mRNA-seq was processed to correct for confounding factors such as cell size, cell cycle and read depth and then analyzed to screen for heterogeneity between different populations of cells. Tumors were analyzed by flow cytometry for both tumor and immune cells and additionally the single cell suspension was seeded into 3-D culture to generate organoids. Finally, organs from tumor bearing animals were analyzed for metastases. With the Vortex platform, we detected CTCs from a majority of our PDOX tumor-bearing mice. The total number of CTCs varied over a wide range between different PDOX tumors. There was a clear heterogeneity in CTCs in terms of CK and Vim expression. In CTCs from one of the PDOX tumors, we detected a small population of CTCs that were either CK+ or Vim+ but the major fraction that was double positive (Vim+ CK+). Probing the bulk tumor from different PDOX models revealed heterogeneity in the levels and number of cells positive for cell surface markers like EpCAM and a difference in the levels of infiltrating myeloid cells (CD11b+). mRNA-seq analyses of individual tumor cells from the bulk tumor belonging to different PDOX models will be described. Additionally, lung and brain metastases were identified. 3D organoid cultures from our PDOX models were successfully grown and their gene expression profiles will be analyzed. In summary, PDOX models of TNBC will help advance our understanding of the molecular basis of this deadly cancer.

Citation Format: Vishnu C. Ramani, Rakhi Gupta, Gerald Quon, Melanie Triboulet, Corinne Renier, Cassandra Greene, Chad Sanada, Tracy Lu, Lukasz Szpankowski, Naveen Ramalingam, Ameen A. Salahudeen, Sean de la O, Ranjani Rajapaksa, Shoshana Levy, Anne A. Leyrat, Jay A. West, Elodie Sollier-Christen, Calvin J. Kuo, George W. Sledge, Stefanie S. Jeffrey. Evaluating the metastatic potential and the molecular heterogeneity of patient-derived orthotopic xenograft models of triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1847. doi:10.1158/1538-7445.AM2017-1847

Abstract 2822: Establishing the use of Vortex technology for investigating circulating tumor cells in mouse models of breast cancer

Background: Circulating tumor cells (CTCs) are precursors of metastatic disease and are an important indicator of the disease progression and outcome of many cancers. Though several recent studies have advanced our understanding of CTCs, many critical areas of CTC biology remain largely unexplored. Murine models of cancer offer a unique opportunity to address this issue. However, small sample volumes, low number of CTCs, difficulty to access ports for blood collection are challenges that diminish the utility of mouse models for studying CTCs. In our previous studies, we had validated the use of Vortex technology for the label-free capture of CTCs from blood samples of different cancers. In this current study, we now report our recent, unpublished data on the adaptation of Vortex platform for enriching and characterizing murine and human tumor cells from mouse blood.

Methods: By spiking tumor cells into small volumes of mouse blood (200-400 µl) from cardiac puncture, we tested the impact of i) different dilutions of mouse blood (10X, 20X, 40X); ii) varying numbers of tumor cells; iii) different cell types (MDA-MB-231, 4T1 and EMT6); and iv) sample recycling on capture efficiency and purity. Blood was processed through the Vortex plastic chip and, to accurately identify and enumerate the enriched tumor cells, we developed a staining protocol that labels human- or murine-specific cytokeratin, vimentin, and CD45.

Results: Our results reveal that over a range of dilutions tested, just after one cycle, 10X dilution of mouse blood was superior, yielding a capture efficiency of 38.83% and a purity of 33% for MDA-MB-231 cells, compared to 20X (34.16% efficiency, 31.1% purity), and 40X (31.83% efficiency, 31% purity) dilutions. We are currently testing whether recycling the blood flow-through would increase the recovery. Even when as many as ~7500 tumor cells were spiked in mouse blood, the Vortex platform was able to successfully enrich tumor cells with high consistency and purity. Importantly, we were now able to successfully isolate human and murine tumor cell lines with varying levels of epithelial cell adhesion molecule (EpCAM) expression (4T1 - high, MDA-MB-231 - moderate to low) spiked into mouse blood. Experiments confirming the viability and growth rate of cancer cells isolated from mouse blood using MTT assay will also be presented.

Conclusion: In summary, our results reveal the use of the Vortex technology for studying CTCs in murine models of cancer, with the ability to handle volumes of blood as low as 200uL while having a capacity to capture extremely large number of CTCs. While this study was focused on breast cancer, our workflow is easily adapted to other malignancies. Studies are underway to grow viable CTCs from tumor bearing animals and isolated by this platform for subsequent growth in 3D culture systems for future biologic and drug testing studies.

Citation Format: Vishnu Ramani, Rakhi Gupta, Melanie Triboulet, Corinne Renier, Steve C. Crouse, Elodie Sollier-Christen, Stefanie S. Jeffrey. Establishing the use of Vortex technology for investigating circulating tumor cells in mouse models of breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2822. doi:10.1158/1538-7445.AM2017-2822

Label-free isolation of prostate circulating tumor cells using Vortex microfluidic technology

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.

Abstract 4967: Label-free collection of prostate circulating tumor cells using microfluidic Vortex technology

BACKGROUND

Prostate cancer is among the most common cancers in men worldwide. Better markers than Prostate Specific Antigen (PSA) are still needed for the detection and monitoring of disease progression. Circulating Tumor Cells (CTCs) are shed into the blood stream from primary tumor(s) and may play key roles in the metastatic process. Liquid biopsies have emerged as a promising approach, with a correlation between the CTC numbers and patient prognosis for prostate cancer. CTCs have also been shown to enable early detection of recurrence, and could be potential candidates for guiding cancer therapy in real-time [1]. Current CTC enrichment technologies, including immuno-affinity and size-based filtration methods, have focused on high capture efficiency with sometimes tedious sample preparation and overall low purity.

