bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4117: Imaging hypoxia: Development of a PET-optical smart probe
Authors: Klockow Jessica L. , Hettie Kenneth S. , Chin Frederick T. 
Published: August 2018

Abstract
Hypoxia is a characteristic trait of many aggressive tumors. Identification of hypoxic tissues is important for establishing patient treatment plans and prognoses. We show progress towards the development of a hypoxia-activated molecular probe that combines near-infrared (NIR) fluorescence and positron emission tomography (PET) imaging. The fluorescence emission enables facile scrutiny of probe function in vitro and positron emission facilitates translation for clinical use. The probe is a small molecule that possesses a nitro-aromatic group which is sensitive to hypoxic environments. The caged smart probe is non-fluorescent due to photo-induced electron transfer from the nitro-aromatic group. Nitroreductase, an enzyme which is upregulated in hypoxic environments, activates the fluorescence by reducing the nitro group, thereby disabling the quenching effect. Wet chemistry techniques were used to develop the probe which was analyzed by UV/Vis and fluorescence spectroscopies. In vitro and in vivo imaging experiments were also performed. The probe demonstrated membrane permeability and lysosomal accumulation in glioblastoma cells. Additional favorable characteristics include NIR emission and low toxicity to cells. The fluorescence was detected in subcutaneous murine cancer models providing evidence of potential clinical translation toward applications like image-guided surgery. In short, the probe was synthesized in good yield from commercially-available materials and showed promising optical characteristics in cells and animal models. Future work involves F-18 radiolabeling of the probe followed by microPET imaging.
Citation Format: Jessica L. Klockow, Kenneth S. Hettie, Frederick T. Chin. Imaging hypoxia: Development of a PET-optical smart probe [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 4117.
Abstract 4123: Pancreatic cancer imaging and interventional PTT with a human bispecific scfv antibody via click chemistry
Authors: wang qian , li dan , wang kun , liu chunyan , gao mingyuan , zhao xinming , tian jie 
Published: August 2018

Abstract
Early diagnosis and therapy intervention remains a meaningful task for prolonging pancreatic cancer lifetime and improving prognosis. Successful development of so many highly specific targets emerge, for accurate diagnosis and precise treatment. Herein, we generated bispecific antibody fragment by connecting anti-EGFR scfv and anti-VEGF scfv, via click ligation of TCO and tetrazine. Firstly, Cellvizo imaging was acquired by AF488/647 labeled anti-EGFR scfv and anti-VEGF scfv, respectively, displayed overexpression and metabolic process in real time. IVIS and 3D MSOT imaging of mice bearing anthropogenic cell line of bxpc3(EGFR+/VEGF+) subcutaneous and orthotopic and tumors with Irdye800 labeled Bs-(scfv)2 revealed a more significantly enhancement and long circulation of tumor uptake and tumor-to-background ratio compared with each special scfv group(T/B ratio of 12.1±3.4 at 4h post-injection, n=5 in IVIS image). Thus, we validated that dual targeting of VEGF and EGFR provides a high affinity and specificity by Irdye800-labeled-Bs-(scfv)2. Finally, we successfully replaced irdye800 with PLA-PEG-NHS@ICG (combined or uncombined GEM) and conjugated Bs-(scfv)2 for interventional PTT, compared with GEM treatment, a 18% higher median survival rate of PTT combined GEM has been achieved. Our finding offer a preclinical proof concept for Bs-(scfv)2 PTT in clinical trial in future, due to effective bio-distribution and high affinity.
Citation Format: qian wang, dan li, kun wang, chunyan liu, mingyuan gao, xinming zhao, jie tian. Pancreatic cancer imaging and interventional PTT with a human bispecific scfv antibody via click chemistry [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 4123.
Abstract 413: Emerging principles in synthetic lethality in glioblastoma
Authors: Hoellerbauer Pia , Arora Sonali , Kufeld Megan , Carter Lucas , Girard Emily J. , Feldman Heather , Corrin Philip , Olson James M. , Paddison Patrick J. 
Published: August 2018

