tbuckley/cabot-search huggingface dataset:
High-Definition Analysis of Host Protein Stability during Human Cytomegalovirus Infection Reveals Antiviral Factors and Viral Evasion Mechanisms
Authors: Katie Nightingale, Kai-Min Lin, Benjamin J. Ravenhill, Colin Davies, Luis Nobre, Ceri A. Fielding, Eva Ruckova, Alice Fletcher-Etherington, Lior Soday, Hester Nichols, Daniel Sugrue, Eddie C.Y. Wang, Pablo Moreno, Yagnesh Umrania, Edward L. Huttlin, Robin Antrobus, Andrew J. Davison, Gavin W.G. Wilkinson, Richard J. Stanton, Peter Tomasec, Michael P. Weekes
Journal: Cell Host & Microbe (2018)

Human cytomegalovirus (HCMV) is an important pathogen with multiple immune evasion strategies, including virally facilitated degradation of host antiviral restriction factors. Here, we describe a multiplexed approach to discover proteins with innate immune function on the basis of active degradation by the proteasome or lysosome during early-phase HCMV infection. Using three orthogonal proteomic/transcriptomic screens to quantify protein degradation, with high confidence we identified 35 proteins enriched in antiviral restriction factors. A final screen employed a comprehensive panel of viral mutants to predict viral genes that target >250 human proteins. This approach revealed that helicase-like transcription factor (HLTF), a DNA helicase important in DNA repair, potently inhibits early viral gene expression but is rapidly degraded during infection. The functionally unknown HCMV protein UL145 facilitates HLTF degradation by recruiting the Cullin4 E3 ligase complex. Our approach and data will enable further identifications of innate pathways targeted by HCMV and other viruses.
Abstract 5589: Detection of epidermal growth factor receptor mutations from circulating tumor DNA versus archival tissue of lung cancer
Authors: In-Jae Oh, Hyeong-Won Seo, Hyun-Ju Cho, Ha-Young Park, Bo-Gun Kho, Jin-Sun Chang, Tae-Ok Kim, Hong-Jun Shin, Cheol Kyu Park, Jung-Hwan Lim, Yong-Soo Kwon, Yu-Il Kim, Sung-Chul Lim, Young-Chul Kim, Yoo-Duk Choi
Journal: Cancer Research (2018)

Abstract Background: Epidermal growth factor receptor (EGFR) mutations are well known predictive marker of targeted therapy. We compared the sensitivity of EGFR mutation detection techniques between matched achival lung cancer tissue and peripheral blood sample. Methods: We collected the paired samples from plasma and paraffin-embedded tumor tissue obtained before EGFR-tyrosine kinase inhibitor (EGFR-TKI). DNA extraction was performed using the QIAamp MinElute virus spin kit and EGFR mutation analysis was done by two detection methods. The current standard test is the PNAClampTM (Clamp) which is the PNA-based PCR clamping that selectively amplifies only the mutated target DNA sequence. The new technique is the PANAMutyperTM EGFR test (Mutyper), which use PNA clamping-assisted fluorescence melting curve analysis. Results: A total of 295 (188 male and 107 female) patients were analyzed in this study. The histologic types were composed of 258 adenocarcinoma, 22 squamous cell carcinoma and 15 others. Most were clinical stage IV (137, 46.4%) and the EGFR mutation rate of tissue sample by standard Clamp test was 25.7%. Plasma sensitivity was significantly higher in Mutyper than Clamp (71.2% vs. 30.0%, p&amp;lt;0.001) with tissue as reference. The overall concordance and degree of agreement between two samples were better in Mutyper (91.9%, k=0.762, p&amp;lt;0.001) than Clamp (81.7%, k=0.344, p&amp;lt;0.001). In tissue sample, the median progression-free survival (PFS) of EGFR sensitive group was significantly longer than negative group regardless of the two methods. In plasma sample, the median PFS was significantly longer only by Mutyper (9.9 vs. 2.2 months, p=0.001), not by Clamp (9.8 vs. 7.6 months, p=0.968). Conclusions: Mutyper was useful liquid biopsy technique with better sensitivity than standard Clamp test. Citation Format: In-Jae Oh, Hyeong-Won Seo, Hyun-Ju Cho, Ha-Young Park, Bo-Gun Kho, Jin-Sun Chang, Tae-Ok Kim, Hong-Jun Shin, Cheol Kyu Park, Jung-Hwan Lim, Yong-Soo Kwon, Yu-Il Kim, Sung-Chul Lim, Young-Chul Kim, Yoo-Duk Choi. Detection of epidermal growth factor receptor mutations from circulating tumor DNA versus archival tissue of lung cancer [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 5589.
Abstract 1396: Pathway-directed DNA demethylation as an epithelial to mesenchymal targeting strategy
Authors: HAO HUANG, Qing Yu, Maooj Kandpal, Ramana V. Davuluri, Daniela Matei
Journal: Cancer Research (2018)

