tbuckley/cabot-search huggingface dataset:
Abstract 416: Tumor cell isolation using antibody/aptamer-based multivalent binding
Authors: Z. Hugh Fan, Jinling Zhang, Weian Sheng
Journal: Cancer Research (2016)

Abstract Isolation and enumeration of circulating tumor cells (CTCs) in peripheral blood have been used for cancer diagnosis, prognosis, and theragnosis. The majority of the CTC isolation methods, including the FDA-approved CellSearch®, employ one antibody to capture tumor cells. Using such a monovalent-binding capture agent likely results in lower cell capture efficiency than multivalent-binding methods, which tend to have stronger binding force (or lower dissociation constant). We have investigated in a multivalent-binding-based tumor cell isolation method by immobilizing a mixture of aptamers and antibodies on the surfaces of microfluidic devices. Since aptamers are much smaller in the size (8-15 kDa) than antibodies (150 kDa), aptamers and antibodies could interact with different receptors on cell surfaces, resulting in a configuration that one cell simultaneously interacts with multiple different types of capture agents. The microfluidic devices we used are in the size of a microscope slide and each of them consists of an inlet, eight parallel channels connected via consecutive bifurcation, and an outlet. There are micromixers inside the channels for enhanced interactions. Biotinylated aptamers and biotinylated antibodies were coated onto microchannel surfaces using avidin-biotin chemistry. We tested the devices by isolating human leukemia cells (CCRF-CEM) in devices immobilized with a mixture of sgc8 aptamers and protein tyrosine kinase-7 (PTK7) antibodies. Both sgc8 aptamers and anti-PTK7 exhibited strong binding with CCRF-CEM cells according to flow cytometry. An antibody-to-aptamer ratio of 1:300 showed the highest capture efficiency among the range we studied (from 1:30 to 1:3000). We found that the antibody-aptamer surfaces had higher capture efficiency than antibody-alone or aptamer-alone surfaces; the degree of enhancement increased with the flow rate. Control experiments using non-specific aptamer (TD05) and non-specific antibody (anti-EpCAM) were carried out to verify the benefits of multivalent binding. We also found that the multivalent-binding surfaces have higher specificity than monovalent-binding surface, especially at a high flow rate. A calibration curve was obtained by spiking leukemia cells into human whole blood. In summary, antibody/aptamer-coated multivalent-binding surfaces in microfluidic devices showed higher capture efficiency and specificity than monovalent-binding surfaces, suggesting their potential for the isolation and enumeration of CTCs for clinical applications. Citation Format: Z. Hugh Fan, Jinling Zhang, Weian Sheng. Tumor cell isolation using antibody/aptamer-based multivalent binding. [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 416.
Abstract 445: Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic TP53 mutations in noncancerous tissues
Authors: Jeffrey D. Krimmel, Michael W. Schmitt, Scott R. Kennedy, Maribel I. Harrell, Kathy J. Agnew, Larry A. Loeb, Elizabeth M. Swisher, Rosa Ana Risques
Journal: Cancer Research (2016)

Abstract The detection of subclonal tumor-specific somatic mutations in clinical samples could revolutionize cancer diagnostics, but is limited by insufficiently sensitive sequencing methods. Duplex Sequencing is a novel next-generation sequencing (NGS) technology that implements single-molecule barcoding of both strands of DNA to allow internal error correction. This modification reduces the error rate of NGS from 1 in 1000 to less than 1 in 10 million nucleotides, an unprecedented sensitivity that enables accurate ultra-deep sequencing for clinical applications. In this study we sought to determine whether Duplex Sequencing could detect extremely rare TP53 mutated cancer cells disseminated into the peritoneal cavity of women with high-grade serous ovarian carcinoma (HGSOC). HGSOC is the most common and most aggressive type of ovarian cancer, shows early transperitoneal dissemination, and is characterized by near-universal prevalence of driver TP53 mutations. We analyzed 17 peritoneal fluid samples from women with HGSOC and known TP53 tumor mutation (cases) and 20 peritoneal fluid samples from women without cancer (controls). The tumor-specific TP53 mutation was detected in matched peritoneal fluid from 94% of cases (16/17), including 2 patients with occult tubal intraepithelial neoplasia, 7 patients with early stage HGSOC, and 8 with negative peritoneal fluid cytopathology. Tumor-specific alleles were detected as low as &amp;lt;1/25,000. Surprisingly, we also detected additional extremely low-frequency somatic TP53 mutations in peritoneal fluid from nearly all (35/37) cases and controls. These mutations were more abundant in cases than in controls, and in the latter correlated with age. The total burden of somatic TP53 mutations (tumor specific and non-specific) in a peritoneal fluid sample could distinguish cases from controls with 82% sensitivity (14/17) and 90% specificity (18/20). Duplex Sequencing also revealed low-frequency, age-associated somatic TP53 mutations in 100% (15/15) of matched peripheral blood samples. Our results demonstrate the ability of Duplex Sequencing to detect very rare cancer cells, but also provide evidence of widespread, low frequency somatic TP53 mutation in non-cancerous tissue. This compromises the specificity of TP53 mutation tests for cancer detection in liquid biopsies. Citation Format: Jeffrey D. Krimmel, Michael W. Schmitt, Scott R. Kennedy, Maribel I. Harrell, Kathy J. Agnew, Larry A. Loeb, Elizabeth M. Swisher, Rosa Ana Risques. Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic TP53 mutations in noncancerous tissues. [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 445.