Abstract
Synthetic lethality occurs when mutations in two otherwise nonessential genes are combined to cause lethality. Because cancer is a disease of genetic alteration, synthetic lethality has been heralded as a method to identity candidate therapeutic targets, e.g., where a target gene could be "synthetic lethal" with a cancer driver mutation. To define synthetic lethal relationships in glioblastoma (GBM), we have performed multiple focused-set and genome-wide CRISPR-Cas9 lethality screens in patient-derived GBM stem-like cells (GSCs) and nontransformed human neural progenitor cells. Because GSCs isolates likely represent a sub-clone of the original tumor and we can determine GSCs' genetic and epigenetic makeup, it is possible to address the concept of synthetic lethality for GBM. To this end, we recently performed comprehensive CRISPR-Cas9 retests of all scoring GBM lethal genes (&gt;900) from screens in three patient isolates with different and overlapping genetic drivers. We then performed secondary retests of high-priority gene targets in 13 GSC harboring various alterations commonly found in GBMs, e.g., EGFRamp, NF1mut, PIK3CAmut, PTENloss/mut, TP53mut, etc. The results were surprising, first in what we did not find. We failed to find synthetic lethal targets for TP53loss/mut, RB1mut, or TERT expression, suggesting that synthetic lethal relationships for these alterations may not exist for GBM. Second, NF1mut interactors defined a broader class of synthetic lethal targets with general overactivity of the RTK/Ras pathway, which can arise from various activating lesions. Third, candidate synthetic lethal relationships can be observed, but, so far, only with EGFRamp, MYC/MYCNamp, and PTEN/PIK3CA alterations. Thus, in general our results suggest that the majority of synthetic lethal relationships in GBM arise from oncogenic activation of the RTK/Ras and PI-3 kinase pathway or amplification of MYC/MYCN. (Synthetic lethal targets will be revealed and discussed at the meeting.)
Citation Format: Pia Hoellerbauer, Sonali Arora, Megan Kufeld, Lucas Carter, Emily J. Girard, Heather Feldman, Philip Corrin, James M. Olson, Patrick J. Paddison. Emerging principles in synthetic lethality in glioblastoma [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 413.
Abstract 4131: Plasticity of transcriptional and epigenetic cellular states in neuroblastoma is driven by core lineage transcription factors
Authors: Nes Johan V. , Groningen Tim V. , Koster Jan , Valentijn Linda , Zwijnenburg Danny , Westerhout Ellen M. , Hamdi Mohamed , Versteeg Rogier 
Published: August 2018

Abstract
Background: Core Regulatory Circuitries (CRCs) of lineage transcription factors associate with super-enhancers and are drivers of cellular identity. We recently showed that most neuroblastomas include two types of tumor cells with divergent gene expression profiles. Undifferentiated mesenchymal (MES) cells and committed adrenergic (ADRN) tumor cells resemble cells from developmental stages of the adrenergic lineage.
Results: We identified the unique super-enhancer (SE) landscapes of MES and ADRN-type cells. SEs associated with lineage transcription factors that identified the Core Regulatory Circuitries (CRC) for each cell type. MES cells were resistant to chemotherapy. Accordingly, MES cells were strongly enriched in post-treatment samples, suggesting that MES cells could play a role in resistance and relapse development. MES and ADRN cells of isogenic origin spontaneously interconverted, showing the transcriptional plasticity of CRCs. We studied the mechanism of MES and ADRN transdifferentiation. The MES TFs PRRX1 and NOTCH were expressed as single genes in ADRN cells. Each of the genes induced a step-wise reprogramming of the ADRN transcriptome towards a MES state. The transcriptional switch was accompanied by genome-wide remodeling of the epigenome to a MES enhancer state. MES TFs repressed super-enhancers of ADRN core TFs, leading to transcriptional downregulation of the ADRN CRC. Deregulated enhancers associated with Polycomb repression. The transdifferentiation was initially reversible, but became gradually stabilized. The transgenes activated an endogenous feed-forward loop including ligands, receptors and co-factors from the NOTCH signaling route. Ultimately, this endogenous NOTCH-cascade maintained a transgene-independent MES state. Super-enhancers in stable MES cell lines associated with NOTCH receptors and co-factors, consistent with NOTCH driving MES lineage identity. Both NOTCH-induced MES cells and ADRN cells were tumorigenic in vivo.
Conclusions: Our results demonstrate that single TFs from the MES CRC impose transdifferentiation via remodeling of the epigenetic and transcriptional landscape of ADRN cells, mimicking spontaneous interconversion. Plasticity of CRCs and lineage identity may have profound implications for treatment strategies in neuroblastoma.
Citation Format: Johan V. Nes, Tim V. Groningen, Jan Koster, Linda Valentijn, Danny Zwijnenburg, Ellen M. Westerhout, Mohamed Hamdi, Rogier Versteeg. Plasticity of transcriptional and epigenetic cellular states in neuroblastoma is driven by core lineage transcription factors [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 4131.
Abstract 4139: SNAI2 inhibition promotes myogenic differentiation and prevents tumorigenic features of embryonal rhabdomyosarcoma
Authors: Pomella Silvia , Carcarino Elena , Cossetti Cristina , Locatelli Franco , Rota Rossella 
Published: August 2018