Abstract It has been proposed that by silencing tumor suppressor genes, DNA methylation plays an important function in cancer initiation and progression. DNA hypomethylating agents are being developed as anti-cancer agents. However, this approach causes unrestricted hypomethylation, which could potentially activate tumor-promoting mechanisms. Therefore a strategy capable of inducing hypomethylation of selected genes is needed. Towards this goal, we designed a strategy to induce demethylation of a coordinated gene program by using Ten-eleven translocation (TET1) dioxygenase, which converts 5 -methylcytosine to 5-hydroxymethylcytosine. We constructed a fusion gene TET1-DBD containing the catalytic domain of TET1 and the DNA binding domain of Snail, the transcription factor that regulates epithelial-to-mesenchymal transition (EMT). We hypothesized that this fusion gene will bind to promoters targeted by Snail, induce hypomethylation, reactivate gene expression, and block EMT. To test this hypothesis, we used TET1-DBD and measured induction of EMT in an ovarian (SKOV3) and breast cancer (MCF10A) model driven by TGF-β. Genome-wide DNA methylation was assessed by Reduced Representation Bisulfite Sequencing (RRBS) to measure the downstream targets of TET1-DBD. TET1-DBD increased mRNA and protein expression levels of E-cadherin in transfected cells and prevented TGF-β induced expression of fibronectin and vimentin in MCF10A and SKOV3 cells. RRBS analysis demonstrated hypomethylation of genes targeted by Snail-DBD. Our results suggest that TET1-DBD selectively binds to and hypomethylates promoters of genes targeted by Snail, resulting in inhibition of the EMT program. We propose a novel approach to induce selective promoter hypomethylation and to block key oncogenic processes by using TET1 fused to a transcription factor “carrier”. Citation Format: HAO HUANG, Qing Yu, Maooj Kandpal, Ramana V. Davuluri, Daniela Matei. Pathway-directed DNA demethylation as an epithelial to mesenchymal targeting strategy [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 1396.
Abstract 752: CovisoLinK: New bacterial transglutaminase Q-Tag substrate for the development of site specific antibody-drug conjugates
Authors: Eva Sivado, Vincent Thomas, Meddy El Alaoui, Anne-Catherine Jallas, Mike R. Dyson, John McCafferty, Said El Alaoui, Sandrine Valsesia-Wittmann
Journal: Cancer Research (2018)

Abstract CovIsoLink™ (Covalently Isopeptide crosslinking) relates to methods for enzymatic covalently coupling drugs and other compounds through transglutaminase site specific generated in the targeted proteins including, polypeptides, proteins and immunoglobulins (patent pending1). Transglutaminases (TGases) catalyze covalent cross- linking of specific glutamine residues to the primary amine of peptide-bound lysine residues or primary amines of other compounds such as polyamines2. Using an in house peptide library and the transglutaminase colorometric assay3, we identified several amino acid sequences that were recognized as glutamine donor substrates. The optimum peptide sequences were selected and we further confirmed that these sequences have improved affinity compared with the conventional small peptides Z-QG. In different experiments we engineered Fc-containing polypeptide at the C-terminal domain and showed that mTG incorporates with high efficiency several types of amine donors to the engineered antibodies. CovIsoLink™ is now used to develop new antibody drug conjugates (ADCs) since the major advantage of this method is to obtain a homogenous immunoconjugate with uniform stoichiometry. We developed and characterized different recombinant anti Her2 IgG1 Mab carrying optimized enzymatic substrates (tag) by genetic insertion in the coding sequence of MAb. We then evaluated the best linkers and conformation to incorporate different compounds through bacterial Transglutaminase (mTG) enzymatic reaction. We set up experimental conditions, production, purification, HPLC/MS analysis and control of the immunoreactivity of CovIsoLink™ Her2-ADC. Using mTG, we obtained site specific conjugation of different modified drugs with optimized linker on the anti Her2 IgG1 antibody. By HIC analysis, we validated a specific and reproducible DAR reaching DAR2 depending on drugs and experimental conditions. In vitro and In vivo characterization and dose response studies of CovIsolink-ADC specificity and reactivity are currently performed in Her2 positive models demonstrating an improved efficacy by comparison with Kadcyla (T-DM1).1) PCT/EP2014/0792278, 2) El Alaoui S et al, Int J Cancer, 1991; 3) Perez AM et al, Anal Biochem, 2009. Citation Format: Eva Sivado, Vincent Thomas, Meddy El Alaoui, Anne-Catherine Jallas, Mike R. Dyson, John McCafferty, Said El Alaoui, Sandrine Valsesia-Wittmann. CovisoLinK: New bacterial transglutaminase Q-Tag substrate for the development of site specific antibody-drug conjugates [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 752.
Diet as a risk factor for antimicrobial resistance in community-acquired urinary tract infections in a middle-aged and elderly population: a case–control study
Authors: M. Mulder, J.C. Kiefte-de Jong, W.H.F. Goessens, H. de Visser, M.A. Ikram, A. Verbon, B.H. Stricker
Journal: Clinical Microbiology and Infection (2018)
Abstract 1020: Characterization of the immune landscape and analysis of tumor response after anti-PD-1 blockade in a 3D <i>ex vivo</i> system of non-small lung cancer
Authors: Melanie Mediavilla-Varela, Melba Marie Page, Jenny Kreahling, Soner Altiok
Journal: Cancer Research (2018)

