Supplementary Table 3. List of Genes Defined in the Literature As Significant in Monocyte-To-Macrophage Differentiation and Polarization
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Serum Scd163 As a Biomarker of Adipose Tissue Inflammation in Obstructive Sleep Apnoea Patients: Limits and Perspectives
AGORA | CORRESPONDENCE Serum sCD163 as a biomarker of adipose tissue inflammation in obstructive sleep apnoea patients: limits and perspectives To the Editor: Recently, MURPHY et al. [1] demonstrated, through a challenging animal, cellular and human translational approach, that intermittent hypoxia induces a pro-inflammatory activation of adipose tissue macrophages (ATMs), promoting insulin resistance. They confirmed that intermittent hypoxia lowers insulin-mediated glucose uptake in 3T3-L1 adipocytes, and evidenced the interrelationship between inflammation and insulin resistance in the adipose tissue of mice exposed to intermittent hypoxia. They then measured the concentration of serum soluble CD163 (sCD163), an assumed pro-inflammatory biomarker reflecting macrophage activation, in obstructive sleep apnoea (OSA) patients classified according to their BMI and apnoea/hypopnoea index (AHI). This is the first time serum sCD163 has been evaluated in OSA patients, and its association with AHI is promising. With the aim of enhancing its relevance in further studies, we wish to discuss the following points. 1) Activation of adipose tissue macrophages (ATMs) towards M1 phenotype in OSA patients. MURPHY et al. [1] made the assumption that circulating sCD163 levels in OSA patients reflect the intermittent hypoxia-dependent polarisation of ATMs towards a M1 phenotype. As appropriately cited, KRAČMEROVÁ et al. [2] showed that circulating sCD163 concentrations are associated with both macrophage content in human adipose tissue, and insulin sensitivity. However, the assumption that serum sCD163 reflects such a polarisation based on the ADAM-17-dependent cleavage, as hypothesised by ETZERODT et al. [3], is unconvincing since only shown in HEK293 cells. Human ATMs are characterised by a high expression of CD163 which, in contrast, is weakly expressed in differentiated M1 macrophages [4]. -
PARSANA-DISSERTATION-2020.Pdf
DECIPHERING TRANSCRIPTIONAL PATTERNS OF GENE REGULATION: A COMPUTATIONAL APPROACH by Princy Parsana A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2020 © 2020 Princy Parsana All rights reserved Abstract With rapid advancements in sequencing technology, we now have the ability to sequence the entire human genome, and to quantify expression of tens of thousands of genes from hundreds of individuals. This provides an extraordinary opportunity to learn phenotype relevant genomic patterns that can improve our understanding of molecular and cellular processes underlying a trait. The high dimensional nature of genomic data presents a range of computational and statistical challenges. This dissertation presents a compilation of projects that were driven by the motivation to efficiently capture gene regulatory patterns in the human transcriptome, while addressing statistical and computational challenges that accompany this data. We attempt to address two major difficulties in this domain: a) artifacts and noise in transcriptomic data, andb) limited statistical power. First, we present our work on investigating the effect of artifactual variation in gene expression data and its impact on trans-eQTL discovery. Here we performed an in-depth analysis of diverse pre-recorded covariates and latent confounders to understand their contribution to heterogeneity in gene expression measurements. Next, we discovered 673 trans-eQTLs across 16 human tissues using v6 data from the Genotype Tissue Expression (GTEx) project. Finally, we characterized two trait-associated trans-eQTLs; one in Skeletal Muscle and another in Thyroid. Second, we present a principal component based residualization method to correct gene expression measurements prior to reconstruction of co-expression networks. -
Gene Expression Polarization
Transcriptional Profiling of the Human Monocyte-to-Macrophage Differentiation and Polarization: New Molecules and Patterns of Gene Expression This information is current as of September 27, 2021. Fernando O. Martinez, Siamon Gordon, Massimo Locati and Alberto Mantovani J Immunol 2006; 177:7303-7311; ; doi: 10.4049/jimmunol.177.10.7303 http://www.jimmunol.org/content/177/10/7303 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2006/11/03/177.10.7303.DC1 Material http://www.jimmunol.org/ References This article cites 61 articles, 22 of which you can access for free at: http://www.jimmunol.org/content/177/10/7303.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 27, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2006 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Transcriptional Profiling of the Human Monocyte-to-Macrophage Differentiation and Polarization: New Molecules and Patterns of Gene Expression1 Fernando O. -