METHOD

Here, we describe the use of the microfluidic Vortex Chip [2] for rapid and size-based isolation of CTCs from the blood of 23 patients with advanced prostate cancer, and 10 healthy donors; 5 being &lt;30 years old, 5 age-matched with the patient cohort. Requiring no upstream sample preparation, blood was diluted 10-fold and processed through the highly parallelized Vortex Chip at 8 mL/min (800 μL/min whole blood). Larger cells (predominantly CTCs) were captured in microscale vortices produced on the Chip, released into a small volume and collected off-chip for CK, PSA, CD45 and DAPI immunostaining and enumeration.

RESULTS

Preliminary work with LNCaP prostate cancer cells spiked in blood showed a 29% capture efficiency and 50% purity. In vitro cell assays confirmed that cells enriched with Vortex chip were alive and proliferating for up to 7 days. For 23 patient samples, CTCs were captured (0.5 - 20 CTCs/mL) with high purity (3.6 - 72.3%), in less than 1H, without prior sample preparation. 11.5% of the cells collected were CK and PSA-negative, but some were identified as undergoing epithelial-mesenchymal transition (EMT) following staining for vimentin and N-cadherin. Few atypical cells were also isolated from age-matched healthy donors (0.7 - 2.8 CTCs/mL), while none was detected in younger healthy donors. Using a threshold calculated from the age-matched healthy donors (3.31 CTCs/mL = mean + 2CV), 70% of the patients were characterized as “positive for CTCs”. No correlation was found between CTC counts and elevated PSA level.

CONCLUSION

These results demonstrate the ability to rapidly collect pure populations of CTCs in metastatic prostate cancer, independent of surface marker expression, without prior sample preparation. Future studies will use chips with optimized capture performance, sample recycling, and will include CTC molecular analysis by targeted panel sequencing. A larger cohort of healthy donors is also being examined to determine a statistically-robust CTC baseline for this size-based capture approach.

[1] Scher Hi, et al., J. Clin. Oncol. 2015

[2] Sollier E, et al., Lab Chip 2014

Citation Format: Edward Pao, Corinne Renier, Clementine Lemaire, James Che, Melissa Matsumoto Di Carlo, Melanie Triboulet, Sandy Srivinas, Stefanie S. Jeffrey, Rajan P. Kulkarni, Matthew Rettig, Elodie Sollier, Dino Di Carlo. Label-free collection of prostate circulating tumor cells using microfluidic Vortex technology. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4967.

High efficiency vortex trapping of circulating tumor cells

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.

Abstract 1997: Label-free concentration of viable breast cancer CTCs for single cell Western blotting

The isolation of circulating tumor cells (CTCs) in blood can aid in cancer prognosis, characterize genetic mutations for targeted therapies, and elucidate the biological mechanisms of metastasis. While CTCs provide clinical utility, there are still several technical difficulties with CTC isolation and analysis. CTCs are very rare (1-10 cells/mL of blood) and current isolation methods rely on immunocapture, require long sample preparation, and fail to deliver viable cells. Further, recent advances in single cell analysis of CTCs have been limited to genomic studies, in which DNA/mRNA does not provide a complete picture of CTCs at the functional level, as mRNA expression may only account for a portion of protein expression. The ability to study and measure the protein expression of CTCs could provide insight into the mechanisms driving cancer progression and signaling dysregulation. Unfortunately, conventional proteomic tools (e.g. immunocytochemistry and Western blot) either do not provide sufficient specificity or sensitivity toward single cell levels. Thus, there is a lack of tools that can provide quantitative protein analysis for rare CTCs.

To address this gap, we enable rare cell Western blotting by combining isolation and proteomic technologies in a unique workflow:

(i) Label-free Vortex enrichment of rare larger cells from blood samples. Larger cancer cells are trapped within an array of microscale fluid vortices that form in simple rectangular reservoirs, while smaller blood cells pass through. The cancer cells are stably maintained in the vortices, allowing for solution exchange, followed by release upon lowering the flow rate. With this device, we were able to release a small volume (∼500 μL) of concentrated, viable cancer cells (MCF7) from healthy blood, at high throughput, capture efficiency (35%), purity (&gt;80%), and ∼10,000 fold enrichment. CTCs were also successfully extracted and enumerated from the blood of patients with breast cancer (N = 18, from 0.75 to 23.25 CTCs/mL).

(ii) High-specificity and multiplexed protein analysis of rare cancer cells with single cell Western blotting (scWB). Enriched CTCs are placed into microwells patterned into a polyacrylamide gel for the scWB assay (in-situ chemical lysis in the microwells, electrophoresis into bulk gel layer, photo-immobilization, and subsequent antibody-probing of immobilized proteins). Here, we demonstrate scWB compatibility with rare cells by spiking MCF7s into normal blood and performing protein separations. The scWB is multiplex and can assay several target proteins simultaneously. Cells stained for surface markers (anti-EpCAM) are also compatible, and the scWB can resolve complete immunocomplexes without disrupting the location of the intracellular targets (GAPDH, ERK).

