tbuckley/cabot-search huggingface dataset:
Abstract 3832: Optimization strategy for fluorescent multiplex immunohistochemistry tissue staining
Authors: Yi zheng, Carla Coltharp, Ryan Dilworth, Linying Liu, Darryn Unfricht, Cliff Hoyt, Milind Rajopadhye, Peter Miller
Journal: Cancer Research (2017)

Abstract Introduction: Recent insights into the tumor microenvironment have fueled the need for additional information beyond the one or two phenotypes provided by traditional immunohistochemistry (IHC). As a response, manual and automated fluorescent multiplex immunohistochemistry (fIHC) techniques have been recently developed and accepted by the immuno-oncology space. Fluorescent multiplex immunohistochemistry (fIHC) assays are designed to simultaneously measure multiple biomarkers in tissue sections with visual context that is lost in other methods, such as flow cytometry. Here we describe a novel optimization strategy to achieve quantitative, robust, and specific multiplex fIHC staining results with both manual and automated multiple-color Opal procedures. Methods: Formalin-fixed paraffin-embedded samples of primary tumors were immunostained using Opal™ reagents both manually and on a fully automated Leica BOND RX™ stainer. The impact of different reagent concentrations and quantities were analyzed in respect to signal specificity and robustness, stripping efficiency, signal co-localization, signal to noise, and color separation. Images were acquired on a Vectra 3.0® automated imaging system, and analyzed with inForm® software. Results: The goals of this study were two-fold: -to understand the impact of Opal reagent concentrations/quantities on fluorescent signal intensities acquired from cells within the context of tissue. -to develop an Opal reagent optimization method that yields more consistent, quantitative results from separated and co-localized fluorescent signals. We’ve applied this novel fIHC experimental approach and optimization strategy to Opal monoplex and multiplex assays and explored staining robustness, contextual specificity, staining order independence, and co-localized signal separation. Using the novel optimization strategy, we have achieved optimal staining patterns with improved confidence in the quantitative characteristics of the assay. Tissue sections stained after optimization have exhibited staining order independence and closely align with traditional IHC patterns. Conclusion: This novel optimization strategy, developed for Opal fIHC assays, is more quantitative, improves staining results, and minimizes interference between co-localized biomarkers. Citation Format: Yi zheng, Carla Coltharp, Ryan Dilworth, Linying Liu, Darryn Unfricht, Cliff Hoyt, Milind Rajopadhye, Peter Miller. Optimization strategy for fluorescent multiplex immunohistochemistry tissue staining [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 3832. doi:10.1158/1538-7445.AM2017-3832
Cap on legal fees for clinical negligence work does not go far enough, defence organisations warn
Authors: Abi Rimmer
Journal: BMJ (2017)

Proposals to limit the amount lawyers can claim in costs on medical negligence cases worth less than £25 000 (€28 000; $33 000) do not go far enough, medical defence organisations have said.

In a review of civil litigation costs,1 Lord Justice Jackson has recommended that the Department of Health and the Civil Justice Council should set up a working party to develop a process for handling clinical negligence claims of under £25 000.

He said that the process should have a grid of fixed recoverable costs …
<i>NSD1</i> Inactivation and <i>SETD2</i> Mutation Drive a Convergence toward Loss of Function of H3K36 Writers in Clear Cell Renal Cell Carcinomas
Authors: Xiaoping Su, Jianping Zhang, Roger Mouawad, Eva Compérat, Morgan Rouprêt, Frederick Allanic, Jérôme Parra, Marc-Olivier Bitker, Erika J. Thompson, Banumathy Gowrishankar, Jane Houldsworth, John N. Weinstein, Jorg Tost, Bradley M. Broom, David Khayat, Jean-Philippe Spano, Nizar M. Tannir, Gabriel G. Malouf
Journal: Cancer Research (2017)

