bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4009: Characterization of M2 macrophage subtype content in cancer and normal tissues
Authors: Dauffenbach Lisa M. , Sia Gela C. , Zheng Jianping , Jun Natalia , Olsen Eric P. , Kerfoot Christopher A. 
Published: July 2017

Abstract
Tumor-associated macrophages play an important role in presenting tumor antigens to T cells and are being investigated for their role in sensitivity to immune checkpoint inhibitors such as PD-1 inhibitors. The M2 macrophage subtype, characterized by CD163 expression, is immunosuppressive and associated with poor prognosis. A multiplex CD68/CD163 immunohistochemical assay was developed to characterize the density of cells expressing each marker and determine the percentage of macrophages that are of the M2 subtype. The assay was used to analyze 22 normal tissue types and 50 tumor tissues within 5 different indications. The results were analyzed by image analysis and results were analyzed as percent positive and density per mm2. Cancer tissues expressed a greater percentage of CD163+ macrophages than normal tissues.
Citation Format: Lisa M. Dauffenbach, Gela C. Sia, Jianping Zheng, Natalia Jun, Eric P. Olsen, Christopher A. Kerfoot. Characterization of M2 macrophage subtype content in cancer and normal tissues [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 4009. doi:10.1158/1538-7445.AM2017-4009
Abstract 401: Designing for success: the right CRISPR design strategies for the right experiment
Authors: Brody Leigh , Humphryes-Kirilov Neil , Dillard Victor , Doyle Riley 
Published: July 2017

Abstract
CRISPR design is a complex multivariate problem. The weight of each variable differs depending on the experiment under consideration. Current methods of designing CRISPR experiments are based on a single-variable, resulting in poor experimental outcomes. From the numerous experiments enabled by the DESKGEN platform, we can demonstrate key design improvements to maximise experimental outcome.
Our current scoring methods were tested and validated using an sgRNA library of over 3,500 sgRNAs in essential genes with a variety of predicted sgRNA activities and specificities. The predicted 'good' sgRNAs achieved significantly higher read depletion for essential genes, with fewer failing sgRNAs, compared to sgRNAs that didn't meet the scoring criteria. Our scoring algorithm incorporates multiple published observations for choosing effective sgRNAs, which differs from other CRISPR tools that tend to focus on one factor such as sgRNA sequence or specificity. We were unable to find correlations for some currently accepted sgRNA selection criteria, such as position within a gene, which demonstrates the need to constantly challenge and improve sgRNA design rules.
Citation Format: Leigh Brody, Neil Humphryes-Kirilov, Victor Dillard, Riley Doyle. Designing for success: the right CRISPR design strategies for the right experiment [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 401. doi:10.1158/1538-7445.AM2017-401
Abstract 4013: A novel multifunctional protein tag enables simple and sensitive bioluminescent quantification of tagged proteins
Authors: Eggers Christopher , Butler Braeden , Hurst Robin , Hall Mary , Binkowski Brock , Encell Lance , Schwinn Marie , Machleidt Thomas , Wood Keith , Fan Frank 
Published: July 2017