Abstract
Pediatric Rhabdomyosarcoma (RMS) is a soft tissue sarcoma of childhood that in its high risk form has a dismal prognosis. RMS includes two histological subtypes, embryonal and alveolar, which differ clinically and molecularly. Both are characterized by the expression of Myogenic Regulatory Factors (MRFs) such as MYOD and MYOG but tumor cells are unable to differentiate in skeletal muscle cells and proliferate indefinitely. For this reason, differentiation therapies have anticancer potential in this tumor. Interestingly, one of the cause of the inability of MRFs in inducing myogenic-like differentiation is related to the loss of transcriptional activity of these factors partly due to the lack of availability of DNA binding sites and/or of capability to form transcriptional complexes. We demonstrate here that the repressor SNAI2 is upregulated in embryonal RMS (ERMS) patients and cells lines compared to their normal counterparts. Silencing of SNAI2 in 2 ERMS patient-derived cell lines using a puromycin pLKO lentiviral vector expressing a SNAI2 shRNA results in a slowdown of cell proliferation associated to p21Cip1 and Myogenin upregulation starting 3 days post-selection, as compared to control vector. These molecular changes are followed by the induction of Myosin-Heavy Chain and the formation of myogenic-like multinucleated structures reminiscent of myogenic fibers. Moreover, colony formation and anchorage independent growth are both strongly impaired. Finally, SNAI2 depleted cells form smaller spheres when cultured in cancer stem cells conditions. Therefore, SNAI2 down-regulation could have therapeutic value in ERMS. Studies are ongoing to verify the restoring of MYOD transcriptional activity and to identify genes regulated by SNAI2 in our system.
The work is supported by Associazione Italiana Ricerca sul Cancro project IG15312 to RR.
Citation Format: Silvia Pomella, Elena Carcarino, Cristina Cossetti, Franco Locatelli, Rossella Rota. SNAI2 inhibition promotes myogenic differentiation and prevents tumorigenic features of embryonal rhabdomyosarcoma [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 4139.
Abstract 414: Broad range chromosomal abnormality detection through Bionano genome mapping
Authors: Hastie Alex R. 
Published: August 2018

