tbuckley/cabot-search huggingface dataset:
Flow cytometry-based FRET identifies binding intensities in PPARγ1 protein-protein interactions in living cells
Authors: Verena Trümper, Andreas von Knethen, Annegret Preuß, Eugeny Ermilov, Steffen Hackbarth, Laura Kuchler, Sandra Gunne, Anne Schäfer, Tobias Bornhütter, György Vereb, Lázló Ujlaky-Nagy, Bernhard Brüne, Beate Röder, Michael Schindler, Michael J. Parnham, Tilo Knape
Journal: Theranostics (2019)

PPARγ is a pharmacological target in inflammatory and metabolic diseases.Upon agonistic treatment or following antagonism, binding of co-factors is altered, which consequently affects PPARγ-dependent transactivation as well as its DNA-independent properties.Therefore, establishing techniques to characterize these interactions is an important issue in living cells.Methods: Using the FRET pair Clover/mRuby2, we set up a flow cytometry-based FRET assay by analyzing PPARγ1 binding to its heterodimerization partner RXRα.Analyses of PPARγ-reporter and co-localization studies by laser-scanning microscopy validated this system.Refining the system, we created a new readout to distinguish strong from weak interactions, focusing on PPARγ-binding to the co-repressor N-CoR2.Results: We observed high FRET in cells expressing Clover-PPARγ1 and mRuby2-RXRα, but no FRET when cells express a mRuby2-RXRα deletion mutant, lacking the PPARγ interaction domain.Focusing on the co-repressor N-CoR2, we identified in HEK293T cells the new splice variant N-CoR2-ΔID1-exon.Overexpressing this isoform tagged with mRuby2, revealed no binding to Clover-PPARγ1, nor in murine J774A.1 macrophages.In HEK293T cells, binding was even lower in comparison to N-CoR2 constructs in which domains established to mediate interaction with PPARγ binding are deleted.These data suggest a possible role of N-CoR2-ΔID1-exon as a dominant negative variant.Because binding to N-CoR2-mRuby2 was not altered following activation or antagonism of Clover-PPARγ1, we determined the effect of pharmacological treatment on FRET intensity.Therefore, we calculated flow cytometry-based FRET efficiencies based on our flow cytometry data.As with PPARγ antagonism, PPARγ agonist treatment did not prevent binding of N-CoR2.Conclusion: Our system allows the close determination of protein-protein interactions with a special focus on binding intensity, allowing this system to characterize the role of protein domains as well as the effect of pharmacological agents on protein-protein interactions.
Abstract 11119: Systolic Blood Pressure Control Improves Cardiovascular Outcomes and Influences Risk for Renal Events in Patients Without Kidney Disease
Authors: Nicholas Chiu, Jackson Steinkamp, Haares Mirzan, Rahul Aggarwal
Journal: Circulation (2018)

Introduction: SPRINT and ACCORD are the two largest randomized controlled trials (RCTs) examining intensive systolic blood pressure (SBP) targets of 120 mmHg. Both studies enrolled non-CKD patients...
How Payment for Research Participation Can Be Coercive
Authors: Joseph Millum, Michael Garnett
Journal: The American Journal of Bioethics (2019)

The idea that payment for research participation can be coercive appears widespread among research ethics committee members, researchers, and regulatory bodies. Yet analysis of the concept of coercion by philosophers and bioethicists has mostly concluded that payment does not coerce, because coercion necessarily involves threats, not offers. In this article we aim to resolve this disagreement by distinguishing between two distinct but overlapping concepts of coercion. Consent-undermining coercion marks out certain actions as impermissible and certain agreements as unenforceable. By contrast, coercion as subjection indicates a way in which someone's interests can be partially set back in virtue of being subject to another's foreign will. While offers of payment do not normally constitute consent-undermining coercion, they do sometimes constitute coercion as subjection. We offer an analysis of coercion as subjection and propose three possible practical responses to worries about the coerciveness of payment.
Tumor-derived DNA from pleural effusion supernatant as a promising alternative to tumor tissue in genomic profiling of advanced lung cancer
Authors: Lin Tong, Ning Ding, Xiaoling Tong, Jiamin Li, Yong Zhang, Xiaodan Wang, Xiaobo Xu, Maosong Ye, Chun Li, Xue Wu, Hairong Bao, Xin Zhang, Qunying Hong, Yuanlin Song, Yang W. Shao, Chunxue Bai, Jian Zhou, Jie Hu
Journal: Theranostics (2019)