Abstract
Dysregulation of protein expression is a key mechanism of tumorigenesis. The most commonly used approach to monitor changes in expression is to perform SDS-PAGE, followed by immunoblotting, a labor-intensive process that requires high-quality antibodies to detect proteins at endogenous levels of expression. We have developed a novel protein tag utilizing NanoLuc Binary Technology (NanoBiT), a binary complementation system based on NanoLuc luciferase. The tag, designated High BiT (HiBiT), is only 11 amino acids in length, which minimizes potential interference with protein function. The amount of HiBiT-tagged protein is measured using a lytic detection reagent containing Large BiT (LgBiT), which binds with high affinity to HiBiT (KD~1 nM) to reconstitute a bright, luminescent enzyme. HiBiT-tagged proteins can be quantified in cell lysates over 7 orders of magnitude of linear dynamic range with a limit of detection of less than 10-19 moles (3 fg of 30 kDa protein). The simple add-mix-read assay protocol can be completed in minutes, providing an assay that is compatible with high-throughput applications. The sensitivity of the assay allows quantification of expression at endogenous levels, and the small tag size is ideal for CRISPR-mediated genome editing. HiBiT-tagged proteins separated by SDS-PAGE can be detected on blots at sub-picogram levels with a detection reagent containing LgBiT. By eliminating the multiple steps of blocking, binding, and washing of traditional blotting techniques, the protocol takes minutes instead of hours. Additionally, the cell surface expression, internalization, or secretion of HiBiT-tagged proteins can be measured in minutes using a non-lytic detection reagent containing the cell-impermeable LgBiT protein. HiBiT represents a next-generation protein tag that allows simple quantification of proteins of interest in their cellular context or following SDS-PAGE.
Citation Format: Christopher Eggers, Braeden Butler, Robin Hurst, Mary Hall, Brock Binkowski, Lance Encell, Marie Schwinn, Thomas Machleidt, Keith Wood, Frank Fan. A novel multifunctional protein tag enables simple and sensitive bioluminescent quantification of tagged proteins [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 4013. doi:10.1158/1538-7445.AM2017-4013
Abstract 4022: Validation of label-free impedance analysis as a versatile tool for cancer molecular therapeutics screening
Authors: Cerignoli Fabio , Xi Biao , Lamarche Brandon , Zhao Leyna , Abassi Yama 
Published: July 2017

Abstract
In vitro monitoring cancer cells response to treatment often involves laborious sample processing and collects single data points that are against the dynamic nature of cancer cells. Here we present the adaptation of an impedance-based methodology to dynamically monitor cancer cell behavior and therapeutic response. The technology detects cell death, proliferation or migration by measuring changes in conductance of microelectrodes embedded in 96 and 384-wells cell culture plates. It avoids sample labeling and processing and allows continuous monitoring of cell response. Our data shows validation with cancer cell lines and primary cells monitored for cell invasion/migration, anticancer drug response and receptor signaling activation, with similar results over end point assays. Easy experiment set up and minimal sample processing make the technology ideal for applications in large screening campaigns, while label-free technology allows further analysis on the same samples through orthogonal assays.
Citation Format: Fabio Cerignoli, Biao Xi, Brandon Lamarche, Leyna Zhao, Yama Abassi. Validation of label-free impedance analysis as a versatile tool for cancer molecular therapeutics screening [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 4022. doi:10.1158/1538-7445.AM2017-4022
Abstract 4026: Bioluminescent metabolite assays enable easy measurement of changes in tumor biology
Authors: Valley Michael , Sobol Mary , Leippe Donna , Vidugiriene Jolanta 
Published: July 2017

Abstract
Tumor cells rely on metabolic reprogramming to meet their increased demands for energy and biomass. Such reprogramming is exemplified by increased rates of glucose uptake, greater utilization of glycolysis, and a reliance on glutaminolysis. Cancer cells also have a strong dependence on lipids and cholesterol and thus feature enhanced rates of biosynthesis and uptake of these molecules as well. We have developed a suite of bioluminescent assays that can monitor metabolites in all of these important pathways. These assays share a core technology that couples the production of NAD(P)H to the generation of light through a variety of metabolite specific dehydrogenases. Changes in glycolysis and glutaminolysis can be followed by measuring glucose, lactate, glutamate, and/or glutamine through their respective dehydrogenases (and glutaminase). Glucose uptake is typically monitored through the accumulation and phosphorylation of 2-deoxyglucose to produce 2-deoxyglucose-6-phosphate, and this can be measured by employing glucose-6-phosphate dehydrogenase. These bioluminescent assays are homogeneous and can be multiplexed with viability, cytotoxicity, and protein quantitation assays. Metabolites can be measured extracellularly (i.e. from media) or intracellularly and the assays can be performed in 96- or 384-well plates. These assays are simple and sensitive and can provide a greater understanding of how various treatments affect the metabolic state of a tumor cell.
Citation Format: Michael Valley, Mary Sobol, Donna Leippe, Jolanta Vidugiriene. Bioluminescent metabolite assays enable easy measurement of changes in tumor biology [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 4026. doi:10.1158/1538-7445.AM2017-4026
Abstract 4028: Analysis and recovery of functionally defined single immune cell clones through opto-electro-positioning technology
Authors: Wang Xiaohua , Bronevetsky Yelena , Beaumont Kristin , Stadler Guido , Bao Xiaoyan R. , Smith Duane , Beemiller Peter , Chapman Kevin 
Published: July 2017