Abstract Background: Immuno-oncology drugs face the challenge that cell lines and animal models cannot recapitulate the full intimacies of the tumor microenvironment. Although these models have aided in the discovery of new medical modalities, only 8% of these models have had a successful translation. Furthermore, the phenotype of the microenvironment of various tumor types has not been assessed in depth. Nilogen Oncosystems' proprietary 3D-EX vivo drug screening platform analyzes fresh patient tumor tissue that remains embedded in its natural environment. With our model, the characteristics of the tumor microenvironment can be accurately revealed in response to checkpoint inhibitors in non-small cell lung cancer (NSCLC) and correlates can be found among different platforms. Methods: For the 3D-EX vivo platform, microspheres were produced from procured fresh tumor tissue from NSCLC cancer patients. They were then treated with Keytruda ex vivo and treatment-mediated changes in TIL subpopulations were analyzed using flow cytometric analysis, cytokine release by Bio-Rad's 17-plex cytokine assay as well as gene expression by NanoString's 770 gene Immune Panel. Results: Ex vivo treatment of the 3D microspheres with Keytruda, showed significant changes in T-cell activation and immune cell populations in 26% of NSCLC tumors. This was observed by the simultaneous increase in IFN-γ and TNF-α upon cytokine analysis. Furthermore, we found a differential expression of signature genes such as CD8, CXCL10, CXCL9, EOMES, Granzyme A/B, IFN-γ, related to T-cell subpopulations via Nanostring analysis, which was accompanied by an increase in Granzyme B via flow cytometry. Conclusion: The positive and negative associations between expression of immune function genes, TIL activation, and cytokine production by ex vivo treatment shows that Nilogen Oncosystems' 3D-Ex vivo platform can accurately recapitulate the tumor microenvironment and exhibits the importance of a comprehensive analysis of the tumor immune microenvironment for a better understanding of the mechanism of action of immuno-oncology drugs that may aid in developing biomarkers that can be used for patient selection. Citation Format: Melanie Mediavilla-Varela, Melba Marie Page, Jenny Kreahling, Soner Altiok. Characterization of the immune landscape and analysis of tumor response after anti-PD-1 blockade in a 3D ex vivo system of non-small lung cancer [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 1020.
Abstract 13252: DNA-Dependent Protein Kinase (DNA-PK) Regulates TNF-Induced VCAM-1 Expression Independently of its Function in DNA Repair: A Novel Role of DNA-PK and its Involvement in Athrogenesis
Authors: Jihang Ju, Hogyoung Kim, Amarjit S Naura, Anna M Wilk, Krzysztof Reiss, Jack Strong, Hamid A Boulares
Journal: Circulation (2012)