Abstract Extensive dysregulation of chromatin-modifying genes in clear cell renal cell carcinoma (ccRCC) has been uncovered through next-generation sequencing. However, a scientific understanding of the cross-talk between epigenetic and genomic aberrations remains limited. Here we identify three ccRCC epigenetic clusters, including a clear cell CpG island methylator phenotype (C-CIMP) subgroup associated with promoter methylation of VEGF genes (FLT4, FLT1, and KDR). C-CIMP was furthermore characterized by silencing of genes related to vasculature development. Through an integrative analysis, we discovered frequent silencing of the histone H3 K36 methyltransferase NSD1 as the sole chromatin-modifying gene silenced by DNA methylation in ccRCC. Notably, tumors harboring NSD1 methylation were of higher grade and stage in different ccRCC datasets. NSD1 promoter methylation correlated with SETD2 somatic mutations across and within spatially distinct regions of primary ccRCC tumors. ccRCC harboring epigenetic silencing of NSD1 displayed a specific genome-wide methylome signature consistent with the NSD1 mutation methylome signature observed in Sotos syndrome. Thus, we concluded that epigenetic silencing of genes involved in angiogenesis is a hallmark of the methylator phenotype in ccRCC, implying a convergence toward loss of function of epigenetic writers of the H3K36 histone mark as a root feature of aggressive ccRCC. Cancer Res; 77(18); 4835–45. ©2017 AACR.
Abstract 3302: Autophagy is required for cell survival under L-asparaginase-induced metabolic stress in acute lymphoblastic leukemia cells
Authors: Jun Inoue, Hiroyoshi Takahashi, Kimiyoshi Sakaguchi, Masatoshi Takagi, Shuki Mizutani, Johji Inazawa
Journal: Cancer Research (2017)

Abstract L-asparaginase has been used for more than three decades in acute lymphoblastic leukemia (ALL) patients and remains an essential drug in the treatment of ALL. Poor response to L-asparaginase is associated with increased risk of therapeutic failure in ALL. However, both the metabolic perturbation and molecular context of L-asparaginase-treated ALL cells has not been fully elucidated. Here we identify that treatment with L-asparaginase results in metabolic shutdown via the reduction of both glycolysis and oxidative phosphorylation, accompanied by mitochondrial damage and activation of autophagy. The autophagy is involved in reducing reactive oxygen species (ROS) level by eliminating injured mitochondria. Inhibition of autophagy enhances L-asparaginase-induced cytotoxicity and overcomes the acquired resistance to L-asparaginase in ALL cells. The ROS-p53 positive feedback loop is an essential mechanism of this synergistic cytotoxicity. Thus, our findings provide the rationale for the future development of combined treatment of L-asparaginase and anti-autophagy drug in ALL patients. Citation Format: Jun Inoue, Hiroyoshi Takahashi, Kimiyoshi Sakaguchi, Masatoshi Takagi, Shuki Mizutani, Johji Inazawa. Autophagy is required for cell survival under L-asparaginase-induced metabolic stress in acute lymphoblastic leukemia 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 3302. doi:10.1158/1538-7445.AM2017-3302
Abstract 5500: KMT2C directs estrogen receptor activity in normal and transformed mammary cells
Authors: Kinisha Gala, Amit Sinha, Francisco Sanchez-Vega, Young Rock Chung, James Hseih, Michael Berger, Nikolaus Schultz, Alessandro Pastore, Omar Abdel-Wahab, Sarat Chandarlapaty
Journal: Cancer Research (2017)

Abstract Estrogen receptor alpha (ERα) is a ligand-activated nuclear receptor that regulates proliferation and differentiation in mammary epithelial cells. ERα activity is likely dependent on the actions of pioneer factors and H3K4 methyltransferases which can establish a genomic landscape permissive for ERα binding. Here, we identify the H3K4 methyltransferase KMT2C as essential for ERα activity in mammary gland development and ER+ breast cancer growth. KMT2C suppression decreases estrogen-dependent gene expression and causes H3K4me1 loss at ERα target gene enhancers. Consequently, KMT2C loss selectively suppresses estrogen-driven breast cancer proliferation. Moreover, mammary-specific Kmt2c knockout mice have defects in pubertal ductal formation similar to Esr1 deficient mice. Although KMT2C loss disrupts estrogen-driven proliferation, it conversely promotes tumor outgrowth under hormone-depleted conditions. Consistent with this, gene expression signatures of KMT2C loss are associated with poor outcomes. We conclude that KMT2C is a key regulator of ERα activity whose loss uncouples mammary phenotypes from hormone availability. Citation Format: Kinisha Gala, Amit Sinha, Francisco Sanchez-Vega, Young Rock Chung, James Hseih, Michael Berger, Nikolaus Schultz, Alessandro Pastore, Omar Abdel-Wahab, Sarat Chandarlapaty. KMT2C directs estrogen receptor activity in normal and transformed mammary 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 5500. doi:10.1158/1538-7445.AM2017-5500
Abstract 4621: Metabolic activation of macrophages by CpG stimulates anti-tumor activity and overcomes CD47-independent inhibition by tumor cells in pancreatic ductal adenocarcinoma
Authors: Mingen Liu, Gregory Beatty
Journal: Cancer Research (2017)