With the integration of these technologies, we push the limits of quantitative protein analysis of CTCs, an essential step to better understand these rare populations.

Citation Format: Elly Sinkala, Elodie Sollier, Corinne Renier, James Che, Stefanie S. Jeffrey, Amy E. Herr. Label-free concentration of viable breast cancer CTCs for single cell Western blotting. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1997. doi:10.1158/1538-7445.AM2015-1997

Abstract 477: Evaluation of tumor uptake and retention in a mouse model of breast cancer brain metastases by I-124 positron emission tomography (PET) imaging

The central nervous system (CNS) is emerging as the first site of metastatic disease in women with breast cancer. Women with hormone unresponsive tumors and/or HER-2 overexpressing tumors are disproportionately affected. Breast cancer brain metastasis represents a unique therapeutic challenge because of the limited access to the CNS of many anticancer drugs.

Radioiodide (131I) therapy may provide a therapeutic alternative since over 70% of invasive breast cancers, and some brain metastases express the sodium-iodide symporter (NIS). The rationale for this approach is based on the success of 131I radioablative therapy for thyroid cancers.

Objectives: To evaluate CNS permeability, kinetics of radioiodine uptake and retention in our NIS expressing breast cancer brain metastasis (BCBM) mouse model.

Methods: A brain-seeking clone of the hormone independent ((ER-/PR-/HER2-) human breast cancer cell line MDA-MB-231 (231BR) was transduced with a lentiviral vector carrying a bicistronic cassette with NIS and the firefly luciferase (Fluc) genes separated by an internal ribosomal entry site (IRES). Single cell clones were selected and characterized for iodide uptake and bioluminescence. 1 Million NIS-Fluc-MDAMB231 cells were implanted subcutaneously in the mammary fat pad (mfp) of nude mice (NCr nude) and tumor growth was monitored by serial in vivo bioluminescent imaging and external tumor volume measurements. NIS-Fluc mfp tumor xenografts were then explanted, 1×1 mm pieces excised and inserted stereotactically into the basal ganglia of the mouse. Bioluminescence imaging was used to follow intracranial tumor growth over time. Kinetics of 123I uptake and biodistribution in mfp xenografts mice was evaluated by ex vivo radioactive count and biodistribution of 124I was evaluated in vivo by positron emission tomography (PET) imaging on BCBM mice.

Results: Brain tumors 124I uptake was evident on the PET 1 hour post injection of the tracer, with values ranging from 1.60 to 3.25 % injected dose/gram of tissue (%ID/g) whereas thyroid uptake was between 6.99 and 11.19 %ID/g. At 20 hours post injection, the brain tumors showed a sustained 124I retention while uptake in most other organs (except thyroid and stomach) was close to background levels; brain tumor to normal brain tissue mean uptake ratio was ranging from to 217.12 to 541.50 (versus 2.02 to 2.68 at 1 hour post injection). The kinetics of 124I uptake was in agreement with the data obtained from the ex vivo counts in mfp xenografts.

Conclusions: We have characterized the kinetics of iodide uptake and retention in a model of breast cancer brain metastases. We showed that NIS expressing BCBM are able to concentrate and retain 124I for prolonged period of time. These results together with dosimetric calculations will allow us to adjust the dosage and timing for 131I therapy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 477.

Breast cancer brain metastases express the sodium iodide symporter

Breast cancer brain metastases are on the rise and their treatment is hampered by the limited entry and efficacy of anticancer drugs in this sanctuary. The sodium iodide symporter, NIS, actively transports iodide across the plasma membrane and is exploited clinically to deliver radioactive iodide into cells. As in thyroid cancers, NIS is expressed in many breast cancers including primary and metastatic tumors. In this study NIS expression was analyzed for the first time in 28 cases of breast cancer brain metastases using a polyclonal anti-NIS antibody directed against the terminal C-peptide of human NIS gene and immunohistochemical methods. Twenty-five tumors (84%) in this retrospective series were estrogen/progesterone receptor-negative and 15 (53.6%) were HER2+. Overall 21 (75%) cases and 80% of HER2 positive metastases were NIS positive. While the predominant pattern of NIS immunoreactivity is intracellular, plasma membrane immunopositivity was detected at least focally in 23.8% of NIS-positive samples. Altogether, these findings indicate that NIS expression is prevalent in breast cancer brain metastases and could have a therapeutic role via the delivery of radioactive iodide and selective ablation of tumor cells.

Endogenous NIS expression in triple-negative breast cancers

BACKGROUND

The sodium iodide symporter (NIS) mediates iodide transport into cells and has been identified in approximately 70% of breast cancers. Functional NIS expression raises the possibility of using (131)I for therapeutic targeting of tumor cells. Treatment of triple-negative breast cancers [estrogen/progesterone receptor-negative and HER2-negative (ER-/PR-/HER2-)] is primarily limited to chemotherapy. Our aim was to characterize NIS expression in this subset of tumors.

METHODS

Archival tissue sections from 23 women with triple-negative breast cancer were analyzed for NIS expression using immunohistochemical methods and an anti-human NIS antibody. Tumors were evaluated for the presence of plasma membrane immunoreactivity. One patient with a NIS-expressing positive tumor underwent (123)I scintigraphic imaging with dosimetric analysis.