Pleural effusion (PE) is commonly observed in advanced lung cancer and was suggested to contain both cell-free tumor DNA and tumor cells. Molecular profiling of PE represents a minimally invasive approach of detecting tumor driver mutations for clinical decision making, especially when tumor tissues are not available. The objective of this study is to investigate the efficacy and precision of detecting gene alterations in PE samples to address the feasibility in clinical use. Methods: Sixty-three metastatic lung cancer patients with (n=30, cohort 1) or without (n=33, cohort 2) matched tumor tissues were enrolled in this study. PE and plasma samples of each patient were collected simultaneously. Supernatant and cell precipitate of PE were processed separately to extract cfDNA (PE-cfDNA) and sediment DNA (sDNA). All samples were subjected to targeted next-generation sequencing (NGS) of 416 cancer-related genes. Results: PE supernatants contain more abundant tumor DNA than PE sediments and plasma samples, suggested by higher mutant allele frequencies (MAF) and elevated mutation detection rate in PE-cfDNA (98.4% vs. 90.5% in PE sDNA vs. 87% in plasma cfDNA). In Cohort 1 with matched tumor tissue, tumor mutational burden (TMB) of PE-cfDNA was similar as tumor tissues (6.4 vs. 5.6), but significantly higher than PE sDNA (median TMB: 3.3) and plasma cfDNA (median TMB: 3.4). Ninety-three percent (27 out of 29) of tissue-determined driver mutations were detected in PE-cfDNA, including alterations in ALK, BRAF, EGFR, ERBB2, KRAS, NF1, PIK3CA, and RET, while only 62% were captured in plasma cfDNA. PE-cfDNA also has the highest detection rate of EGFR driver mutations in the full cohort (71% vs. 68% in PE sDNA vs. 59% in plasma cfDNA). Mutation detection from cytological negative and hemorrhagic PE is challenging. Comparatively, PE-cfDNA demonstrated absolute superiority than PE sDNA in such a scenario, suggesting that it is an independent source of tumor DNA and therefore less influenced by the abundance of tumor cells. Conclusion: Genomic profiling of PE-cfDNA offers an alternative, and potentially more meticulous approach in assessing tumor genomics in advanced lung cancer when tumor tissue is not available. Our data further demonstrate that in hemorrhagic or cytologically negative PE samples, PE-cfDNA has higher mutation detection sensitivity than sDNA and plasma cfDNA, and therefore is a more reliable source for genetic testing.
RhoB plays an essential role in CXCR2 sorting decisions
Authors: Nicole Neel, Lynne Lapierre, James Goldenring, Ann Richmond
Journal: Cancer Research (2007)