Abstract 5271: Optimization and detection of focal somatic copy number variants in whole genome, whole exome and panel sequencing for tumor/normal matched pairs and tumor only analysis
Authors: Jessica Aldrich, Jonathan J. Keats, Austin Christofferson, Winnie S. Liang, John D. Carpten, Lisa Baumbach-Reardon, David W. Craig
Journal: Cancer Research (2016)

Abstract Often in the clinical setting, tumor samples may be derived from historical tissue or from fresh frozen tissue and it may not be feasible to obtain normal tissue from the individual. Comparing unmatched tissues from different individuals possess a unique challenge of addressing common copy number variations not faced when comparing matched samples. In addition to the challenges of comparing unmatched samples, DNA extracted from samples preserved as formalin-fixed, paraffin-embedded (FFPE) tissue is often highly degraded and when compared to more intact DNA extracted from different source (e.g. blood) can increase the inherent noise in the system. Here we analytically characterize the accuracy and performance of algorithmic approaches for separating germline inherited copy number variation from somatic copy number changes, focusing on both filtering approaches and use of pooled reference samples sequenced under similar conditions. Example approaches include filtering known common copy number variation within 1000 Genomes Phase 3 and Database of Genomic Variants (DGV) Gold Standard. Additionally, we utilized a tumor/reference pool based analysis where a reference pool was constructed by equimolar pooling of multiple individuals. Determination of fold changes between tumor and reference was calculated by determining physical coverage of read pair fragments in 100 bases increments. Next, to address differences in sequencing performance between tumor and reference, the read depth data for each sample is collapsed/averaged into a lower resolution according to user-selected parameters (e.g. distance between points and read depth). Normalized log2 fold-changes between tumor and reference samples are then calculated and an adjustable smoothing window is applied. In addition, we utilize tumor allele frequencies of known heterozygous germline SNPs identified within the normal to both evaluate potential false positives and correct biases. Lastly, a segmentation algorithm is applied to summarize the individual log2 fold-changes into intervals with a constant copy number state. We will present the advantages and limitations of these approaches both when a germline normal is available and when tumor only analysis is necessary. Citation Format: Jessica Aldrich, Jonathan J. Keats, Austin Christofferson, Winnie S. Liang, John D. Carpten, Lisa Baumbach-Reardon, David W. Craig. Optimization and detection of focal somatic copy number variants in whole genome, whole exome and panel sequencing for tumor/normal matched pairs and tumor only analysis. [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 5271.