Abstract
Current methods for detection of balanced structural variation can be broken down into two categories: traditional cytogenetics and molecular methods. Cytogenetics may include chromosomal karyotyping, fluorescence in situ hybridization (FISH), chromosomal microarray and adaption of them. Molecular methods primarily include NGS sequencing based methods. Bionano genome mapping, an optical mapping approach in a NanoChannel array system, is a method that combines the advantages of different categories while solving many of the limitations. Compared to cytogenetics, Bionano mapping is high throughput and removes manual interpretation, it also has much higher resolution, detecting balanced events as small as about 30 kbp compared to multi-megabases needed for cytogenetic approaches, and unbalanced events starting at 1 kbp. NGS based methods often are limited by read lengths that cannot provide unambiguous information across repeat elements longer than individual reads. This limitation results in significantly reduced sensitivity for balanced variation and abnormalities as well as for insertions and even some categories of larger deletions. This is particularly true in highly medically relevant locations where segmental duplications mediate chromosomal abnormalities. Genome mapping using Bionano Genomics' Saphyr System offers high-throughput, genome-wide visualization of extremely long DNA molecules in their native form. It allows researchers to interrogate genomic structural variations (SVs) in the range of one kilobase pair and above. We present several in silico and biological validation experiments that demonstrate the sensitivity and specificity of Bionano mapping for the detection of insertions, deletions, inversions and translocations compared to benchmark studies using short read and long read sequencing. We also show a new direct labeling method that dramatically improves assembly contiguity such that chromosome arms can be assembled into single maps. Bionano mapping is a fast and cost effective method for the detection of a broad range of traditionally refractory SVs across the human genome.
Citation Format: Alex R. Hastie. Broad range chromosomal abnormality detection through Bionano genome mapping [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 414.
Abstract 4142: Conformational dynamics of the chimeric kinase DNAJB1-PRKACA, the driver for fibrolamellar hepatocellular carcinoma
Authors: Tomasini Michael D. , Wang Yingiie , Karamafrooz Adak , Hall James , Taylor Susan S. , Beuming Thijs , Veglia Gianluigi , Simon Sanford M. 
Published: August 2018

Abstract
In fibrolamellar hepatocellular carcinoma (FLC) there is a single common genetic alteration in all tumors: A deletion in one copy of chromosome 19 resulting in the fusion of the first exon of DNAJB1, encoding the J-domain of heat shock protein 40, with exons 2-10 of the catalytic subunit of protein kinase A, PRKACA [1]. This produces an enzymatically active chimeric protein. Expression of the chimera in mouse liver either by recreating the deletion by CRISPR/Cas9, or expression, in trans, by a transposon is sufficient to produce FLC [2]. We used molecular dynamics simulations, NMR, and SAXS to analyze the conformational dynamics of the native and chimeric kinase. The most significant differences were in the amino domain with the chimera in an ensemble of conformations. Some structures had the J-domain tucked under the large lobe of the kinase, similar to that reported in the crystal structure, and in others the J-domain was dislodged from the core of the kinase, swinging free in solution. These simulated dislodged states were captured experimentally both by NMR and small angle X-ray scattering. Modeling of the different conformations onto the RIIβ holoenzyme revealed no obvious steric interactions suggesting that the J-domain does not preclude formation of the holoenzyme. The flexible conformations appear to be independent of the nucleotide/substrate binding mode as they were observed in ATP, ADP, Apo, and ATP-PKI bound states.
[1] Honeyman, J. N. et al. Detection of a recurrent DNAJB1-PRKACA chimeric transcript in fibrolamellar hepatocellular carcinoma. Science 343, 1010-1014 (2014).
[2] Kastenhuber, E. R. et al. DNAJB1-PRKACA fusion kinase interacts with β-catenin and the liver regenerative response to drive fibrolamellar hepatocellular carcinoma. Proc. Natl. Acad. Sci. 201716483 (2017). doi:10.1073/pnas.1716483114
Citation Format: Michael D. Tomasini, Yingiie Wang, Adak Karamafrooz, James Hall, Susan S. Taylor, Thijs Beuming, Gianluigi Veglia, Sanford M. Simon. Conformational dynamics of the chimeric kinase DNAJB1-PRKACA, the driver for fibrolamellar hepatocellular carcinoma [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 4142.
Abstract 4149: Inhibition of ribonucleotide reductase (RNR) in Ewing sarcoma cells results in suppression of protein synthesis
Authors: Koppenhafer Stacia , Goss Kelli , Gordon David 
Published: August 2018