2032  Chemokines largely contribute to the process of tumorigenesis through their roles in inflammation, angiogenesis, and tumor growth and metastasis. The elucidation of the mechanisms that regulate the cellular responses mediated by chemokines is crucial for the identification of novel therapeutic targets. An important aspect of chemokine receptor function is the intracellular trafficking of these receptors. The CXCR2 chemokine receptor is a G protein-coupled receptor that undergoes clathrin-mediated endocytosis upon ligand binding. The trafficking of CXCR2 is critical for cells to maintain a proper chemotactic response. The mechanisms that regulate the recycling/degradation sorting decision are largely unknown. The small GTPases RhoB regulates the trafficking of the EGF receptor. We sought to investigate whether RhoB also regulates CXCR2 trafficking. In our studies, we utilized dominant negative (T19N) and GTPase-deficient activated (Q63L) RhoB mutants, as well as RhoB siRNA to investigate the role of RhoB in CXCR2 trafficking. Expression of both RhoB mutants and RhoB siRNA severely impaired CXCR2-mediated chemotaxis. Expression of RhoB T19N and RhoB siRNA impaired sorting of CXCR2 to the lysosome after 3h CXCL8 stimulation and RhoB T19N impaired CXCL8-induced CXCR2 degradation. In cells expressing the RhoB Q63L mutant, CXCL8 stimulated CXCR2 recycling through the Rab11a perinuclear recycling compartment was impaired but CXCR2 degradation was not induced after 30min of CXCL8 stimulation. CXCR2 co-localized with Rab4, a marker for the rapid recycling pathway, and with mannose-6-phosphate receptor, which traffics between the trans-Golgi network and endosomes, in RhoB Q63L expressing cells, suggesting that CXCR2 is recycled through alternative pathways. These data suggest that RhoB plays a key role in CXCR2 recycling/degradation sorting decisions. [This work was supported by NCI CA34590 and Multidisciplinary Basic Research Training in Cancer T32CA09592]
Immunotherapy in Ovarian Cancer: Are We There Yet?
Authors: Lana E. Kandalaft, Kunle Odunsi, George Coukos
Journal: Journal of Clinical Oncology (2019)

Article Tools REVIEW ARTICLES Gynecologic Cancer Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES No companion articles ARTICLE CITATION DOI: 10.1200/JCO.19.00508 Journal of Clinical Oncology - published online before print August 12, 2019 PMID: 31403857 Immunotherapy in Ovarian Cancer: Are We There Yet? Lana E. Kandalaft, PharmD, PhD1xLana E. KandalaftSearch for articles by this author; Kunle Odunsi, MD, PhD2xKunle OdunsiSearch for articles by this author; and George Coukos, MD, PhD1xGeorge CoukosSearch for articles by this author Show More 1Ludwig Institute for Cancer Research and University of Lausanne, Lausanne, Switzerland2Roswell Park Comprehensive Cancer Center, Buffalo, NY https://doi.org/10.1200/JCO.19.00508 First Page Full Text PDF Figures and Tables © 2019 by American Society of Clinical Oncology
IL-1R3 blockade broadly attenuates the functions of six members of the IL-1 family, revealing their contribution to models of disease
Authors: Jesper Falkesgaard Højen, Marie Louise Vindvad Kristensen, Amy S. McKee, Megan Taylor Wade, Tania Azam, Lars P. Lunding, Dennis M. de Graaf, Benjamin J. Swartzwelter, Michael Wegmann, Martin Tolstrup, Karsten Beckman, Mayumi Fujita, Stephan Fischer, Charles A. Dinarello
Journal: Nature Immunology (2019)
Comparison of mucosal and cutaneous melanoma in the head and neck region: Different clinical features and similar outcomes.
Authors: Rumeysa Ciftci, Serkan Keskin, Senem Karabulut, Ibrahim Yildiz, Leyla Kilic, Fatma Sen, Didem Tastekin, Faruk Tas
Journal: Journal of Clinical Oncology (2013)