Abstract Macrophages dominate the immune infiltrate present in pancreatic ductal adenocarcinoma (PDAC). Although tumor-infiltrating macrophages have the potential to mediate anti-tumor activity, they most commonly acquire an immunosuppressive role in cancer. We have found that CpG oligonucleotides - containing unmethylated cytosine-guanine motifs - potently induce macrophages to phagocytose PDAC cells and mediate anti-tumor effects. When delivered in vivo, in a fully immunocompetent murine model of PDAC, CpG increased the presence of macrophages within PDAC tumors and suppressed tumor outgrowth in a macrophage-dependent manner. Though CpG did not polarize macrophages toward classical anti-tumor (M1) or pro-tumor (M2) phenotypes, CpG treatment increased the basal rate of oxygen consumption in macrophages. Reversing this metabolic shift by inhibiting fatty acid oxidation abolished pro-phagocytic and anti-tumor effects by macrophages in vitro and in vivo. We investigated the impact of CpG in overcoming anti-phagocytic signals from CD47, a membrane protein overexpressed in multiple malignancies, including PDAC. While targeted knockout of CD47 in PDAC cells was not sufficient to activate in vitro phagocytosis by macrophages or anti-tumor effects in vivo, delivery of CpG potentiated anti-tumor and phagocytic activity that was independent of CD47 expression by tumor cells. However, the combination of CD47 loss in tumor cells and systemic CpG treatment enhanced the survival of tumor-bearing mice, indicating that disruption of CD47 can sensitize tumors to macrophage-directed immunotherapy. Together, our findings demonstrate a key role for cellular metabolism in directing the anti-tumor functions of macrophages and overcoming negative regulatory signals imposed by malignant cells. Citation Format: Mingen Liu, Gregory Beatty. Metabolic activation of macrophages by CpG stimulates anti-tumor activity and overcomes CD47-independent inhibition by tumor cells in pancreatic ductal adenocarcinoma [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 4621. doi:10.1158/1538-7445.AM2017-4621
Abstract 1566: Differential expression of Epstein Barr virus miRNAs in triple-negative breast cancer
Authors: Alexander Blanchard, Tiffany Walls, Ramon Vidal, Stefan Bonn, Scott Harrison, Perpetua Muganda
Journal: Cancer Research (2017)

