tbuckley/cabot-search huggingface dataset:
Abstract 2045: Exploring the potential of cellular thermal shift assay (CETSA) to study drug resistance during cancer therapy
Authors: Lekshmy Kunjamma Usha Sreekumar, Yan Ting Lim, Saranya Veerappan, Par Nordlund
Journal: Cancer Research (2017)

Abstract The aim of this project is to understand the various mechanisms contributing to drug resistance development in cancer therapy. The efficacy of therapeutics is dependent on a drug binding to its target. We have developed a method that allows for the first time to directly evaluate drug binding to target proteins in cells and tissue samples the cellular thermal shift assay (CETSA) (Martinez Molina et al. Science, 341:84). CETSA is based on the biophysical principle of ligand-induced thermal stabilization of target proteins. By monitoring the drug occupancy in the target protein, CETSA can be used to study processes of drug transport and metabolism in cancer cells. We have used CETSA to study the acquired drug resistance of, antifolate and fluropyrimidine drugs in pairs of parental and resistant cell lines. CETSA shifts and isothermal dose response fingerprint (ITDRF) were used to study the relative drug target engagement in these cells. Quantitative mass spectrometry was used to monitor differences in protein expression levels across the cell lines. Based on the CETSA measurements, resistant cells clearly showed a higher drug dose threshold as compared to the parent cell lines, typically requiring 8-50 times higher dose to establish similar target engagement. Several potential mechanism for drug resistant emerged - we, for example, observed up-regulation of thymidylate synthase and down regulation of reduced folate carrier (RFC) protein associated with antifolate transport, in some resistant cell lines. The data supports that CETSA is a potential valuable tool to dissect various mechanisms those contribute to resistant development in cancer cells. Citation Format: Lekshmy Kunjamma Usha Sreekumar, Yan Ting Lim, Saranya Veerappan, Par Nordlund. Exploring the potential of cellular thermal shift assay (CETSA) to study drug resistance during cancer therapy [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 2045. doi:10.1158/1538-7445.AM2017-2045
Abstract 2766: Esophageal stenting in resource-limited settings
Authors: Michael M. Mwachiro, Robert K. Parker, Stephen Burgert, Justus Lando, Sinkeet Rankeeti, Robert Chepkwony, Emmanuel Kiniga, Sanford Dawsey, Mark Topazian, Russell E. White
Journal: Cancer Research (2017)

Abstract Background: Esophageal cancer is the 6th leading cause of cancer death globally, with geographical high-risk areas in Asia, the Middle East, and eastern and southern Africa. Esophageal squamous cell carcinoma (ESCC) is the more common variant in Africa. In Kenya, its incidence is 2nd in men after prostate cancer and 3rd in women after breast and cervix-uteri cancers. Late presentation is a common occurrence in developing countries and is multifactorial due to challenges in access to health care, low socioeconomic status and delayed or missed diagnosis. A large percentage of these tumors are thus unresectable and are only eligible for palliative care via stenting. Our hospital is a 300-bed referral center in southwestern Kenya, which is a hotspot for ESCC, and we see over 400 cases of ESCC annually. Methods: We have developed a technique for placement of esophageal self-expanding metallic stents (SEMS) without fluoroscopy that is safe and easily reproducible. This is an outpatient procedure, with the majority done under conscious sedation, and routine followup is not necessary. The tumor margins are noted at time of video endoscopy, a guidewire is placed, and dilation done with Savary dilators as required. The SEMS are then loaded on the stent delivery device and deployed into the proper position based on measurements, and placement is subsequently confirmed via endoscopic visualization. Results: A total of 3000 SEMS have been placed to date at our hospital, without using fluoroscopy. The male: female ratio has been 1.5:1, and the average age has been 60.4 years. The distribution of tumor locations was 67% in the middle and distal third. The most common complications were tumor overgrowth with obstruction and stent migration. Procedure related mortality was 0.3%. Post-procedure improvement in dysphagia score was seen in over 80% , and patient satisfaction was high. Initial data puts our post stent survival time around 8 months/ 250 days Conclusions: Placement of SEMS for ESCC, without fluoroscopy, is a safe and reproducible procedure which has a low rate of adverse events. This procedure results in effective palliation of a difficult disease and can easily be done in resource-limited settings which have endoscopy capabilities. Current efforts are ongoing to increase opportunities for training endoscopists in this procedure and for provision of affordable stents in Africa. Citation Format: Michael M. Mwachiro, Robert K. Parker, Stephen Burgert, Justus Lando, Sinkeet Rankeeti, Robert Chepkwony, Emmanuel Kiniga, Sanford Dawsey, Mark Topazian, Russell E. White. Esophageal stenting in resource-limited settings [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 2766. doi:10.1158/1538-7445.AM2017-2766
Ambient Ionization and Miniature Mass Spectrometry Systems for Disease Diagnosis and Therapeutic Monitoring
Authors: Wenpeng Zhang, Xiao Wang, Yu Xia, Zheng Ouyang
Journal: Theranostics (2017)