Vascular cell adhesion molecule (VCAM)-1 plays a dominant role in the initiation of atherosclerosis. Our group has recently reported that the DNA-dependent protein kinase (DNA-PK) regulates TNF-induced expression of VCAM-1 in glioblastoma cells via phosphorylation of p50NF-kppaB at serine-20. Such modification is crucial for the interaction of the transcription factor with p65NF-kappa B and VCAM-1 gene promoter occupancy. In this study, we examined the role of DNA-PK in VCAM-1 expression in vascular cells and the mechanism by which TNF-kappa activates the kinase. DNA-PK is required for TNF-induced VCAM-1 expression in human vein (HUVEC) and aortic (HAEC) endothelial cells. Inhibition of DNA-PK kinase activity blocked p50NF-kappa B phosphorylation at serine-20 using newly-generated antibodies targeting the phosphorylated form of the protein. Inhibition of DNA-PK markedly reduced monocyte adhesion to TNF-stimulated endothelial cells strongly suggesting a potential involvement in atherosclerosis. Indeed, pho...
Plasma Matrix Metalloproteinase-9 as a Marker of Blood Stasis in Varicose Veins
Authors: Marie-PauleJacob, MichèleCazaubon, AnthonyScemama, DominiquePrié, FrançoiseBlanchet, Marie-ClaudeGuillin, Jean-BaptisteMichel
Journal: Circulation (2002)

Background— Possible intermediate circulating markers linking blood stasis to vein remodeling were explored in patients with varicose veins in the lower limbs. Methods and Results— Blood was sampled at rest (supine position) and after a stasis of 30 minutes both in the varicose vein (limbs hanging down) and in the brachial vein (arm hanging down) as a paired control. Several endothelial and leukocyte markers were measured in plasma with the use of ELISA kits. Angiotensin-converting enzyme activity was determined by use of a specific substrate. Matrix metalloproteinases (MMPs) 9 and 2 were evaluated with the use of gelatin zymography. No markers were significantly modified after 30 minutes of blood stasis in the brachial vein. After 30 minutes of blood stasis in the varicose vein, oxygen partial pressure decreased (P<0.01). Although thrombomodulin, von Willebrand factor, vascular endothelial growth factor, and MMP-2 were not modified in these conditions, the proteins released by proteolysis from the endoth...
Abstract 4083: Intrahepatic cholangiocarcinoma and gallbladder carcinoma mouse model based on transplantation of syngeneic tumor-initiating cells
Authors: Akiyoshi Kasuga, Takashi Semba, Hiromasa Takaishi, Takanori Kanai, Hideyuki Saya, Yoshimi Arima
Journal: Cancer Research (2018)

Abstract Biliary tract cancers (BTCs) are relatively rare in the Western world, but the rates of BTCs have risen worldwide in the past few decades. BTCs, which arise from epithelial cells in bile ducts, include intrahepatic and extrahepatic cholangiocarcinomas, gallbladder carcinomas, and ampullary carcinomas. The differences between these subtypes are not fully understood because of the limited number of genetically engineered mouse models for BTCs. Genetic mutations in the KRAS gene and the epigenetic changes in Ink4a/Arf genes have been frequently detected in BTCs, and it has been considered that those alterations are associated with the development and maintenance of human BTCs. To clarify the biological features of intrahepatic cholangiocarcinomas and gallbladder carcinomas, we developed syngeneic mouse models based on a combination of organoid 3D cultures and the transplantation of oncogene-expressed syngeneic bile duct epithelial cells. We isolated the epithelial cell adhesion molecule (EpCAM)-positive intrahepatic bile duct epithelial cells and the gallbladder epithelial cells from the Ink4a/Arf knockout C57BL/6 mice, and the cells were maintained as organoids under 3D culture conditions. Those cells were then infected with retroviruses expressing KRASG12V. Lethal metastatic adenocarcinomas having differentiated components formed in our mice when we transplanted the KRASG12V-expressing cells into the livers of wild-type C57BL/6 mice. The tumors resembled human desmoplastic intrahepatic cholangiocarcinomas and gallbladder carcinomas. Our mouse models can be useful for investigating pathogenesis and therapeutic strategies for human BTCs. Citation Format: Akiyoshi Kasuga, Takashi Semba, Hiromasa Takaishi, Takanori Kanai, Hideyuki Saya, Yoshimi Arima. Intrahepatic cholangiocarcinoma and gallbladder carcinoma mouse model based on transplantation of syngeneic tumor-initiating cells [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 4083.
Abstract 4190: Synergistic anticancer effect of sulforaphane and cisplatin on sirtuins-mediated epithelial-to-mesenchymal signaling in triple negative breast cancer
Authors: SONAM SINHA, Neeta Shrivastava
Journal: Cancer Research (2018)