RESULTS

Fifteen cases (65.2%) demonstrated NIS-positivity with 11 tumors (47.8%) exhibiting strong expression. Plasma membrane immunoreactivity was observed in four breast cancers and was equivocal in another four tumors. Tumor-specific radioiodide uptake was demonstrated by (123)I scintigraphy in a patient with a large primary breast cancer unresponsive to neoadjuvant therapy. The tumor concentrated 2.05, 1.53, and 1.96 times more isotope than normal breast tissue at 1, 5, and 21 h. The relative increased uptake is consistent with positive NIS expression in the tumor on definitive surgery; however, the cumulative concentration in the tumor was not sufficient to achieve a therapeutic effect, had the isotope been (131)I.

CONCLUSIONS

NIS is strongly expressed in a significant proportion of triple-negative breast cancer cells, suggesting a potential role for NIS-directed (131)I-radioablative strategies in this patient population.

Development of a breast cancer brain metastases model to study 131I radioablative therapy

Abstract #2011

Background: An increasing number of women develop brain metastases (BM) after breast cancer (BC) treatment. A large proportion of these are estrogen/progesterone receptor-negative (ER-/PR-) and/or Her-2/neu overexpressing tumors. 131I radioablative therapy may provide a therapeutic alternative to treat metastases at this anatomic sanctuary since over 70% of invasive breast cancers, including a majority of ER- tumors and some brain metastases (unpublished data) express the sodium-iodide symporter (NIS). This approach relies on the success of radioiodide as a targeted treatment for thyroid cancers. To test this concept, we developed a BC BM model using tumor cells engineered to express NIS.&#x2028; Methods: MDAMB231 and SKBr3 cell lines were transduced with a lentiviral vector carrying a bicistronic cassette with NIS and the firefly luciferase (Fluc) genes separated by an internal ribosomal entry site. Single cell clones were selected and characterized for iodide uptake and bioluminescence. NIS-Fluc-MDAMB231 or NIS-Fluc SKBr3 cells (2.5 x 106 cells) were implanted subcutaneously (sc) in the mammary fat pad (mfp) of nude mice (NCr nude; 5-6 weeks old; n=5). NIS-Fluc mfp tumor xenografts were then explanted, 1x1 mm pieces excised and inserted stereotactically into the basal ganglia of the animal. All tumor development was monitored by serial in vivo bioluminescent imaging. Once established, brain tumors were excised, dissociated, established in tissue culture and re-implanted sc in the mfp of a new set of mice. Successive passages in the mfp then in the brain were performed in an attempt to increase tumor take. A second strategy tested with MDAMB231 cells consisted of direct implantation of cells into the basal ganglia. NIS expression was evaluated on tissue sections with a polyclonal antibody raised against the C-terminus of the human NIS.&#x2028; Results: All mice survived and were healthy in appearance. Intracranial implantation of mfp xenografts was highly successful with 66% take in both MDAMB231 (after two passages) and SKBr3 (after first passage). Bioluminescent imaging revealed sustained growth of tumors for more than 4 weeks. Microscopically, the explanted brain tumors had a cellular appearance without stromal cell or lymphocytic infiltration and were congruent with the histology of mfp xenografts. However, the tumor cell population was heterogeneous as NIS expression was present with plasma membrane staining in about 50% of SKBr3 and 15% of MDAMB231 cells. Direct cell implantations failed as no discernible bioluminescence was noted over a period of 3 weeks and no visible tumor at necropsy.&#x2028; Conclusions: A BCBM model has been developed by implanting intracranially mfp xenografts obtained with ER-/PR- +/- Her-2/neu overexpressing cells. Using this model, it will be possible to evaluate the effects of 131I on NIS-expressing BCBM.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2011.

Genomic and functional conservation of sedative-hypnotic targets in the zebrafish

OBJECTIVES

The zebrafish is an ideally suited vertebrate animal model for large-scale genetic screens and is emerging as a model organism in pharmacological and behavioral research. We investigated the effects of sedative hypnotics commonly used in humans on zebrafish locomotor activity and identified the corresponding genomic and receptor binding targets.

METHODS

We studied radioreceptor binding and behavioral responses to compounds with known sedative hypnotic properties representing multiple pharmacological classes. These included GABAergic hypnotics such as benzodiazepines, barbiturates, and baclofen; alpha-2 adrenergic agonists; and histaminergic H1 antagonists. An automated system was used to quantify behavioral effects. Zebrafish homologs of histamine receptor H1, gamma-amino-n-butyric acid type A (alpha-subunit), and gamma-amino-n-butyric acid type B (1 and 2) receptor genes were identified through translating queries of the zebrafish Zv4 database with human receptor protein sequences. A pilot screen of 154 N-ethyl-N-nitroso-urea-mutagenized F2 families was conducted with pentobarbital, flurazepam and mepyramine.

RESULTS

Radioreceptor binding studies revealed high affinity binding sites for known gamma-amino-n-butyric acid type A, gamma-amino-n-butyric acid type B, and histaminergic ligands. Drug immersion of 5-7-day-old larvae reduced mobility and, in some cases, produced a complete state of unresponsive immobility similar to anesthesia. These effects were dose-dependent and rapidly reversible in water. As established in mammals, (R)-baclofen was more active behaviorally and had higher affinity in binding studies when compared with (S)-baclofen. In this model, (S)-baclofen only partially reduced activity at high dose and blocked (R)-baclofen behavioral hypnotic effects. Genomic sequences with high similarity to the corresponding pharmacological targets were identified, but no mutants were found in the pilot screen.