Mass spectrometry has become a powerful tool in the field of biomedicine.The combination of ambient ionization and miniature mass spectrometry systems could most likely fulfill a significant need in medical diagnostics, providing highly specific molecular information in real time for clinical and even point-of-care analysis.In this review, we discuss the recent development of ambient ionization and miniature mass spectrometers as well as their potential in disease diagnosis and therapeutic monitoring, with an emphasis on their capability in analysis of biofluids and tissues.We also speculate the future development of the integrated, miniature MS systems and provide our perspectives on the challenges in technical development as well as possible solutions for path forward.
Population and allelic variation of A-to-I RNA editing in human transcriptomes
Authors: Eddie Park, Jiguang Guo, Shihao Shen, Levon Demirdjian, Ying Nian Wu, Lan Lin, Yi Xing
Journal: Genome biology (2017)

A-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism for generating transcriptome diversity. However, there remain significant knowledge gaps about the variation and function of RNA editing. In order to determine the influence of genetic variation on A-to-I RNA editing, we integrate genomic and transcriptomic data from 445 human lymphoblastoid cell lines by combining an RNA editing QTL (edQTL) analysis with an allele-specific RNA editing (ASED) analysis. We identify 1054 RNA editing events associated with cis genetic polymorphisms. Additionally, we find that a subset of these polymorphisms is linked to genome-wide association study signals of complex traits or diseases. Finally, compared to random cis polymorphisms, polymorphisms associated with RNA editing variation are located closer spatially to their respective editing sites and have a more pronounced impact on RNA secondary structure. Our study reveals widespread cis variation in RNA editing among genetically distinct individuals and sheds light on possible phenotypic consequences of such variation on complex traits and diseases.
Abstract 327: EpCAM/EpEX regulate tumor progression through EGFR signaling in colon cancer cells
Authors: Kang-Hao Liang, Jun-Kai Lai, I-I Kuan, Hsien-Cheng Tso, Han-Chung Wu
Journal: Cancer Research (2017)

Abstract Epithelial cell adhesion molecule (EpCAM) is highly expressed in advanced epithelial cancers and tumor-initiated cells (TICs), but its roles in cancer progression remain to be elucidated. Here, we showed that the extracellular domain of EpCAM (EpEX) could bind to EGFR through EGF-like domain I, and subsequently activated its downstream molecules, ERK1/2 and Akt. EGFR inhibitor and knockdown of EGFR by shRNA ablated EpEX-induced ERK1/2 phosphorylation. Regulated intramembrane proteolysis (RIP) of EpCAM was induced similarly by EpEX and EGF through EGFR-dependent activation of ERK pathway. MEK inhibitor, U0126, could abolish ADAM17 and PS2 phosphorylation induced by EpEX. EpAb2-6, an anti-EpEX neutralizing monoclonal antibody, inhibits EpEX-activated EGFR-PI3K-AKT pathway in detached colon cancer cells. Moreover, intracellular domain of EpCAM (EpICD), the product of RIP-induced cleavage of EpCAM, is necessary for nuclear accumulation of β-catenin, and their target gene expressions in vitro and in mouse xenograft models. We also found that an increase of nuclear EpICD observed in CRCs predicted metastasis and poor prognosis in CRC patients. Finally, in animal model studies, EpAb2-6 therapy exhibited an enhanced antitumor effect and markedly extended the survival time of mice with human colorectal cancer in metastatic and orthotopic models. These results demonstrate that EpEX works as a growth factor in activating EGFR-mediated signaling, and as a potential target for treatment of colon cancer. This research was supported by grants from Academia Sinica and Ministry of Science and Technology [MOST 104-0210-01-09-02,MOST 105-0210-01-13-01], and the National Science Council (NSC103-2321-B-001-064), Taiwan (to H-C Wu). Citation Format: Kang-Hao Liang, Jun-Kai Lai, I-I Kuan, Hsien-Cheng Tso, Han-Chung Wu. EpCAM/EpEX regulate tumor progression through EGFR signaling in colon cancer cells [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 327. doi:10.1158/1538-7445.AM2017-327
Abstract 5641: Effects of G1T48, a novel orally bioavailable selective estrogen receptor degrader (SERD), and the CDK4/6 inhibitor, G1T38, on tumor growth in animal models of endocrine resistant breast cancer
Authors: Suzanne E. Wardell, Alexander P. Yllanes, Jennifer G. Baker, Robert M. Baldi, Taylor K. Krebs, Jessica Sorrentino, John Bisi, Jay Strum, John D. Norris
Journal: Cancer Research (2017)