Abstract 3501: Puma/pBcl-2 axis influences sensitivity of cancer cells to multiple stimuli
Authors: Yubo Liu
Journal: Cancer Research (2016)

Abstract Bcl-2 is a central regulator of cell survival that is overexpressed in the majority of cancers cells.Previous reports indicated that Bcl-2 phosphorylation (S70) may provide a switch by which cellscan regulate the pro-survival functions of Bcl-2. But there is still controversy over the function of phosphorylatedBcl-2 (pBcl-2).In the presentstudy, Puma/pBcl-2 axis was found to play a key role in regulating the sensitivity of cancer cells to multiple stimuli.Based on immunoprecipitation, weobserved that the pro-apoptoticBH3-only protein Puma which was induced by paclitaxel competitively bound pBcl-2 (S70) and displaced Bim and Bax from pBcl-2(S70) in Hela and HL60 cells.Further study showed thatdepletion of Puma (siRNA), but not other BH3 only proteins, significantlydecreased paclitaxel-induced apoptosis.Bim/pBcl-2 and Bax/pBcl-2 complexeswere largely maintained when Pumawas reduced. These data indicated that the phosphorylation of Bcl-2(S70) enhancedits anti-apoptotic function and the induction of Puma could neutralize this effect. Similarly,the induced Puma was also responsible for Bim and Bax displacement from pBcl-2 (S70) when Hela and HL60 cellswere treated with DNA damage agents(cisplatin and etoposide).However, Pumacannot displace Bax or Bim when pBcl-2 (S70) was redundant in the cells expressedphospho-mimetic S70E-Bcl-2. It demonstrated that DNA damage induced apoptosis could be inhibit by pBcl-2 (S70) and the induction of Puma could antagonize pBcl-2 (S70). In a cell free system, mitochondria from Hela and HL60 cells which expressing the S70E-Bcl-2 wereincubated with different BH3 peptides. Cytochrome c release couldbe induced by a low concentration of Puma-BH3 peptide, but a higher concentrationwas necessary during Bimengagement.By contrast, Bad-BH3 and Noxa-BH3cannot initiate the release of cytochrome c.In conclusion, multiple stimuli activates the mitochondrial apoptoticpathway in cancer cells, in which Puma/pBcl-2(S70) axisplay a key role in a novel mechanism involving the displacement of Bim and Bax from pBcl-2 (S70)by Puma. In contrast with the debatable function of Bcl-2 phosphorylation (S70), this study provided evidence that the phosphorylation of Bcl-2 at S70 enhanced cell survivalin multiplestimuli triggered apoptosis. Citation Format: Yubo Liu. Puma/pBcl-2 axis influences sensitivity of cancer cells to multiple stimuli. [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 3501.
Abstract 2622: A LC-MS/MS method to quantify specific dietary isothiocyanates in human urine for epidemiological studies
Authors: Marcin Dyba, Jian-Min Yuan, Jennifer Adams-Haduch, Fung-Lung Chung
Journal: Cancer Research (2016)

Abstract Epidemiological studies have demonstrated an inverse relationship between the intake of cruciferous vegetables and risk of cancers. The protective effects may be attributed to glucosinolates and glucobrassicins in these vegetables. While glucosinolates and glucobrassicins are not chemopreventive, their metabolites, isothiocyanates (ITCs), indole-3-carbinol (I3C), and 3,3′-diindolylmethane (DIM), have been shown to inhibit tumorigenesis in rodent models. In the past studies the total ITCs intake was estimated through food frequency questionnaires and/or urinary total ITC by a HPLC-based method. Self-reported intake of cruciferous vegetables has inherent limitations in estimating the intake of ITCs because of differences in the contents of their precursors present in different kinds of cruciferous vegetables, different locations and methods of cultivation, or different methods of food preparation. Animal and cell culture studies have shown that different types of ITCs have different anticancer properties and potency, suggesting that they are not equal in protecting against the development of cancers. The lack of a reliable method to quantify specific ITCs derived from dietary intake of cruciferous vegetables hinders the investigation of the role of specific ITCs against the development of cancer in human populations. To address this deficiency, we developed a flexible, highly sensitive, fast and reliable quantitative liquid chromatography mass spectrometry method (LC-MS/MS) for detecting and quantifying common dietary ITCs plus DIM in human urine. Urinary ITCs are measured as mercapturic acid conjugates (ITCs-NAC), predominant metabolite of ITCs, using multiple reaction monitoring (MRM) technique and deuterated [2H3]-ITCs-NAC as internal standards. DIM is quantified in separate experiment using [2H2]-DIM internal standard. The method was validated by a small set of previously analyzed samples from Singapore Chinese Health Study. We found an excellent correlation between previously reported total ITCs levels and sum of ITCs detected by newly developed method. The combination of minimal sample preparation, ultra-performance liquid chromatography, and highly sensitive mass spectrometer resulted in a method that is fast (below 10 min for ITCs and 12 min for DIM) and sensitive (low femtomolar LOQ) amenable to population studies. Citation Format: Marcin Dyba, Jian-Min Yuan, Jennifer Adams-Haduch, Fung-Lung Chung. A LC-MS/MS method to quantify specific dietary isothiocyanates in human urine for epidemiological studies. [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 2622.