e20016 Background: Mucosal melanoma (MM) of head and neck (H&amp;N) is a relatively rare and different disease from cutaneous melanoma (CM). We aimed to define clinical features and outcomes of patients with MM of H&amp;N and to emphasize its differences from CM. Methods: The medical records of patients (n= 41 for MM, n=94 for CM) between 2000 and 2010 were assesed. Results: In MM group, 21 patients had primary oral cavity (OCM) and 20 had sinonasal melanoma (SNM). The median age was 60 years and gender distribution was similar. Thirty-two (78%) of patients had stage I, 4 (10%) had stage II, and 5 (12%) patients had stage III disease. One and 5-year overall survival (OS) rates were 81% and 58%, and similar for SNM and OCM (p=0.67). Among CM patients, primary sites were face (53%), scalp (28%) and ear region (19%). Facial melanoma (FM) patients were older (p=0.001) than scalp (SM) or ear melanoma (EM). Male gender was more frequent among SM patients (81%) than FM (42%, p=0.001) and EM (50%, p=0.03). Most of FM patients had localized disease (84%), while most of EM (72%) and SM (46%) patients had advanced disease. One and 5-year OS rates of CM were 86% and 43%, respectively. Five-year OS rates were 72% for FM, 27% for EM and 17% for SM (FM v SM, p&lt;0.001; FM v EM, p=0,012; EM v SM, p=0.40). Advanced disease (stage III and IV) had significant impact on OS (p=0.001) for only SM patients. In addition, male patients with CM had poorer prognosis than female patients (p=0.034). However, age of patient did not affect OS. MM group was older (median 60 v 54 years, p= 0.008) and had a higher rate of localized disease than CM (78% v 65%, p=0.06). Advanced disease had a significant impact on OS for both MM and CM (p= 0.03). OS rates of CM and MM were similar (p=0.53). Conclusions: Melanoma of H&amp;N region is a very heterogeneous disease. MM has different clinicopathologic features from CM. Primary site of melanoma in this region is also important for prognosis and biological behaviour of tumour. Therefore, approaches to these melanomas should be different.
Abstract 37: Mir-590 Promotes Transdifferentiation of Porcine and Human Fibroblasts Towards a Cardiomyocyte-like Fate by Directly Repressing Specificity Protein 1 (Sp1)
Authors: Vivek P Singh, Megumi Mathison, Vivekkumar Patel, Deepthi Sanagasetti, Lina Yang, Mostafa R Naguib, Sonal Somvanshi, Lisa K Mullany, Brian W Gibson, Jianchang Yang, Todd K Rosengart
Journal: Circulation Research (2016)

Objective: Transdifferentiation of cardiac fibroblasts into cardiomyocyte-like cells (iCMs) represents a promising strategy in treating human heart disease. However, despite encouraging reprogramming data obtained from rodent models, the transgenes used in those models are not sufficient to reprogram human cells. We therefore sought to optimize a cocktail of factors which can efficiently transdifferentiate human cells. A porcine model was included to test its potential as a surrogate for human reprogramming studies. Methods: Lentivirus expressing Gata4 (G), Mef2c (M), Tbx5 (T), Hand2 (H), Myocardin (My), or two microRNAs miR-590, miR-199, were transduced into cultured porcine cardiac fibroblasts (PCFs) and human cardiac fibroblasts (HCFs) in different combinations. Two weeks after transduction, qRT-PCR, immunofluorescence (IF), and FACS assays were performed, and the efficiency of iCM production was evaluated by the expression of cardiomyocyte markers cardiac troponin T (cTnT) and α-sarcomeric actinin. Results: Combined G, M, T treatment alone was insufficient to transdifferentiate PCFs or HCFs into iCMs, despite the capability of GMT transduction to transdifferentiate up to 7% of treated rat cardiac fibroblasts, as assessed by FACS analysis for cTNT. However, the addition of H, My and miR-590 to GMT resulted in the transdifferentiation of approximately 5% of HCFs and PCFs, as measured by cTnT expression. IF analysis likewise demonstrated high expression of cTNT and α-actinin in these cells. Importantly, the transdifferentiated PCFs exhibited spontaneous contractions when co-cultured with murine cardiomyocytes. qPCR showed that administration of GMT plus either miR-590 or HMy upregulated cardiac genes MYH6 and TNNT2, and downregulated the fibroblast genes Collagen I and Collagen III. Mir-590 also directly suppressed Sp1, a fibrosis inducer and putative inhibitor of cellular reprogramming in the heart. Conclusions: Our data suggest that the porcine model can serve as an appropriate surrogate for human fibroblasts reprogramming studies. Enhanced transdifferentiation associated with miR-590-mediated repression of Sp1 suggests a novel pathway that may be targetable to enhance cardiac cellular reprogramming clinically.
Intense interseasonal influenza outbreaks, Australia, 2018/19
Authors: Ian G Barr, Yi Mo Deng, Miguel L Grau, Alvin X Han, Robin Gilmour, Melissa Irwin, Peter Markey, Kevin Freeman, Geoff Higgins, Mark Turra, Naomi Komadina, Heidi Peck, Robert Booy, Sebastian Maurer-Stroh, Vijaykrishna Dhanasekaran, Sheena Sullivan
Journal: Eurosurveillance (2019)