CONCLUSIONS

These results demonstrate conservation of gene, protein and function for many established sedative hypnotic pathways. The results indicate feasibility of conducting large-scale pharmacogenomic screens to isolate novel proteins modulating susceptibility to hypnotic compounds in a vertebrate system.

Comparison of the canine and human olfactory receptor gene repertoires

In this study, 817 novel canine olfactory receptor (OR) sequences were identified, and 640 have been characterized. Of the 661 characterized OR sequences, representing half of the canine repertoire, 18% are predicted to be pseudogenes, compared with 63% in human and 20% in mouse.

Background

Olfactory receptors (ORs), the first dedicated molecules with which odorants physically interact to arouse an olfactory sensation, constitute the largest gene family in vertebrates, including around 900 genes in human and 1,500 in the mouse. Whereas dogs, like many other mammals, have a much keener olfactory potential than humans, only 21 canine OR genes have been described to date.

Results

In this study, 817 novel canine OR sequences were identified, and 640 have been characterized. Of the 661 characterized OR sequences, representing half of the canine repertoire, 18% are predicted to be pseudogenes, compared with 63% in human and 20% in mouse. Phylogenetic analysis of 403 canine OR sequences identified 51 families, and radiation-hybrid mapping of 562 showed that they are distributed on 24 dog chromosomes, in 37 distinct regions. Most of these regions constitute clusters of 2 to 124 closely linked genes. The two largest clusters (124 and 109 OR genes) are located on canine chromosomes 18 and 21. They are orthologous to human clusters located on human chromosomes 11q11-q13 and HSA11p15, containing 174 and 115 ORs respectively.

Conclusions

This study shows a strongly conserved genomic distribution of OR genes between dog and human, suggesting that OR genes evolved from a common mammalian ancestral repertoire by successive duplications. In addition, the dog repertoire appears to have expanded relative to that of humans, leading to the emergence of specific canine OR genes.

THEGENETICS OFNARCOLEPSY

Human narcolepsy is a genetically complex disorder. Family studies indicate a 20-40 times increased risk of narcolepsy in first-degree relatives and twin studies suggest that nongenetic factors also play a role. The tight association between narcolepsy-cataplexy and the HLA allele DQB1*0602 suggests that narcolepsy has an autoimmune etiology. In recent years, extensive genetic studies in animals, using positional cloning in dogs and gene knockouts in mice, have identified abnormalities in hypothalamic hypocretin (orexin) neurotransmission as key to narcolepsy pathophysiology. Though most patients with narcolepsy-cataplexy are hypocretin deficient, mutations or polymorphisms in hypocretin-related genes are extremely rare. It is anticipated that susceptibility genes that are independent of HLA and impinge on the hypocretin neurotransmitter system are isolated in human narcolepsy.

A 1-Mb resolution radiation hybrid map of the canine genome

The purebred dog population consists of >300 partially inbred genetic isolates or breeds. Restriction of gene flow between breeds, together with strong selection for traits, has led to the establishment of a unique resource for dissecting the genetic basis of simple and complex mammalian traits. Toward this end, we present a comprehensive radiation hybrid map of the canine genome composed of 3,270 markers including 1,596 microsatellite-based markers, 900 cloned gene sequences and ESTs, 668 canine-specific bacterial artificial chromosome (BAC) ends, and 106 sequence-tagged sites. The map was constructed by using the RHDF5000-2 whole-genome radiation hybrid panel and computed by using MULTIMAP and TSP/CONCORDE. The 3,270 markers map to 3,021 unique positions and define an average intermarker distance corresponding to 1 Mb. We also define a minimal screening set of 325 highly informative well spaced markers, to be used in the initiation of genome-wide scans. The well defined synteny between the dog and human genomes, established in part as a function of this work by the identification of 85 conserved fragments, will allow follow-up of initial findings of linkage by selection of candidate genes from the human genome sequence. This work continues to define the canine system as the method of choice in the pursuit of the genes causing mammalian variation and disease.

Mapping and sequencing of the canine NRAMP1 gene and identification of mutations in leishmaniasis-susceptible dogs

The NRAMP1 gene (Slc11a1) encodes an ion transporter protein involved in the control of intraphagosomal replication of parasites and in macrophage activation. It has been described in mice as the determinant of natural resistance or susceptibility to infection with antigenically unrelated pathogens, including Leishmania. Our aims were to sequence and map the canine Slc11a1 gene and to identify mutations that may be associated with resistance or susceptibility to Leishmania infection. The canine Slc11a1 gene has been mapped to dog chromosome CFA37 and covers 9 kb, including a 700-bp promoter region, 15 exons, and a polymorphic microsatellite in intron 1. It encodes a 547-amino-acid protein that has over 87% identity with the Slc11a1 proteins of different mammalian species. A case-control study with 33 resistant and 84 susceptible dogs showed an association between allele 145 of the microsatellite and susceptible dogs. Sequence variant analysis was performed by direct sequencing of the cDNA and the promoter region of four unrelated beagles experimentally infected with Leishmania infantum to search for possible functional mutations. Two of the dogs were classified as susceptible and the other two were classified as resistant based on their immune responses. Two important mutations were found in susceptible dogs: a G-rich region in the promoter that was common to both animals and a complete deletion of exon 11, which encodes the consensus transport motif of the protein, in the unique susceptible dog that needed an additional and prolonged treatment to avoid continuous relapses. A study with a larger dog population would be required to prove the association of these sequence variants with disease susceptibility.

Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes

We present here the first fully integrated, comprehensive map of the canine genome, incorporating detailed cytogenetic, radiation hybrid (RH), and meiotic information. We have mapped a collection of 266 chromosome-specific cosmid clones, each containing a microsatellite marker, to all 38 canine autosomes by fluorescence in situ hybridization (FISH). A 1500-marker RH map, comprising 1078 microsatellites, 320 dog gene markers, and 102 chromosome-specific markers, has been constructed using the RHDF5000-2 whole-genome radiation hybrid panel. Meiotic linkage analysis was performed, with at least one microsatellite marker from each dog autosome on a panel of reference families, allowing one meiotic linkage group to be anchored to all 38 dog autosomes. We present a karyotype in which each chromosome is identified by one meiotic linkage group and one or more RH groups. This updated integrated map, containing a total of 1800 markers, covers >90% of the dog genome. Positional selection of anchor clones enabled us, for the first time, to orientate nearly all of the integrated groups on each chromosome and to evaluate the extent of individual chromosome coverage in the integrated genome map. Finally, the inclusion of 320 dog genes into this integrated map enhances existing comparative mapping data between human and dog, and the 1000 mapped microsatellite markers constitute an invaluable tool with which to perform genome scanning studies on pedigrees of interest.

Isolation of DNA markers informative in purebred dog families by genomic representational difference analysis (gRDA)

Genomic Representational Difference Analysis (gRDA) is a subtractive DNA method to clone the differences between two related genomes, called tester and driver. We have evaluated this method to obtain polymorphic DNA markers for pedigree dogs. Amplified size-selected genomic restriction fragments (amplicons) of two dog littermates were repeatedly hybridized to each other in order to remove (subtract) those restriction fragments common to both sibs. Already after two rounds of subtractive hybridization, a clear enrichment of presumably tester-specific restriction fragments was observed, which was even more pronounced after the third round of subtraction. A plasmid library of 3000 recombinant clones was constructed of the second round and of the third round difference product. DNA sequence determination of randomly chosen clones of each difference product showed that approximately 1000 unique clones were obtained in the second-round difference product and approximately 500 in the third-round difference product. About half of the clones identified in the second-round difference product were also present in the third-round difference product. Of the second-round difference product, 39 different gRDA fragments could be identified, of which 21 were tester specific. In the third-round difference product, 22 different gRDA fragments were identified, of which 18 were tester specific. There were 13 fragments in common, resulting in a total of 48 different fragments. In order to establish the localization of these markers, we performed mapping using the dog radiation hybrid panel RHDF5000. Of 39 mapped clones, 29 were mapped to 20 existing RH groups, and 10 remained unlinked. It is concluded that gRDA is suitable to generate DNA markers to track disease genes within lines of pedigree dogs.

Cloning, characterization, and physical mapping of the canine Prop-1 gene (PROP1): exclusion as a candidate for combined pituitary hormone deficiency in German shepherd dogs

Abnormalities in the genes encoding Pit-1 and Prop-1 have been reported to cause combined pituitary hormone deficiency (CPHD) in mice and humans. In dogs, a similar phenotype has been described in the German shepherd breed. We have previously reported that the Pit-1 gene (POU1F1) is not mutated in affected German shepherd dogs. In this study, we report the isolation and mapping of the canine Prop-1 gene (PROP1), and we assessed the involvement of PROP1 in German shepherd dog dwarfism. The canine PROP1 gene was found to contain three exons, encoding a 226 amino acid protein. The deduced amino acid sequence was 79% and 84% homologous with the mouse and human Prop-1 protein, respectively. Using fluorescence in situ hybridization, PROP1 was mapped to canine chromosome 11. Further mapping with a canine radiation hybrid panel showed co-localization with the polymorphic DNA marker AHT137. Sequence analysis of genomic DNA from dwarf German shepherd dogs revealed no alterations in the PROP1 gene. Moreover, linkage analysis of AHT137 revealed no co-segregation between the PROP1 locus and the CPHD phenotype, excluding this gene as candidate for canine CPHD and providing a new spontaneous model of hypopituitarism.

Cloning of the canine gene encoding transcription factor Pit-1 and its exclusion as candidate gene in a canine model of pituitary dwarfism

Combined pituitary hormone deficiency (CPHD) is an autosomal recessive inherited disease of German shepherd dogs characterized primarily by dwarfism. In mice and humans a similar genetic disorder has been described that results from an alteration in the gene encoding the transcription factor Pit-1. In this study we characterized the canine Pit-1 gene, determined the chromosomal localization of the Pit-1 gene, and screened dwarf German shepherd dogs for the presence of mutations in this gene. The full-length canine Pit-1 cDNA contained an open reading frame encoding 291 amino acids, 92 bp of 5'-untranslated region, and 1959 bp of 3'-untranslated region. The deduced amino acid sequence was highly homologous with Pit-1 of other mammalian species. Using a Pit-1 BAC clone as probe, the Pit-1 gene was mapped by FISH to canine Chromosome (Chr) 31. In dwarf German shepherd dogs a C to A transversion was detected, causing a Phe (TTC) to Leu (TTA) substitution at codon 81. This alteration was present neither in other canine breeds analyzed nor in other mammalian species. However, healthy German shepherd dogs were also homozygous for the mutant allele, indicating that it is not the primary disease-causing mutation. In addition, linkage analysis of polymorphic DNA markers flanking the Pit-1 gene, 41K19 and 52L05, revealed no co-segregation between the Pit-1 locus and the CPHD phenotype. These findings suggest that a gene other than Pit-1 is responsible for the pituitary anomaly in dwarf German shepherd dogs.