<sup>89</sup>zr-GC1008 PET imaging and GC1008 treatment of recurrent glioma patients.
Authors: Martha W. den Hollander, Frederike Bensch, Andor W. J. M. Glaudemans, Roelien H. Enting, Sophie Bunskoek, Thijs H. Oude Munnink, Marjolijn N. Lub-de Hooge, Joseph Pearlberg, Jourik A. Gietema, Elisabeth G. E. de Vries, Annemiek M.E. Walenkamp
Journal: Journal of Clinical Oncology (2013)

2050 Background: Transforming growth factor-β (TGF-β) signaling is involved in glioma development. GC1008 is a monoclonal antibody that has demonstrated significant neutralization of all mammalian isoforms of TGF-β in preclinical models (Lonning, Curr Pharm Biotechnol 2011). The aim of this study was to investigate whether GC1008 uptake in brain tumors can be visualized using the 89 Zirkonium (Zr)-GC1008 PET scan and to assess treatment outcome in patients with recurrent glioma treated with GC1008 (NCT01472731). Methods: Patients with WHO II-IV glioma who presented with recurrent disease were eligible. After iv administration of 37 MBq (5 mg) 89 Zr-GC1008, 89 Zr-GC1008 PET scans were performed on day 2 and day 4 post injection. Thereafter, patients were treated with 5 mg/kg GC1008 iv every 3 weeks. MRI scans were made for response evaluation after 3 courses or as clinically indicated. Results: Twelve patients with 1 st -8 th recurrent disease were included (10 glioblastoma, 1 anaplastic oligodendroglioma, 1 anaplastic astrocytoma), all underwent an 89 Zr-GC1008 PET scan on day 4, 4 patients also underwent a PET scan on day 2 after tracer injection. Median SUVmax on day 4 was in tumor lesions 4.6 (range 1.5-13.9) and median SUVmean in normal brain tissue 0.3 (range 0.2-0.5). In 3 out of 4 patients who underwent a day 2 and day 4 whole body scan uptake decreased in most normal organs but not in tumor lesions, supporting tumor specific 89 Zr-GC1008 uptake. No major toxicity of GC1008 treatment was observed, but all patients showed clinical and/or radiological progressive disease after 1-3 cycles. Median progression free survival was 61 days (range 25-80) and median overall survival 106 days (range 37-287+). Conclusions: 89 Zr-GC1008 showed excellent uptake by recurrent gliomas. Clinical benefit of GC1008 treatment was not observed in this limited study population. Clinical trial information: 01472731.
Abstract 522: Role and regulation of Aurora A in radiation resistance mechanisms in glioblastoma
Authors: Brinda Ramasubramanian, Kamalakannan Palanichamy, Disha Patel, Saikh Jaharul Haque, Arnab Chakravarti
Journal: Cancer Research (2016)

Abstract Glioblastoma (GBM) is the most aggressive tumor of the human brain, which inevitably escapes the standard treatment modalities that include surgery, radiotherapy and chemotherapy. Consequently, the median survival of GBM patients remains 12-15 months despite these aggressive treatments. Therefore, to develop effective therapies, it is important to understand how GBM cells develop therapeutic resistance. Aurora A is a ubiquitously expressed serine/threonine kinase, which plays essential roles in mitotic regulation. This protein kinase, which phosphorylates p53, PP1, CEBP, and histone H3 among other regulators of cell division, is overexpressed in various neoplasms including GBM and invariably associated with poor prognosis. Recent studies have demonstrated that Aurora A contributes to radio-resistance in various solid neoplasm including GBM. Importantly, Aurora A inhibitors are currently in phase I/II clinical trials for solid cancer. Notably, Aurora A inhibitor MLN8237 that crosses the blood brain barrier specifically inhibits Aurora A at concentrations ≤ maximally tolerated dose in animal models and in phase I clinical trials. We found that Aurora A protein level is upregulated by ionizing radiation in GBM cells. This was, in part, mediated by radiation-induced inhibition of 26S-proteosomal degradation of Aurora A. Aurora A was silenced using both lentiviral