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Nguyen WNT, Jacobsen EA, Finney CAM, Colarusso P, Patel KD. Intravital imaging of eosinophils: Unwrapping the enigma. J Leukoc Biol 2020; 108:83-91. [PMID: 32170880 DOI: 10.1002/jlb.3hr0220-396r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/16/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
Eosinophils are traditionally associated with allergic and parasitic inflammation. More recently, eosinophils have also been shown to have roles in diverse processes including development, intestinal health, thymic selection, and B-cell survival with the majority of these insights being derived from murine models and in vitro assays. Despite this, tools to measure the dynamic activity of eosinophils in situ have been lacking. Intravital microscopy is a powerful tool that enables direct visualization of leukocytes and their dynamic behavior in real-time in a wide range of processes in both health and disease. Until recently eosinophil researchers have not been able to take full advantage of this technology due to a lack of tools such as genetically encoded reporter mice. This mini-review examines the history of intravital microscopy with a focus on eosinophils. The development and use of eosinophil-specific Cre (EoCre) mice to create GFP and tdTomato fluorescent reporter animals is also described. Genetically encoded eosinophil reporter mice combined with intravital microscopy provide a powerful tool to add to the toolbox of technologies that will help us unravel the mysteries still surrounding this cell.
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Affiliation(s)
- William N T Nguyen
- Departments of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
| | - Elizabeth A Jacobsen
- Division of Allergy and Clinical Immunology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Constance A M Finney
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Pina Colarusso
- Departments of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
| | - Kamala D Patel
- Departments of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada.,Biochemistry and Molecular Biology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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2
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Kalina T, Fišer K, Pérez-Andrés M, Kuzílková D, Cuenca M, Bartol SJW, Blanco E, Engel P, van Zelm MC. CD Maps-Dynamic Profiling of CD1-CD100 Surface Expression on Human Leukocyte and Lymphocyte Subsets. Front Immunol 2019; 10:2434. [PMID: 31708916 PMCID: PMC6820661 DOI: 10.3389/fimmu.2019.02434] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/30/2019] [Indexed: 01/12/2023] Open
Abstract
CD molecules are surface molecules expressed on cells of the immune system that play key roles in immune cell-cell communication and sensing the microenvironment. These molecules are essential markers for the identification and isolation of leukocytes and lymphocyte subsets. Here, we present the results of the first phase of the CD Maps study, mapping the expression of CD1–CD100 (n = 110) on 47 immune cell subsets from blood, thymus, and tonsil using an eight-color standardized EuroFlow approach and quantification of expression. The resulting dataset included median antibody binding capacities (ABCs) and percentage of positivity for all markers on all subsets and was developed into an interactive CD Maps web resource. Using the resource, we examined differentially expressed proteins between granulocyte, monocyte, and dendritic cell subsets, and profiled dynamic expression of markers during thymocyte differentiation, T-cell maturation, and between functionally distinct B-cell subset clusters. The CD Maps resource will serve as a benchmark of antibody reactivities ensuring improved reproducibility of flow cytometry-based research. Moreover, it will provide a full picture of the surfaceome of human immune cells and serves as a useful platform to increase our understanding of leukocyte biology, as well as to facilitate the identification of new biomarkers and therapeutic targets of immunological and hematological diseases.