Abstract Triple-negative breast cancers (TNBC) accounts for up to 20% of breast cancer cases. These tumors are negative for estrogen, progesterone, and HER2 receptors, which are markers used for diagnosis and treatment of other types of breast cancer. Clinically, TNBCs are notoriously aggressive, respond poorly to targeted therapies, have high rates of relapse, as well as poor prognosis. The molecular basis of TNBC oncogenesis is currently unknown, but it is possible that viral factors, such as Epstein-Barr Virus (EBV) miRNAs, play a role. EBV miRNAs have been implicated in the oncogenesis of several forms of cancer, including Burkitt’s lymphoma and nasopharyngeal carcinoma. The objective of this study, therefore, was to determine the differential expression of EBV miRNAs in TNBC tumors as compared to normal breast tissue. We conducted a comprehensive profiling of viral miRNAs in 48 TNBC tumors as compared to 15 control normal breast tissues, utilizing deep sequencing analysis software and publically available deep sequencing data. Four EBV miRNAs (BART18-3p, BART 8-5p, BART15, BART22) were significantly expressed in 11-17% of the TNBC tumors, and not in control normal breast tissue. Four novel putative EBV miRNAs were found to be differentially expressed in TNBC tumors as compared to control normal cells. Two of the novel putative EBV miRNAs were differentially expressed above 125 reads per million (RPM) in 20% and 27% of the TNBC tumors as compared to 0% and 6.6% of normal breast tissues, respectively. One novel putative EBV miRNA was expressed above 125 RPM in 83% of TNBC tumors as compared to 13% of normal breast tissue. One novel putative EBV miRNA was expressed above 125 RPM in 66% of the normal breast tissue as compared to 2% of the TNBCs. These putative EBV miRNAs localize within genomic regions of EBV, including the LMP-2 region. Ongoing work has so far computationally validated one of these miRNAs as a novel EBV miRNA; in vitro validation studies are in progress. This is the first report on the differential expression of EBV miRNAs in TNBC tumors. Since TNBC tumors are extremely heterogeneous, it is intriguing that 20% of TNBC tumors specifically express the same EBV miRNA. Our findings suggest that these differentially expressed EBV miRNAs may potentially play a role in the pathogenesis of TNBC. Citation Format: Alexander Blanchard, Tiffany Walls, Ramon Vidal, Stefan Bonn, Scott Harrison, Perpetua Muganda. Differential expression of Epstein Barr virus miRNAs in 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 1566. doi:10.1158/1538-7445.AM2017-1566
Abstract 2584: The UCSC Xena system for cancer genomics data visualization and interpretation
Authors: Mary Goldman, Brian Craft, Jingchun Zhu, David Haussler
Journal: Cancer Research (2017)

Abstract The UCSC Xena platform (http://xena.ucsc.edu/) allows biologists and bioinformaticians to securely analyze and visualize their private functional genomics data in the context of public genomic and clinical data sets. The Xena platform consists of a set of federated data hubs and the Xena browser, which integrates across hubs, providing one location to analyze and visualize all data. Our expanding public Xena Data Hubs currently hosts 1400+ data sets from more than 35 cancer types, as well as Pan-Cancer data sets. Our public data hubs serve seminal cancer genomics and functional genomics data set to the scientific community, including the latest TCGA, TARGET, ICGC, and GTEx data sets. We support most data types including somatic and germline SNPs, INDELs, large structural variants, CNV, gene-, transcript-, exon- protein-, miRNA-expression, DNA methylation, phenotypes, clinical data, subtype classifications and genomic biomarkers. Additionally, investigators’ own functional genomics data can be hosted on private hubs running on their laptop or behind the firewall. Data is integrated on the UCSC Xena Browser, allowing biologists to view and interpretation of their genomic data in the context of a large collection of cancer genomics data sets such as TCGA. The lightweight Xena data hubs are straightforward to install on Windows, Mac and Linux operating systems and loading data is easy using either our application or command line interface. This system of the browser and hubs helps researchers combine new or preliminary results from their laptops or internal servers, or even data from a new paper, securely with vetted data from the public sphere. Visualizations and analyses include dynamic Kaplan-Meier survival analysis to assess survival stratification by any information in addition to our visual spreadsheet, scatter plots and bar graphs. We seek feedback at our poster on new visualizations and functionalities. Citation Format: Mary Goldman, Brian Craft, Jingchun Zhu, David Haussler. The UCSC Xena system for cancer genomics data visualization and interpretation [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 2584. doi:10.1158/1538-7445.AM2017-2584
Abstract 1886: mGluR1 drives invasion of proneural subtype of glioblastoma cells
Authors: Alena Gladwin, Sen Peng, Jeff Kiefer, Seugchan Kim, Michael Berens, Harshil D. Dhruv
Journal: Cancer Research (2017)