mediated shRNA expression and a specific Aurora A inhibitor in three different established cell lines, and were treated with 6 gy radiation. We found that pharmacological inhibition and RNAi-mediated knockdown of Aurora A sensitized the GBM cells to radiation therapy resulting in reduced cell proliferation and increased apoptosis. Interestingly, we observed that RNAi-mediated down-regulation of Aurora A was associated with a decrease in X-linked inhibitor of apoptosis (XIAP) expression in GBM cells. We also found that Aurora A and XIAP were co-localized in GBM cells. Taken, together our results reveal a mechanism by which Aurora A confers radio-resistance in GBM cells and further rationalize the use of Aurora A inhibitors as radio-sensitizer in solid neoplasms including GBM. Funding sources: This work was supported by R01CA108633 (To AC), 1RC2CA148190 (To AC) U10CA180850-01 (To AC), 1R01CA169368 (To AC) from the National Cancer Institute (NCI), Brain Tumor Funders Collaborative Grant (To AC), Ohio State University Comprehensive Cancer Center Award (To AC) Citation Format: Brinda Ramasubramanian, Kamalakannan Palanichamy, Disha Patel, Saikh Jaharul Haque, Arnab Chakravarti. Role and regulation of Aurora A in radiation resistance mechanisms in glioblastoma. [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 522.
Abstract 347: Developing a novel immunotoxin that targets cells overexpressing ErbB2
Authors: Luqun Shen, Kelsey Weigel, Clayton Thomas, Lauren Drapalik, Zachary T. Schafer, Shaun Lee
Journal: Cancer Research (2016)

Abstract Immunotoxins are chimeric proteins comprising a specific cellular targeting domain linked to a cytotoxic factor. Here we describe the design and use of a novel, peptide-based immunotoxin that can initiate selective cytotoxicity on ErbB2-positive cells. ErbB2 is a receptor tyrosine kinase that is overexpressed in the tumor cells of approximately 30% of breast cancer patients. Immunotoxin candidates were designed to incorporate a targeting ligand with affinity for ErbB2 along with a membrane lysin-based toxin domain. The use of a membrane lysin as the toxin domain distinguishes our immunotoxins from numerous others in that internalization of the toxin is not required to induce cell death. One particular peptide candidate, NL1.1-PSA, demonstrated selective cytotoxicity towards ErbB2-overexpressing cell lines. We utilized a bioengineering strategy to show that recombinant NL1.1-PSA immunotoxin expression by Escherichia coli also conferred selective cytotoxicity towards ErbB2-overexpressing cells. Our findings hold significant promise for the use of effective immunotoxins in cancer therapeutics. While Herceptin treatment has been effective in patients with ErbB2 positive breast cancer, our novel immunotoxin may ultimately prove to be a novel and efficacious addition to the arsenal of approaches used to eliminate Herceptin-resistant breast cancer cells. Citation Format: Luqun Shen, Kelsey Weigel, Clayton Thomas, Lauren Drapalik, Zachary T. Schafer, Shaun Lee. Developing a novel immunotoxin that targets cells overexpressing ErbB2. [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 347.
Overexpression of BRE in Pediatric MLL-Rearranged Acute Myeloid Leukemia Associated with t(9;11)(p22;q23).
Authors: Brian Balgobind, C. Michel Zwaan, Susan T.C.J.M. Arentsen-Peters, Dirk Reinhardt, Ursula Creutzig, Valerie de Haas, Gertjan J.L. Kaspers, Jacqueline Cloos, Eveline S.J.M de Bont, Andre Baruchel, Jan Stary, Rob Pieters, Marry M van den Heuvel-Eibrink
Journal: Blood (2009)
Consolidation with High Dose Therapy and Autologous Stem Cell Transplant Improves Survival for Patients with Mantle Cell Lymphoma
Authors: Loretta Nastoupil, Pareen J Shenoy, Alex Ambinder, Miray Seward, Ajay K. Nooka, Edmund K. Waller, Amelia Langston, Jonathan L. Kaufman, Nassoma King, Mary Jo Lechowicz, Sagar Lonial, Rajni Sinha, Christopher R. Flowers
Journal: Blood (2012)