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Affiliation(s)
- Tomas Kalina
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Charles University, Prague, Czechia.,Department of Paediatric Haematology and Oncology, University Hospital Motol, Prague, Czechia
| | - Karel Fišer
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Charles University, Prague, Czechia
| | - Martin Pérez-Andrés
- Department of Medicine, Cancer Research Centre (IBMCC, USAL-CSIC), Cytometry Service (NUCLEUS), Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain.,Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Daniela Kuzílková
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Charles University, Prague, Czechia
| | - Marta Cuenca
- Department of Biomedical Sciences, University of Barcelona, Barcelona, Spain
| | - Sophinus J W Bartol
- Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Elena Blanco
- Department of Medicine, Cancer Research Centre (IBMCC, USAL-CSIC), Cytometry Service (NUCLEUS), Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain.,Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Pablo Engel
- Department of Biomedical Sciences, University of Barcelona, Barcelona, Spain
| | - Menno C van Zelm
- Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department of Immunology and Pathology, Monash University and the Alfred Hospital, Melbourne, VIC, Australia
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3
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Wang Y, Dou X, Jiang L, Jin H, Zhang L, Zhang L, Liu Z. Discovery of novel glycogen synthase kinase-3α inhibitors: Structure-based virtual screening, preliminary SAR and biological evaluation for treatment of acute myeloid leukemia. Eur J Med Chem 2019; 171:221-234. [PMID: 30925338 DOI: 10.1016/j.ejmech.2019.03.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/14/2019] [Accepted: 03/16/2019] [Indexed: 12/26/2022]
Abstract
Glycogen synthase kinase 3α (GSK-3α) plays a constitutive role in various physiological processes and has been proved to be a therapeutic target for acute myeloid leukemia (AML). In this paper, by means of computer-aided drug design, we discovered a novel chemical series of GSK-3α inhibitors with an IC50 value of 0.033-2.804 μM. The preliminary structure-activity relationship was concluded and, notably, the most potent and isoform-selective compound G28_14 was identified with IC50 values of 33 nM and 218 nM against GSK-3α and -3β, respectively, exhibiting a nearly ten-fold isoform-selectivity. Further cell viability assays and colony formation assays revealed that G28_14 suppressed cell survival by impairing cell proliferation by up to 90% in two AML cell lines. Moreover, surface marker expression analysis demonstrated that G28_14 induced terminal differentiation with a high level of CD11b, CD11c, and CD14. Western immunoblotting showed that G28_14 isoform-selectively inhibited the phosphorylation of GSK-3α in-cell without activating Wnt/β-catenin signaling. In addition, to elucidate its structure-activity relationship, the binding mode of this chemical series was proposed using molecular docking and molecular dynamics simulations. Taken together, this chemical series is worth developing as differentiation therapies for the treatment of AML.
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Affiliation(s)
- Yanxing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Xiaodong Dou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Lan Jiang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China.
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China.
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4
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Simon C, Davidsen K, Hansen C, Seymour E, Barnkob MB, Olsen LR. BioReader: a text mining tool for performing classification of biomedical literature. BMC Bioinformatics 2019; 19:57. [PMID: 30717659 PMCID: PMC7394276 DOI: 10.1186/s12859-019-2607-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 01/04/2019] [Indexed: 02/01/2023] Open
Abstract
Background Scientific data and research results are being published at an unprecedented rate. Many database curators and researchers utilize data and information from the primary literature to populate databases, form hypotheses, or as the basis for analyses or validation of results. These efforts largely rely on manual literature surveys for collection of these data, and while querying the vast amounts of literature using keywords is enabled by repositories such as PubMed, filtering relevant articles from such query results can be a non-trivial and highly time consuming task. Results We here present a tool that enables users to perform classification of scientific literature by text mining-based classification of article abstracts. BioReader (Biomedical Research Article Distiller) is trained by uploading article corpora for two training categories - e.g. one positive and one negative for content of interest - as well as one corpus of abstracts to be classified and/or a search string to query PubMed for articles. The corpora are submitted as lists of PubMed IDs and the abstracts are automatically downloaded from PubMed, preprocessed, and the unclassified corpus is classified using the best performing classification algorithm out of ten implemented algorithms. Conclusion BioReader supports data and information collection by implementing text mining-based classification of primary biomedical literature in a web interface, thus enabling curators and researchers to take advantage of the vast amounts of data and information in the published literature. BioReader outperforms existing tools with similar functionalities and expands the features used for mining literature in database curation efforts. The tool is freely available as a web service at http://www.cbs.dtu.dk/services/BioReader Electronic supplementary material The online version of this article (10.1186/s12859-019-2607-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christian Simon
- Disease Systems Biology, Novo Nordisk Center for Protein Research, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Kristian Davidsen
- Department of Health Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Christina Hansen
- Department of Health Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Emily Seymour
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Mike Bogetofte Barnkob
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | - Lars Rønn Olsen
- Department of Health Technology, Technical University of Denmark, 2800, Lyngby, Denmark.