Abstract
Ewing sarcoma is a highly aggressive bone and soft tissue cancer that is caused by the EWS-FLI1 fusion protein. EWS-FLI1 is required for tumor growth and survival. However, directly targeting EWS-FLI1 with drugs has been challenging and an alternative therapeutic approach is to identify unique vulnerabilities incurred by the oncoprotein. In previous work, we identified that Ewing sarcoma cells are uniquely vulnerable to drugs that inhibit ribonucleotide reductase (RNR), which is the rate limiting enzyme in the synthesis of deoxyribonucleotides. Furthermore, we also showed that blocking the function of checkpoint kinase 1 (CHK1), a major regulator of the response to impaired DNA replication, using either a small molecule inhibitor or siRNA-mediated knockdown causes synergistic toxicity with gemcitabine, an irreversible inhibitor of the RRM1 subunit of RNR, in Ewing sarcoma cells. In the current work, we identifiy that inhibition of RNR in Ewing sarcoma cells in vitro and in vivo results in the suppression of protein synthesis. Moreover, we have found that the treatment of Ewing sarcoma cell lines with gemcitabine results in an increase in the active (unphosphorylated) form of 4E-BP1, which is a well-described inhibitor of protein translation. However, in contrast to the Ewing sarcoma cells, treatment of other cell types with gemcitabine did not alter 4E-BP1 phosphorylation or protein synthesis. Currently, ongoing work is focused on the in vivo testing of gemcitabine, alone and in combination with CHK1, ataxia telangiectasia and rad3-related protein (ATR), and protein synthesis inhibitors, as a novel therapeutic approach for the treatment of Ewing sarcoma.
Citation Format: Stacia Koppenhafer, Kelli Goss, David Gordon. Inhibition of ribonucleotide reductase (RNR) in Ewing sarcoma cells results in suppression of protein synthesis [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 4149.
Abstract 415: A single molecule detection system for comprehensive analysis of cancer related cellular pathways
Authors: Furtado Manohar R. , Fang Rixun , Burns Norman , Burich Rebekah , Le Catherine , Ivaturi Soumya , Hartlage Rob , Zizminskas Ed , Jahncke Jim , Mack Philip C. , Staker Bryan P. 
Published: August 2018

Abstract
The purpose of this study was to evaluate the system capabilities of a new single-molecule detection platform capable of both genomic and proteomic analysis of cellular pathways using very small amounts of tumor material. The system has 4-color optics, single-fluorophore detection capability, localization of molecules to within a 20nm area, a flow cell with an area of 940 mm2 and the ability to detect &gt; 109 molecules on the surface. NSCLC cell lines were cultured and untreated or treated with the EGFR tyrosine kinase inhibitor erlotinib. Cells were harvested and used to generate protein lysates, isolate mRNA and gDNA. Cellular molecules were covalently attached to an epoxysilane-coated surface on the flow cell and then repeatedly probed 10-15 times with labeled antibodies and oligonucleotides to detect, count and quantitate proteins, protein phosphorylation levels, mRNAs, fusion transcripts, and DNA mutations. We detected protein phosphorylation changes for EGFR, ERK, MET and MEK comparable to that observed by traditional western blots; however, the system required only 0.5 to 2 cell equivalents of protein lysate, containing sub pico-Molar levels of protein. We demonstrated robust and statistically significant detection of 2-fold changes in protein levels across 3 slides, in triplicate lanes and performed over 3 non-consecutive days by 3 operators (Tukey-Kramer tests). We also detected 8 mRNAs, with no PCR amplification required, in a multiplexed format with relative levels similar to that observed with TaqMan® qPCR tests. We demonstrated protein detection at ~ 100% recovery compared to an ELISA test and nucleic acid recovery at ~ 30% with no amplification. We also detected exon 19 deletions in EGFR, point mutations at L858R, T790M in EGFR and V600E in BRAF, at 0.5% minor allele levels, by using an oligonucleotide ligation assay off-chip and then attaching the ligated product to the surface. mRNA levels were detected using 10-20 cell equivalents of RNA. We believe the system will enable comprehensive analysis of cancer-related pathways, requiring only a few cells, to help decipher cellular pathway activity induced by driver mutations and consequently help with selection of efficacious drugs tailored for specific individuals based on comprehensive molecular analysis.
Citation Format: Manohar R. Furtado, Rixun Fang, Norman Burns, Rebekah Burich, Catherine Le, Soumya Ivaturi, Rob Hartlage, Ed Zizminskas, Jim Jahncke, Philip C. Mack, Bryan P. Staker. A single molecule detection system for comprehensive analysis of cancer related cellular pathways [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 415.