Abstract
Cancer patients mount protective innate and adaptive immune responses against tumor cells. Such responses are able to control or even eliminate tumor burden if harnessed properly. Identifying clonal adaptive immune cells targeting tumor cells with designated function is extremely valuable as these cells are able to either fight the tumor directly or provide tumor targeting immune receptors to engineer other effector cells like autologous CD8 T cells or NK cells. The process of isolating cancer specific immune cells and their receptors, however, remains technically challenging and labor intensive.
Opto-Electro-Positioning (OEP) technology employs a light actuated dielectrophoretic force to maneuver live cells in their culture environment. We have combined OEP with a nanofluidic cell culture system to produce an integrated microfluidic platform that enables multi-dimensional investigation of lymphocyte specificity and function. The system is able to 1) deterministically capture designated lymphocytes, 2) actively maintain and observe colony growth, and 3) conduct cytokine release assays, all in a single enclosed microfluidic chip. The new platform is suitable for high throughput screening to identify and harvest antigen specific and/or functionally defined T cells. We have successfully applied it to isolate primary human T cells targeting either EBV/Tetanus toxin antigens or tumor associated antigens such as MART-1 through tetramer staining or a proliferation assay. The system is also exceptionally efficient for investigating immune cells from clinical specimens typically of low cellularity. From tumor biopsies, we are able to capture tumor infiltrating T cells, stimulate proliferation, investigate their TNF-α secretion on chip, and obtain full transcriptomic analysis after export.
Overall, our data suggest the OEP nano-fluidic environment provides a powerful high throughput screening tool to identify rare lymphocytes against tumor associate antigens or neo-antigens and to investigate precious clinical samples for biomarker discovery.
Citation Format: Xiaohua Wang, Yelena Bronevetsky, Kristin Beaumont, Guido Stadler, Xiaoyan R. Bao, Duane Smith, Peter Beemiller, Kevin Chapman. Analysis and recovery of functionally defined single immune cell clones through opto-electro-positioning technology [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 4028. doi:10.1158/1538-7445.AM2017-4028
Abstract 403: CRISPR/Cas9 genome-wide sgRNA libraries for loss-of-function and gain-of-function genetic screens
Authors: Tedesco Donato , Diehl Paul , Makhanov Mikhail , Baron Sylvain , Chenchik Alex 
Published: July 2017

Abstract
Genome-wide loss-of-function screening is a fundamental method to identify genes responsible for driving biological processes. Complex pooled lentiviral-based libraries expressing large numbers of genetic disruptors, such as shRNAs (RNAi) or sgRNAs (CRISPR), make large-scale cell screening practical. While RNAi-based approaches have proven to be an effective strategy for these screens, recent work has showed CRISPR-based technologies offer not only an effective alternative, but distinct advantage. We will present unpublished data from genetic screens in human cancer cell lines using CRISPR-Knockout (KO), CRISPRi and CRISPRa technologies, as well as RNAi. Although loss-of-function shRNA and sgRNA pooled library screens are similar in concept, the gene loss of function is achieved by different mechanisms (mRNA degradation with RNAi, full gene disruption with CRISPR-KO, transcriptional inhibition with CRISPRi), so some divergences are expected and indeed observed when comparing results obtained using one method versus the other. Furthermore, contrary to RNAi, CRISPR technology can be modified to activate gene expression (CRISPRa), thus enabling the use of genome-wide gain-of-function screening in gene function studies.
Citation Format: Donato Tedesco, Paul Diehl, Mikhail Makhanov, Sylvain Baron, Alex Chenchik. CRISPR/Cas9 genome-wide sgRNA libraries for loss-of-function and gain-of-function genetic screens [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 403. doi:10.1158/1538-7445.AM2017-403
Abstract 4035: A novel combi-molecule engineered to target the putative synthetic lethal interactions between the epidermal growth factor receptor (EGFR) and poly(ADP-ribose)polymerase (PARP)
Authors: Mouhri Zhor Senhaji , Rupp Martin , Jean-Claude Bertrand J. 
Published: July 2017