Background Interseasonal influenza outbreaks are not unusual in countries with temperate climates and well-defined influenza seasons. Usually, these are small and diminish before the main influenza season begins. However, the 2018/19 summer-autumn interseasonal influenza period in Australia saw unprecedented large and widespread influenza outbreaks. Aim Our objective was to determine the extent of the intense 2018/19 interseasonal influenza outbreaks in Australia epidemiologically and examine the genetic, antigenic and structural properties of the viruses responsible for these outbreaks. Methods This observational study combined the epidemiological and virological surveillance data obtained from the Australian Government Department of Health, the New South Wales Ministry of Health, sentinel outpatient surveillance, public health laboratories and data generated by the World Health Organization Collaborating Centre for Reference and Research on Influenza in Melbourne and the Singapore Agency for Science, Technology and Research. Results There was a record number of laboratory-confirmed influenza cases during the interseasonal period November 2018 to May 2019 (n= 85,286; 5 times the previous 3-year average) and also more institutional outbreaks, hospitalisations and deaths, than what is normally seen. Conclusions The unusually large interseasonal influenza outbreaks in 2018/19 followed a mild 2018 influenza season and resulted in a very early start to the 2019 influenza season across Australia. The reasons for this unusual event have yet to be fully elucidated but are likely to be a complex mix of climatic, virological and host immunity-related factors. These outbreaks reinforce the need for year-round surveillance of influenza, even in temperate climates with strong seasonality patterns.
Impaired Ca++ mobilization in rituximab-resistant cells (RRCL) is associated with changes in the structure of CD20 antigen, down-regulation of Bax/Bak pro-apoptotic proteins and up-regulation of the endoplasmic reticulum (ER) Ca++ pump protein SERCA-3
Authors: F. J. Hernandez-Ilizaliturri, H. Kaur, A. Bhinder, S. Olejniczak, J. Knight, M. S. Czuczman
Journal: Journal of Clinical Oncology (2006)

2516 Ca++ mobilization leading to apoptosis has been observed following rituximab biding to CD20 in lymphoma cells. Extending rituximab (R) exposure (e.g. as via R maintenance regimens) could potentially accelerate the emergence of resistance to rituximab. To define the molecular basis for rituximab resistance we developed several RRCL and demonstrated changes in CD20 expression/structure and membrane reorganization following rituximab therapy. Specifically, changes in the N-terminal and the C-terminal region of the internal domain of CD20 were observed in RRCL as determined by Western blotting using various antibodies recognizing epitopes located in the internal (GST77 and 1439) and external domain (B1) of CD20. In our current work we evaluated the effects that CD20 structure/expression changes have upon Ca++ mobilization. Extracellular and intracellular Ca++ mobilization was measured by flow cytometric analysis using FLUO-3 AM (acetoxymethyl ester). Optimization of the Ca++ indicator and calibration curves were performed for each cell line. Raji and RRCL were labeled under optimal conditions with FLUO-3 AM/Pluronic Acid F-127. Subsequently, cells were then re-suspended in HANKS media with or without Ca++ and exposed to rituximab or isotype (10μg/ml) ± human serum (25%). Surface CD20 expression was similar between Raji cells and RRCL. Expression of pro- or anti-apoptotic proteins and Ca++ regulatory proteins SERCA3, SERCA2 and Calreticulin was also determined by western blotting. In vitro exposure of Raji cells to rituximab + HS resulted in Ca++ mobilization even in Ca++ depleted media. Notably, Ca++ mobilization was impaired in RRCL when compared to Raji parental cells. In addition, down-regulation of Bax/Bak and up-regulation of SERCA3 was demonstrated in RRCL. Our data suggest that the acquirement of rituximab resistance is associated with changes in the intracellular domain of CD20 and in Ca++ regulator/pro-apoptotic proteins (SERCA3 and Bax/Bak) resulting in a decrease in the intracellular mobilization of Ca++. No significant financial relationships to disclose.
Diabetes Technology: Review of the 2019 American Diabetes Association Standards of Medical Care in Diabetes
Authors: James J. Chamberlain, Kacie Doyle-Delgado, Lacie Peterson, Neil Skolnik
Journal: Annals of Internal Medicine (2019)