Abstract Purpose: Triple negative breast cancer (TNBC) overexpresses sirtuins (SIRTs), a class III HDACs, which induces epithelial-to-mesenchymal (EMT) transition and facilitates Cisplatin (CIS) resistance. We hypothesized that Sulforaphane (SFN), an HDAC inhibitor, when combined with CIS, could potentiate CIS efficacy against TNBC metastasis and overcome its resistance. Material and Methods: The effect of SFN and CIS combination on cellular proliferation and apoptosis of two TNBC cell lines, MDA-MB-231 and MDA-MB-468 were assessed by MTT assay and Annexin and PI method followed by FACS analysis respectively. The anti-metastatic capabilities of the compounds were evaluated using wound healing assay, invasion assay, chemotaxis assay, colony formation and tumorsphere assay. The regulation of key proteins involved in sirtuin-mediated EMT signaling and metastasis was determined by zymography and western blot analysis. Results: The results revealed that SFN in combination with CIS synergistically inhibited TNBC cells through inhibition of cellular proliferation, induction of apoptosis, in-silico and in-vitro modulation of SIRTs (1-7) expression. Anti-metastatic capabilities of the combinatorial treatment regimen were associated with inhibition of migratory, invasive, mammosphere forming potential and downregulation of matrix metallopeptidase (MMP-9 and MMP-2) activity of TNBC cells. When TNBC cells were treated with SFN, the expression of epithelial marker, E-cadherin was up-regulated, while the expression of mesenchymal markers, ZEB1, SNAIL, TWIST and associated SIRTs were down-regulated. In contrast, when the cells were treated with CIS, the expressions of mesenchymal markers were up-regulated. Interestingly, the combinatorial treatment of SFN and CIS synergistically inhibited EMT transition in TNBC cells. In-vivo studies are warranted to confirm our results. Conclusion: Collectively our findings demonstrated a SIRTs-mediated EMT-suppression leading to synergistic antitumor effect by combination of SFN and CIS in TNBC cells. This combination therapy may serve as a novel therapeutic strategy for TNBC management. Citation Format: SONAM SINHA, Neeta Shrivastava. Synergistic anticancer effect of sulforaphane and cisplatin on sirtuins-mediated epithelial-to-mesenchymal signaling in triple negative breast cancer [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 4190.
Abstract 4425: PARP1 inhibition impedes Warburg effect in breast cancer cells through modulation of the miR-98/STAT3 signaling axis
Authors: Nidhi Shukla
Journal: Cancer Research (2018)

Abstract Cancer cells have increased metabolic autonomy and rewired cellular metabolism in order to meet the bioenergetics, biosynthetic, and redox demands during tumorigenesis. They tend to depend on glycolysis rather than oxidative metabolism to meet their energy demand. Therefore, elucidation of the key regulators of metabolism could potentially aid in devising selective and promising anti-cancer therapies. MicroRNAs (miRNAs) have recently attained prominence as key regulators of cancer cell metabolism. MiRNAs are known to regulate metabolism in cancer cells either through the direct regulation of key metabolic enzymes, tumor suppressors and oncogenes or the indirect modulation of master transcription factors and signalling pathways. Therefore dysregulation of cellular metabolism by miRNAs contributes significantly to cancer progression. Current therapeutic strategies include: (a) targeting metabolic pathways that are strictly required for cancer cells, or (b) impairing an oncogenic signalling axis involved in cancer metabolic rewiring. The poly (ADP-ribose) polymerase (PARP) inhibitors, used in the treatment of DNA repair deficient tumours are also known to facilitate oxidative metabolism. However, the effect of PARP inhibition on glycolytic metabolism is yet to be elucidated. In the present study we aimed to identify novel miRNAs involved in the regulation of glycolytic metabolism after PARP1 inhibition. MiRNA microarray analysis revealed upregulation of the tumor suppressor miR-98 in PARP1 inhibitor treated MDA-MB-231 breast cancer cells. Further mechanistic studies confirmed miR-98 regulation of STAT3 expression and downregulation of key glycolytic enzymes HK2 and PKM2 leading to decreased Warburg effect. MiR-98 overexpression or PARP1 inhibition in combination with miR-98 antagomir showed downregulation of STAT3, HK2 and PKM2. Glucose consumption and HK2 activity were decreased upon PARP1 inhibition associated miR-98 expression. Collectively, these results showed that miR-98 is a critical regulator of PARP1 inhibition associated reduction of Warburg effect in breast cancer cells. Citation Format: Nidhi Shukla. PARP1 inhibition impedes Warburg effect in breast cancer cells through modulation of the miR-98/STAT3 signaling axis [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 4425.