Abstract
Over the past decade, PARP inhibition has been actively pursued as a novel approach for the selective therapy of tumors with BRCA1/2 mutations. The therapeutic benefits of PARP inhibitors have now been proven in the clinic against BRCA1/2 mutant ovarian cancers. This is hitherto limited to BRCA1/2 mutations, which only accounts for 5-10% of all cancers with hereditary mutations in the homologous recombination pathway. Therefore, new strategies are not only required to enhance the potency of PARP inhibitors but also to expand their use beyond BRCA mutation. While several combination modalities have been reported for PARP inhibitors, the concept of targeted PARP inhibitor has not yet been explored. Here using our novel combi-targeting approach, we report on the design of PARP inhibitors targeted to EGFR, a tyrosine kinase receptor overexpressed in several solid tumors. Recently, reports on the relationship between EGFR, PARP and BRCA have begun to emerge, one of which described a contextual synthetic lethality between EGFR and PARP (PloS one 7.10 (2012)). Here we report on the design and synthesis of novel PARP-EGFR combi-molecule based on structural modification of olaparib as a PARP inhibitor warhead and the quinazoline moiety for targeting EGFR. The results showed that: (a) it is capable of inducing a dose-dependent inhibition of PARP in isolated enzyme assay, (b) it induced a dose-dependent inhibition of EGFR in an isolated kinase assay, (c) it showed a dose-dependent inhibition of EGFR phosphorylation and downstream signaling in whole-cell assay, (d) it was selectively potent towards BRCA2 mutant and also EGFR-overexpressing cell lines, (d) it was extremely potent with activities superior to that of olaparib or gefitinib alone and their corresponding equimolar combination in three established triple negative breast cancer cell lines, (e) subcellular distribution analysis showed that it was abundantly localized in the perinuclear region. These results in toto suggest that this new combi-molecule could be developed as a single drug modality emulating the combination of PARP and EGFR inhibitors with the added benefit of being targeted to EGFR-expressing tumor cells.
Citation Format: Zhor Senhaji Mouhri, Martin Rupp, Bertrand J. Jean-Claude. A novel combi-molecule engineered to target the putative synthetic lethal interactions between the epidermal growth factor receptor (EGFR) and poly(ADP-ribose)polymerase (PARP) [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 4035. doi:10.1158/1538-7445.AM2017-4035
Abstract 4041: SUV39H2 inhibition enhances sensitivity of breast cancer cells to doxorubicin through downregulation of γ-H2AX production
Authors: Vougiouklakis Theodore , Saloura Vassiliki , Matsuo Yo , Nakamura Yusuke 
Published: July 2017