Abstract Background: The combination of targeting the CDK4/6 and ER signaling pathways with palbociclib and fulvestrant is a proven therapeutic strategy for the treatment of ER positive breast cancer. However, the poor physicochemical properties of fulvestrant require monthly intramuscular injections to patients, which limit the pharmacokinetic and pharmacodynamic activity of the compound. Therefore, an orally available compound that more rapidly reaches steady state may lead to a better clinical response in patients. Here we report the preclinical characterization of G1T48, a novel, orally bioavailable, non-steroidal small molecule inhibitor of ERα, which is a potent, selective antagonist that down regulates ERα in vitro and in vivo in ER-positive models of breast cancer. Methods: Breast cancer cells expressing clinically relevant ESR1 mutations (ER-Y537S, ER-D538G) were threated with G1T38, G1T48, and mechanistically distinct SERMs/SERDs and cellular proliferation was assessed by measuring DNA content (Hoechst dye). Ovariectomized nu/nu mice bearing xenograft tumors of clinically relevant tamoxifen (TamR) and aromatase (long term estrogen deprived) resistant ER+ breast cancer were treated with G1T38 and G1T48, alone or in combination, with clinically relevant comparators. Time to progression and tumor volume were assessed over a 4 week dosing period. Results: G1T38 and G1T48 significantly inhibited cellular proliferation of MCF7 breast cancer cells bearing endocrine resistant ER mutations, ER-Y537S and ER-D538G. G1T48 treatment led to dramatic reductions in ER protein levels. Importantly, tumor growth inhibition was observed in mouse models of sensitive and resistant human breast cancer when G1T48 was dosed as a single agent or in combination with G1T38, a potent, selective CDK4/6 inhibitor. Conclusions: G1T38, a novel CDK4/6 inhibitor, and G1T48, a novel SERD, either alone or in combination, demonstrated highly potent inhibition of tumor growth in animal models of tamoxifen and aromatase resistance. G1T48 also demonstrated activity in models of endocrine resistance mediated by ER mutation. G1T48 is currently completing IND enabling studies. Citation Format: Suzanne E. Wardell, Alexander P. Yllanes, Jennifer G. Baker, Robert M. Baldi, Taylor K. Krebs, Jessica Sorrentino, John Bisi, Jay Strum, John D. Norris. Effects of G1T48, a novel orally bioavailable selective estrogen receptor degrader (SERD), and the CDK4/6 inhibitor, G1T38, on tumor growth in animal models of endocrine resistant 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 5641. doi:10.1158/1538-7445.AM2017-5641
Abstract 3435: Profiling miRNAs in breast epithelial progenitor cells during branching morphogenesis and EMT in 3D culture
Authors: Eirikur Briem, Bylgja Hilmarsdottir, Zuzana Budkova, Saevar Ingthorsson, Magnus K. Magnusson, Thorarinn Gudjonsson
Journal: Cancer Research (2017)

Abstract In this study we investigate the role of miRNA-203a in branching morphogenesis and epithelial to mesenchymal transition (EMT) in breast cell lines. D492 is a breast epithelial cell line with stem cell properties. D492 generates luminal- and myoepithelial cells and in 3D culture forms structures reminiscent of terminal duct lobular units of the breast. When cocultured with endothelial cells subset of D492 cells undergo EMT as evidenced by spindle shape morphology, E- to N cadherin switch and loss of keratin expression. We have established an endothelial-induced mesenchymal subline from D492 referred to as D492M. Here we use D492 and D492M as a model to investigate miRNA expression patterns during different stages of branching and in EMT. We performed small RNA-sequencing on D492 and D492M in 3D cultures. We were able to pinpoint miRNAs that are associated with epithelial integrity and suppressing EMT. We have recently shown that miRNA-200c-141 convert D492M back to the epithelial phenotype (Hilmarsdottir et al. G&amp;D 2015). MiRNA-203a is also down-regulated in D492M. Here we overexpress miRNA-203a in D492 and D492M. Methylation analysis reveal that the promoter area of miRNA-203a is not methylated in D492M. When miRNA-203a is overexpressed in D492M, cells change phenotype from elongate, mesenchymal-like phenotype to more cuboidal epithelioid phenotype, show reduced cell proliferation, less ability to form colonies in low attachment cultures, less ability to migrate and reduced invasion capability. When D492MmiRNA-203a is co-cultured with endothelial cells in 3D culture they partially regain the ability to form branching structures similar to D492. D492MmiRNA-203a show reduced expression of EMT transcription factors SNAI2 and ZEB1. When cultured on transwell filters, D492M forms stratified squamous epithelial layer while D492MmiRNA-203a form single squamous layer. In conclusion, miRNA-203a induces partial epithelial phenotype in D492M as evidenced by morphology and marker expression. We also conclude that three dimensional cultures of D492 and D492M work well as a model system to investigate miRNA expression during branching morphogenesis and in EMT. Citation Format: Eirikur Briem, Bylgja Hilmarsdottir, Zuzana Budkova, Saevar Ingthorsson, Magnus K. Magnusson, Thorarinn Gudjonsson. Profiling miRNAs in breast epithelial progenitor cells during branching morphogenesis and EMT in 3D culture [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 3435. doi:10.1158/1538-7445.AM2017-3435
Abstract 1563: A machine learning approach to predict platform specific gene essentiality in cancer
Authors: Coryandar M. Gilvary, Neel S. Madhukar, Kaitlyn M. Gayvert, David S. Rickman, Olivier Elemento
Journal: Cancer Research (2017)