Characterization of 463 type I markers suitable for dog genome mapping

In total, 463 canine gene markers were identified and characterized to serve as reagents in canine genome map projects. These markers are distributed over 221 canine gene markers, 139 TOASTs (Traced Orthologous Sequence Tags), 27 canine TOASTs, and 76 huESTs (human Expressed Sequence Tags). Out of 310 canine gene markers, 59%-84% were successfully amplified on dog DNA, the highest rates of success being observed when the exon/intron structure is known. Concerning TOASTs and human ESTs, of the 225 and 300 markers analyzed, 62% and 25% respectively were able to produce a dog positive amplification. As part of an ongoing project to map the canine genome using a dog/hamster radiation hybrid panel, these markers were tested for their specificity on dog versus hamster DNA. Thus 61%, 21%, and 12% of dog gene markers, TOASTs, and huESTs met the criteria required for radiation hybrid mapping, respectively. All of these 463 canine gene markers, however, are available and will be of value to any other mapping strategies.

Toward a dog radiation hybrid map

Dog fibroblasts grown from a biopsy performed in a male mongrel were fused after gamma irradiation with thymidine kinase-deficient hamster cells and cultivated in selection medium. A total of 148 clones were obtained and screened by means of PCR amplification using primers corresponding to a dog-specific short repetitive element and to dog microsatellites and genes. One hundred seven cell lines were selected and grown in roller bottles and the distribution of 39 markers was analyzed in the extracted DNA. The results clearly indicate that this panel of hybrid cell lines should prove invaluable for constructing a map of the canine genome. In parallel, for more than 500 microsatellites present in the databases or screened from two libraries of short inserts, we have determined PCR conditions favoring dog-specific products even in the presence of hamster DNA. These highly polymorphic microsatellites should be useful in further linkage studies. We have also characterized 254 markers: dog genes, human expressed sequenced tags (huESTs), and traced orthologous amplified sequenced tags (TOASTs). Once mapped, these will constitute powerful tools to detect regions of conserved synteny in human and other mammalian genomes.

A whole-genome radiation hybrid map of the dog genome

A whole genome radiation hybrid (RH) map of the canine genome was constructed by typing 400 markers, including 218 genes and 182 microsatellites, on a panel of 126 radiation hybrid cell lines. Fifty-seven RH groups have been determined with lod scores greater than 6, and 180 framework landmarks were ordered with odds greater than 1000:1. Average spacing between adjacent markers is 23 cR5000, an estimated physical distance of 3.8 Mb. Fourteen groups have been assigned to 9 of the canine chromosomes, and a comparison of RH and genetic groups allowed the successful bridging of both types of data on one map composed of 31 RH and 13 syntenic RH groups. Comparison of canine, human, mouse, and pig maps underlined regions of conserved synteny. This integrated map, covering an estimated 80% of the dog genome, should prove a powerful tool for localizing and identifiying genes implicated in pathological and phenotypical traits.

Risk factors for work-related violent victimization

This case-control study used the National Crime Victimization Survey database (a national sample of housing addresses) to examine sociodemographic risk factors for becoming a victim of work-related robbery and assault. Cases (N = 267) reported having been violently victimized in the previous 6 months. Controls (N = 1,783) were chosen from all nonvictims of violent crime at the end of the 6-month period. Risk factors varied by type of victimization, and differences were evident between men and women. Men less than 45 years of age had an increased risk for assault [odds ratio (OR) = 2.0-2.7], compared with those 55 years of age and older; and those with a family income of less than $40,000 had an increased risk for assault (OR = 1.7-1.9), compared with those having a family income of $50,000 or more. We found a decreased risk for those with a high school education (OR = 0.6), compared with those with some college education. For women, an increased risk was seen for ages 16-18 years (OR = 3.3) and 25-34 years (OR = 2.3), compared with those 55 years of age or older. Women who were divorced or separated (OR = 4.4) and never-married (OR = 2.1) were at higher risk than women who were married. We found a decreased risk for nonwhites (OR = 0.5), compared with whites.

Injury from dairy cattle activities

Animals have been implicated as an important source of injury for farm household members. Little is known, however, about the specific activities associated with the animal/livestock operations that place a person at increased or decreased risk for injuries. The primary aim of this case-control study was to identify which dairy cattle operation activities (that is, milking, feeding, cleaning barns, trimming and treating feet, dehorning, assisting with difficult calvings, and doing treatments) were associated with an increased or decreased risk of injury. We found milking to have the greatest increase in risk for injury. The ratios for increasing hours per week spent at milking (0, 1-10, 11-20, 21-30, 31-63) were 1.0, 2.3, 5.5, 10.9, and 20.6, respectively. We also found an increased rate ratio associated with trimming or treating hooves (rate ratio = 4.2).