Abstract
Accumulating evidence has demonstrated the biological importance of protein methyltransferases in human tumorigenesis, and several small molecular inhibitors targeting these enzymes have been developed. Moreover, inhibiting pathways involved in DNA repair has been shown to enhance the cytotoxicity of DNA-damaging agents. Herein, we report the development of a potent SUV39H2 inhibitor (OTS193320) that decreases global histone H3 lysine 9 tri-methylation (H3K9me3) levels in cancer cells and attenuates cancer cell proliferation, and suppresses the tumor growth in mouse xenograft models. SUV39H2 (Suppressor of variegation 3-9 homolog 2), is a protein methyltransferase known to methylate histone H3 at lysine 9 (H3K9), and recently reported to methylate histone H2AX at lysine 134, which enhances the accumulation of phosphorylated H2AX (γ-H2AX) and regulates the DNA repair pathway in human cancer. SUV39H2 is highly expressed in many cancer types, including lung and breast cancers, while its expression levels are restricted to testis in normal adult tissues. Exposure of OTS193320 to two triple negative breast cancer cell lines attenuated H3K9me3 levels in a dose-dependent manner and triggered apoptotic cell death. Combination of OTS193320 and doxorubicin (DOX) resulted in reduction of γ-H2AX levels compared to single agent DOX, as visualized on western blot and immunocytochemical analysis. Furthermore, combination therapy attenuated the levels of p53-binding protein 1, which is reported to co-localize with γ-H2AX foci, compared to single agent DOX. Cell viability assays demonstrated a significant growth suppressive effect when OTS193320 was combined with DOX, compared to single agent treatment of either drug, suggesting chemosensitization to DOX. Importantly, in a mouse xenograft model of A549 lung cancer cells, we observed a tumor growth inhibition of 60.8% at day 14 with 25mg/kg intravenous administration of the inhibitor, without significant body weight loss or toxicity. Immunohistochemical staining of tumors treated with the inhibitor demonstrated a significantly lower number of Ki-67 positive cells and attenuated distribution patterns of H3K9me3 compared to the control tumors. Collectively, our results demonstrate that SUV39H2 inhibition may be a promising approach to develop a novel class of anti-cancer treatment.
Citation Format: Theodore Vougiouklakis, Vassiliki Saloura, Yo Matsuo, Yusuke Nakamura. SUV39H2 inhibition enhances sensitivity of breast cancer cells to doxorubicin through downregulation of γ-H2AX production [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 4041. doi:10.1158/1538-7445.AM2017-4041
Abstract 4043: Design of a novel MGMT inhibitor targeted to EGFR overexpressing tumor cells: a new approach to selectively potentiate temozolomide in refractory tumors
Authors: Rupp Martin , Jean-Claude Bertrand J. 
Published: July 2017

Abstract
Temozolomide (TMZ) is an oral alkylating agent commonly used as a first-line chemotherapeutic agent for the treatment of high-grade gliomas and melanoma. Alkylation of the O6-position of guanine in DNA is mainly responsible for the antitumor effect of TMZ. The primary mechanism of chemoresistance to TMZ has been shown to be the overexpression of the DNA repair enzyme O6-methylguanine methyltransferase (MGMT) that specifically removes the methyl lesions from the O6-position of guanine. While O6-benzylguanine (O6-BG), a potent inhibitor of MGMT, was shown to sensitize tumor cells to TMZ in vitro and in vivo, the O6-BG+TMZ combination failed in clinical trial due to acute hematologic toxicity. To circumvent this problem, we wish to target O6-BG to the epidermal growth factor receptor (EGFR), a receptor that is not generally expressed in the hematological cells but overexpressed in many solid tumors. We have now successfully designed and synthesized one such molecule termed MR30 and showed that: 1) MR30 is capable of blocking EGFR and depleting MGMT levels in whole cells; 2) MR30 is a unique molecule capable of inducing stronger growth inhibition than the 2-drug combination involving clinical EGFR and MGMT inhibitors in a panel of melanoma, lung, prostate and ovarian cancer cell lines; 3) MR30 in vitro potentiated the effect of TMZ on MGMT positive cell lines; 4) its kinase inhibitory profiling over 25 different kinases demonstrated selectivity for EGFR, HER2 and EGFR mutant forms; 5) an isogenic model showed more than 70-fold selectivity towards EGFR expressing cells in growth inhibitory assay; 6) MR30 showed good cell penetration with distribution in the perinuclear region. The results in toto suggest that MR30 has the potential to be developed as a tumor selective potentiator of TMZ.
Citation Format: Martin Rupp, Bertrand J. Jean-Claude. Design of a novel MGMT inhibitor targeted to EGFR overexpressing tumor cells: a new approach to selectively potentiate temozolomide in refractory tumors [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 4043. doi:10.1158/1538-7445.AM2017-4043