Abstract Loss-of-function (LOF) screenings across a set of diverse cancer cell lines has the potential to reveal novel synthetic lethal interactions, cancer-specific vulnerabilities, and guide treatment options. These were traditionally done using shRNAs, but with the recent emergence of CRISPR technology there has been a shift in methodology. The Achilles project is to date the largest cancer LOF screening effort undertaken, however we found a large amount of inconsistency between their shRNA and CRISPR-Cas9 essentiality results for the same set of cell lines. Here we characterize the differences between genes found to be essential in either CRISPR or shRNA screens. We found that certain features such as gene expression, network connectivity and conservation could accurately separate out essential genes that were found exclusively in either one of these screens. This information could be tremendously useful in understanding the differences in the CRISPR and shRNA screening results. Furthermore, one limitation with Project Achilles was that they conducted shRNA screens on 216 cell lines, but only 33 cell lines in CRISPR. Therefore we developed a model that integrates these genetic, network, and population features to predict CRISPR results from shRNA screenings, and found that our model can accurately identify CRISPR essential genes better than approaches just based on the shRNA results (p-value &amp;lt; 10-5, d-statistic =~0.5 ). This potentially eliminates the need for a costly CRISPR screen, predicts essential genes that would be missed in the shRNA screen, and provides new data on thousands of genes in almost 200 cell lines. Additionally we integrated prior screening results to build a second set of models to predict gene essentiality for untested genes with no LOF screening needed. We found this accurately predicted whether a gene would be marked as essential as well as what type of platform (CRISPR or shRNA) was more likely to accurately identify essentiality. When predicting genes which were exclusively essential in CRISPR we observed an area under the receiver operating characteristic curve (AUC) of 0.82. Overall, these methods allow for a more comprehensive essentiality analysis of genes; which is not possible by single screening platforms. Citation Format: Coryandar M. Gilvary, Neel S. Madhukar, Kaitlyn M. Gayvert, David S. Rickman, Olivier Elemento. A machine learning approach to predict platform specific gene essentiality in 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 1563. doi:10.1158/1538-7445.AM2017-1563
Abstract 1369: DNA, protein, and cell line reagents to facilitate RAS pathway drug discovery efforts
Authors: Dominic Esposito
Journal: Cancer Research (2017)

Abstract The RAS Reagents Core within the NCI RAS Initiative produces and distributes qualified DNA vectors, cell lines, and protein production reagents to the external community to facilitate research into RAS biology and development of RAS cancer therapeutics. DNA vectors representing a variety of RAS mutations, as well as a complete collection of 180 genes in the RAS pathway are available as Gateway-compatible Entry clones. These clones represent the most commonly expressed transcript forms of the 180 genes, many of which were not previously available in full-length, wildtype forms. The vectors can be used with the FNLCR combinatorial cloning library to easily generate a large number of different types of expression clones with various promoters, fusion tags, and plasmid backbones. Cell line reagents include a variety of Ras-dependent mouse embryonic fibroblasts (MEFs) which have a defined mutant allele of KRAS and which serve as isogenic cell lines for investigating allele and mutant specific RAS biology, as well as for valuable screening tools. Protein reagents include E. coli and insect cell constructs and cell lines for production of a variety of Ras-related proteins. In particular, we have materials for the high yield production of properly processed, prenylated KRAS protein using a unique engineered insect cell expression system. This system can also be used to produce other prenylated small GTPases at levels not previously attainable. Many of the resources of the RAS Reference Core are readily available to the academic community through repositories or material transfer agreements, and can be licensed to industry scientists as well. The program is also interested in identifying the needs of the community for additional RAS-related resources, and is developing methods for vetting requests from the outside to provide additional reagents. Citation Format: Dominic Esposito. DNA, protein, and cell line reagents to facilitate RAS pathway drug discovery efforts [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 1369. doi:10.1158/1538-7445.AM2017-1369