Effects of brain injury on college academic performance

Brain injury, a leading cause of mortality, morbidity and disability in the United States, has serious consequences and substantial costs. Although previous studies have assessed a variety of outcomes subsequent to brain injury, documentation of performance prior to brain injury using a case-control approach has not been included; preinjury performance differences may confound the estimate of the effects of brain injury on performance. The primary objective of this study was to compare academic performance before and after brain injury in a population of university undergraduate students to determine the extent to which the academic career of the brain-injured person was altered from what would have been expected in the absence of such an injury. Cases included all undergraduate students in a major university, between the ages of 17 and 27, who incurred a brain injury requiring hospitalization between 1980 and 1984 (n = 99). Two comparison groups were used to determine whether changes in academic performance were specifically related to brain injuries or injuries in general: (1) injured controls, i.e. 121 students between the ages of 17 and 27 years, hospitalized for injuries other than to the central nervous system, and (2) uninjured academic controls, i.e. 198 students with out injuries requiring hospitalization during the study period, matched 2:1 to the brain-injured students by age, gender, and completed course credits categorized as < 90, > or = 90. Although there were no differences when the total groups, including both males and females, were compared, there was a significant pre- to postinjury decrease in the grade point average for female cases when compared to their uninjured academic controls (p < 0.02). This difference was related to the effects of brain injury, and not to the effects of injury in general. No such difference was observed for the males. There were also no differences when the total groups, including males and females, were compared relevant to return to school. However, a significantly higher proportion of the female cases, compared with their uninjured academic controls, did not return to school after their injury; similar findings were identified for the injured controls as well. Thus, these differences were not specific to brain injury but rather to injury in general. In spite of this observation, the difference between female cases who returned and those who did not return was associated with neurological deficits, especially upper left limb motor deficits, as the time of hospital discharge. The findings from this effort are suggestive of gender differences in the consequences of brain injury and serve as a basis for further studies to evaluate the magnitude of this problem.

An epidemiological study of roadway fatalities related to farm vehicles: United States, 1988 to 1993

Compared with the estimated injury fatality rate for workers in all occupations (nine in 100,000 in 1988) the farm fatality rate (48 in 100,000) was among the highest in the nation; in 1993, these rates were eight and 35 in 100,000, respectively. On-road farm-vehicle fatalities have been identified as a significant problem, yet these events apparently have not been investigated in a comprehensive manner. The purpose of this study was to investigate the circumstances surrounding all on-road, non-truck, farm-vehicle crash fatalities in the United States form 1988 through 1993. The National Highway Traffic Safety Administration's Fatal Accident Reporting System, which includes data for all US fatal on-road motor vehicle crashes, was the source of data. Driver-related variables were compared among farm vehicles, vehicles in collisions with farm vehicles, and all other vehicles in rural, fatal crashes; environmental variables were compared between rural farm-vehicle and non-farm-vehicle crashes. During 1988 to 1993, in rural areas, 444 farm-vehicle occupants were killed; in addition, 238 occupants of other vehicles or pedestrians were killed in collisions with the farm vehicles. The farm vehicles were disproportionately involved in overturns, rear-end collisions, and incidents in which the injured person fell from the vehicle, when compared with all other non-farm vehicles involved in rural-area fatal crashes. Of the farm vehicles involved in fatal crashes at night, dawn, or dusk, 65% were struck in the rear, compared with 4% of vehicles involved in fatal non-farm-vehicle crashes. Compared with drivers in all other rural crashes, farm-vehicle operators were more likely to be male, have a greater proportion of convictions for driving while intoxicated, and a lower proportion of previous speeding convictions. From this initial investigation, it appears that the fatal-crash involvement of farm vehicles are related to vehicle and environmental factors that are changeable. Given the proportion of overturns associated with farm-vehicle crashes (21%) compared with non-farm vehicles (9%), there is a need to investigate design characteristics of the farm vehicles. The large proportion of farm vehicles struck in the rear during daylight (24%) as well as night, dawn, or dusk hours (65%), compared with non-farm vehicles (4% and 4%, respectively), suggest factors related to visibility and perception of the farm vehicles' speed that provide a basis for further study.

Health care for the uninsured in Duluth

Providing health care for Minnesota's uninsured population continues to be both a clinical and political challenge. Between October 1, 1991, and September 30, 1993, 1,260 previously uninsured people received charity health care in Duluth. No one was excluded because of pre-existing conditions. Their utilization of services and associated costs can help project the health care needs and costs of care for uninsured Minnesotans. This group of uninsured people used a different mix of health care services compared with insured Minnesotans, and their total costs (including prescriptions) were about 15% greater. A large proportion of these uninsured Minnesotans had chronic health conditions and a "pent-up need" for services and medications. This experience demonstrated that it is possible to administer a limited benefits plan in coordination with existing public and private resources.

No involvement of bovine leukemia virus in childhood acute lymphoblastic leukemia and non-Hodgkin's lymphoma

Bovine leukemia virus (BLV) is the causative agent of enzootic bovine lymphosarcoma. Much speculation continues to be directed at the role of BLV in human leukemia. To test this hypothesis rigorously, a case-control study of childhood acute lymphoblastic leukemia and non-Hodgkin's lymphoma was conducted between December 1983 and February 1986. Cases (less than or equal to 16 years at diagnosis) derived from patients diagnosed at the primary institutions and affiliated hospitals were matched (age, sex, and race) with regional population controls. DNA samples from bone marrow or peripheral blood from 157 cases (131 acute lymphoblastic leukemia, 26 non-Hodgkin's lymphoma) and peripheral blood from 136 controls were analyzed by Southern blot technique, under highly stringent conditions, using cloned BLV DNA as a probe. None of the 157 case or 136 control DNA samples hybridized with the probe. The high statistical power and specificity of this study provide the best evidence to date that genomic integration of BLV is not a factor in childhood acute lymphoblastic leukemia/non-Hodgkin's lymphoma.