Description: The American Diabetes Association (ADA) annually updates its Standards of Medical Care in Diabetes to provide clinicians, patients, researchers, payers, and other interested parties with evidence-based recommendations for the diagnosis and management of patients with diabetes. Methods: The ADA Professional Practice Committee comprises physicians, adult and pediatric endocrinologists, diabetes educators, registered dietitians, epidemiologists, pharmacists, and public health experts. To develop the 2019 standards, the committee continuously searched MEDLINE through November 2018 to consider and review studies, particularly high-quality trials including persons with diabetes, for potential incorporation into recommendations. It also solicited feedback from the larger clinical community. Recommendations: This synopsis focuses on selected guidance relating to use of diabetes technology in adults with diabetes. Recommendations address self-monitoring of blood glucose, continuous glucose monitors, and automated insulin delivery systems.
Is EGFR gene sequencing useful in squamous cell lung cancer?
Authors: Ana Antunes, Ana Barroso, Sara Conde, Sofia Neves, Barbara Parente
Journal: Journal of Clinical Oncology (2012)

e18111 Background: NCCN guidelines for NSCLC, currently do not recommend EGFR gene mutation study in squamous cell carcinoma (SLC), based on its low frequency of mutation (only 3% of SLC) and on the assumed low predictive value of these mutations in this population. Aim: To evaluate EGFR mutation rate in SLC, as well as response to treatment with erlotinib (disease control and survival) of patients with SLC, according to the mutational status of the EGFR gene. Methods: Revision of clinical and pathological features of patients with SLC for which we had performed EGFR sequencing. In the group of SLC patients with stage IIIB//IV at diagnosis treated with erlotinib 150 mg/day after at least one line of chemotherapy, comparison of response to erlotinib – disease control, overall survival (OS) and survival after the introduction of erlotinib (SE) – among the mutated and wild-type EGFR was performed. Results: Between January 2006 and December 2011, 98 patients with SLC were subject to EGFR sequencing – 89 males, 9 females; mean age 66.2 ±11.1 years; 82 smokers or former smokers. EGFR mutation was found in 11 patients (11.2%), 10 of which were male. Of these 98 patients, 22 were treated with erlotinib. 18 patients were in stage IIIB/IV at diagnosis and 5 had mutated EGFR. Of these 18 patients, median OS was 21.52 months and median SE was 5.5 months. Disease control was achieved in 6 (33%) patients. Median OS was 27.45 months in EGFR mutated SLC, against 19.5 in wild-type (p&lt;0.05). Median SE was 13.5 months in mutated EGFR against 4.3 months in the wild-type (p&lt;0.05). EGFR mutation was related with disease control – OR 22 (95% CI 1.53-314.3). Conclusions: In spite of the small sample size, this study shows that EGFR mutation rate of SLC in a Caucasian population is not insignificant and its presence is associated to a greater disease control and longer survival, as it has been described to lung adenocarcinoma.
Association Between PNPLA3 rs738409 C&gt;G Variant and Liver-Related Outcomes in Patients With Nonalcoholic Fatty Liver Disease
Authors: Stefania Grimaudo, Rosaria Maria Pipitone, Grazia Pennisi, Ciro Celsa, Calogero Cammà, Vito Di Marco, Maria Rosa Barcellona, Roberta Boemi, Marco Enea, Aurora Giannetti, Federica Spatola, Giulio Marchesini, Antonio Craxì, Salvatore Petta
Journal: Clinical Gastroenterology and Hepatology (2019)
Integrative phosphoproteome and interactome analysis of the role of Ubash3b in BCR-ABL signaling
Authors: Jevon A. Cutler, Savita Udainiya, Anil K. Madugundu, Santosh Renuse, Yaoyu Xu, Jaehun Jung, Kwang Pyo Kim, Xinyan Wu, Akhilesh Pandey
Journal: Leukemia (2019)