Abstract A major cause for the therapeutic failure and subsequent morbidity and mortality of glioblastoma (GBM) is the aggressive invasion of malignant cells into the surrounding normal brain that effectively renders complete surgical resection impossible and virtually assures recurrent tumor growth. Multi-omic profiling of GBM led to their molecular sub-classification into two distinct molecular subtypes: proneural (PN) and mesenchymal (MES). However, very little is known about shared or distinct invasion processes of cells in these genomically different subtypes. Using Microarray gene expression profiles of microdissected paired stationary core and invasive rim samples from 19 patients, we demonstrated that invasive gene signature of MES subtypes differs from PN. Specifically, using three orthogonal but intersecting bioinformatic approaches, i.e. gene set variation analysis, causal network analysis, and iRegulon analysis; we discovered that genes differentially expressed between PN core and rim could, to a meaningful degree, be accounted for based on their annotation as “regulated by the transcription factor REST”. REST functions as a repressor of gene expression. Of the genes repressed by REST, mGluR1 (Metabotropic Glutamate Receptor 1) was significantly overexpressed at the rim of PN glioma cells as compared to the core. Finally, we also investigated the role of mGluR1 in glutamate induced glioma cell migration; our results show that glutamate stimulates migration of proneural-like glioma cells (A172) as compare to non-proneural-like glioma cell (T98G). mGluR1 activation by glutamate has shown to induce activation of Pyk2 and Src in astrocytes; knockout of mGluR1 is not embryonic lethal. In summary, our data demonstrate that glutamate-induced glioma cell migration of PN subtype of GBM is dependent on mGluR1 and thus raises the prospect that therapeutic targeting of mGluR1 may be a novel approach to controlling the invasion of this deadly disease. Citation Format: Alena Gladwin, Sen Peng, Jeff Kiefer, Seugchan Kim, Michael Berens, Harshil D. Dhruv. mGluR1 drives invasion of proneural subtype of glioblastoma 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 1886. doi:10.1158/1538-7445.AM2017-1886
Abstract 5782: A novel method for high-throughput drug screening in 3D tumor organoids
Authors: Nhan Phan, Jessica Huang, David Eisenberg, Sanaz Memarzadeh, Alice Soragni
Journal: Cancer Research (2017)

Abstract 3D tumor organoids are pivotal tools to study tumor development, propagation and invasive properties (Tanner and Gottesman, 2015). They closely recapitulate many characteristics of the tumor of origin in terms of structure, heterogeneity, complexity and response to drug treatment. As such, they are considered an accurate pre-clinical model for drug discovery and development (Nyga et al, 2011; Tanner and Gottesman, 2015; Shroyer, 2016). Nevertheless, reliable methods to perform high-throughput drug screenings using tumor organoids are limited and require extensive manipulation such as sample transfer from plate to plate. In addition, thick 3D matrix supports may hinder drug penetration. Here we introduce a robust method to generate, treat and assay 3D tumor organoids in standard, uncoated 96- or 384-well plates. By plating cells around the rim of the wells we generate an ultrathin layer of Matrigel that allows penetration of small molecules and bulkier peptide drugs. Media change is easily performed from the center of the well without perturbing the organoids. After a 2-day treatment course, organoids are released by dispase treatment and assayed in the same well by performing a CellTiter-Glo assay (Promega). The method exhibits low plate-to-plate, experiment-to-experiment and operator-to-operator variability. In addition, it can be extended to patient-derived tumor organoids (PDTO) generated from primary tumors. We show how PDTO from high-grade serous ovarian carcinoma (HGSOC) specimens are generated with a success rate &amp;gt;95%. Given the low number of cells required and high assay sensitivity, we can seed 200 wells from 1Mio cells derived from a tumor biopsy, and test over 60 different drugs/concentrations in triplicates. Moreover, we show how drug combination studies are feasible and allow assessing treatment synergies. As an example, we combined a peptidic inhibitor of p53 aggregation, ReACp53 (Soragni et al, 2016), with carboplatin in PDTO HGSOC established from a panel of patients harboring different p53 mutations. Drug interaction studies are performed across a range of ReACp53 and carboplatin concentrations and cell viability assessed at day 2 is used to compute drug-response curves, EC50 values and combination indexes. In conclusion, we are introducing an inexpensive, robust, easily automated method to perform high-throughput drug screenings in 3D organoids and PDTO and demonstrate its utility in determining drug sensitivities and optimizing multi-drug combinations in vitro. Citation Format: Nhan Phan, Jessica Huang, David Eisenberg, Sanaz Memarzadeh, Alice Soragni. A novel method for high-throughput drug screening in 3D tumor organoids [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 5782. doi:10.1158/1538-7445.AM2017-5782