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5
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Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D, Valencia A. Automatic identification of informative regions with epigenomic changes associated to hematopoiesis. Nucleic Acids Res 2017; 45:9244-9259. [PMID: 28934481 PMCID: PMC5716146 DOI: 10.1093/nar/gkx618] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/06/2017] [Indexed: 12/19/2022] Open
Abstract
Hematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate a chromatin space that allows to classify 42 human healthy blood epigenomes from the BLUEPRINT, NIH ROADMAP and ENCODE consortia by their cell type. This approach let us to distinguish different cells types based on their epigenomic profiles, thus recapitulating important aspects of human hematopoiesis. The analysis of the orthogonal dimension of the chromatin space identify 32,662 chromatin determinant regions (CDRs), genomic regions with different epigenetic characteristics between the cell types. Functional analysis revealed that these regions are linked with cell identities. The inclusion of leukemia epigenomes in the healthy hematological chromatin sample space gives us insights on the healthy cell types that are more epigenetically similar to the disease samples. Further analysis of tumoral epigenetic alterations in hematopoietic CDRs points to sets of genes that are tightly regulated in leukemic transformations and commonly mutated in other tumors. Our method provides an analytical approach to study the relationship between epigenomic changes and cell lineage differentiation. Method availability: https://github.com/david-juan/ChromDet.
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Affiliation(s)
| | - David Juan
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, 08003, Spain
| | - Vera Pancaldi
- Barcelona Supercomputing Centre (BSC), Barcelona, 08034, Spain
| | - Felipe Were
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Ignacio Martin-Subero
- Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Barcelona, 08036, Spain
| | - Daniel Rico
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Alfonso Valencia
- Barcelona Supercomputing Centre (BSC), Barcelona, 08034, Spain.,ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Spain
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6
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Jones ML, Alfaleh MA, Kumble S, Zhang S, Osborne GW, Yeh M, Arora N, Hou JJC, Howard CB, Chin DY, Mahler SM. Targeting membrane proteins for antibody discovery using phage display. Sci Rep 2016; 6:26240. [PMID: 27189586 PMCID: PMC4870581 DOI: 10.1038/srep26240] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 04/28/2016] [Indexed: 12/21/2022] Open
Abstract
A critical factor in the successful isolation of new antibodies by phage display is the presentation of a correctly folded antigen. While this is relatively simple for soluble proteins which can be purified and immobilized onto a plastic surface, membrane proteins offer significant challenges for antibody discovery. Whole cell panning allows presentation of the membrane protein in its native conformation, but is complicated by a low target antigen density, high background of irrelevant antigens and non-specific binding of phage particles to cell surfaces. The method described here uses transient transfection of alternating host cell lines and stringent washing steps to address each of these limitations. The successful isolation of antibodies from a naive scFv library is described for three membrane bound proteins; human CD83, canine CD117 and bat CD11b.
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Affiliation(s)
- Martina L. Jones
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia Queensland 4072 Australia
| | - Mohamed A. Alfaleh
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia Queensland 4072 Australia
- Faculty of Pharmacy; King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Sumukh Kumble
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia Queensland 4072 Australia
| | - Shuo Zhang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia Queensland 4072 Australia
| | - Geoffrey W. Osborne
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia Queensland 4072 Australia
- Queensland Brain Institute, The University of Queensland, St Lucia Queensland 4072 Australia
| | - Michael Yeh
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia Queensland 4072 Australia
| | - Neetika Arora
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia Queensland 4072 Australia
| | - Jeff Jia Cheng Hou
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia Queensland 4072 Australia
| | - Christopher B. Howard
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia Queensland 4072 Australia
| | - David Y. Chin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia Queensland 4072 Australia
| | - Stephen M. Mahler
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia Queensland 4072 Australia
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7
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Suravajhala P, Benso A, Valadi JK. Editorial: Annotation and curation of uncharacterized proteins: systems biology approaches. Front Genet 2015; 6:224. [PMID: 26175751 PMCID: PMC4485308 DOI: 10.3389/fgene.2015.00224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 06/12/2015] [Indexed: 11/20/2022] Open
Affiliation(s)
- Prashanth Suravajhala
- Bioclues.org Hyderabad, India ; Bioinformatics.org Hudson, MA, USA ; Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Denmark
| | | | - Jayaraman K Valadi
- Bioclues.org Hyderabad, India ; Department of Informatics Center, Shiv Nadar University Noida, India
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