Cellular and Plasma Proteomic Determinants of COVID-19 and Non-COVID-19 Pulmonary Diseases Relative to Healthy Aging
RESOURCE https://doi.org/10.1038/s43587-021-00067-x Cellular and plasma proteomic determinants of COVID-19 and non-COVID-19 pulmonary diseases relative to healthy aging Laura Arthur1,8, Ekaterina Esaulova 1,8, Denis A. Mogilenko 1, Petr Tsurinov1,2, Samantha Burdess1, Anwesha Laha1, Rachel Presti 3, Brian Goetz4, Mark A. Watson1, Charles W. Goss5, Christina A. Gurnett6, Philip A. Mudd 7, Courtney Beers4, Jane A. O’Halloran3 and Maxim N. Artyomov1 ✉ We examine the cellular and soluble determinants of coronavirus disease 2019 (COVID-19) relative to aging by performing mass cytometry in parallel with clinical blood testing and plasma proteomic profiling of ~4,700 proteins from 71 individuals with pul- monary disease and 148 healthy donors (25–80 years old). Distinct cell populations were associated with age (GZMK+CD8+ T cells and CD25low CD4+ T cells) and with COVID-19 (TBET−EOMES− CD4+ T cells, HLA-DR+CD38+ CD8+ T cells and CD27+CD38+ B cells). A unique population of TBET+EOMES+ CD4+ T cells was associated with individuals with COVID-19 who experienced moderate, rather than severe or lethal, disease. Disease severity correlated with blood creatinine and urea nitrogen levels. Proteomics revealed a major impact of age on the disease-associated plasma signatures and highlighted the divergent contri- bution of hepatocyte and muscle secretomes to COVID-19 plasma proteins. Aging plasma was enriched in matrisome proteins and heart/aorta smooth muscle cell-specific proteins. These findings reveal age-specific and disease-specific changes associ- ated with COVID-19, and potential soluble mediators of the physiological impact of COVID-19. -
Anti-OX40 Antibody Directly Enhances the Function of Tumor-Reactive CD8+ T Cells
Author Manuscript Published OnlineFirst on August 1, 2019; DOI: 10.1158/1078-0432.CCR-19-1259 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. 1 Anti-OX40 antibody directly enhances the function of tumor-reactive CD8+ T cells and synergizes with PI3Kβ inhibition in PTEN loss melanoma Weiyi Peng1,5*, Leila J. Williams1, Chunyu Xu1,5, Brenda Melendez1, Jodi A. McKenzie1,6, Yuan Chen1, Heather Jackson2, Kui S. Voo3, Rina M. Mbofung1,7,, Sara E. Leahey1, Jian Wang4, Greg Lizee1, Hussein A. Tawbi1, Michael A. Davies1, Axel Hoos2, James Smothers2, Roopa Srinivasan2, Elaine Paul2, Niranjan Yanamandra2* and Patrick Hwu1* 1Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX. 2Oncology R&D, Immuno-Oncology and Combinations RU, GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, PA 19426, United States 3Oncology Research for Biologics and Immunotherapy Translation Platform, The University of Texas MD Anderson Cancer Center, Houston, TX. 4Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX. 5Present address: Department of Biology and Biochemistry, University of Houston, Houston, TX. 6Present address: Eisai Inc., Woodcliff Lake, NJ. 7Present address: Merck Research Laboratories, Palo Alto, CA. Running Title: OX40 agonist-based cancer immunotherapy Keywords: OX40, PI3K, cancer immunotherapy Downloaded from clincancerres.aacrjournals.org on September 25, 2021. © 2019 American Association for Cancer Research. Author Manuscript Published OnlineFirst on August 1, 2019; DOI: 10.1158/1078-0432.CCR-19-1259 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. 2 *Corresponding Authors: Patrick Hwu, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030. -
Molecular Signatures of G-Protein-Coupled Receptors A
REVIEW doi:10.1038/nature11896 Molecular signatures of G-protein-coupled receptors A. J. Venkatakrishnan1, Xavier Deupi2, Guillaume Lebon1,3,4,5, Christopher G. Tate1, Gebhard F. Schertler2,6 & M. Madan Babu1 G-protein-coupled receptors (GPCRs) are physiologically important membrane proteins that sense signalling molecules such as hormones and neurotransmitters, and are the targets of several prescribed drugs. Recent exciting developments are providing unprecedented insights into the structure and function of several medically important GPCRs. Here, through a systematic analysis of high-resolution GPCR structures, we uncover a conserved network of non-covalent contacts that defines the GPCR fold. Furthermore, our comparative analysis reveals characteristic features of ligand binding and conformational changes during receptor activation. A holistic understanding that integrates molecular and systems biology of GPCRs holds promise for new therapeutics and personalized medicine. ignal transduction is a fundamental biological process that is comprehensively, and in the process expand the current frontiers of required to maintain cellular homeostasis and to ensure coordi- GPCR biology. S nated cellular activity in all organisms. Membrane proteins at the In this analysis, we objectively compare known structures and reveal cell surface serve as the communication interface between the cell’s key similarities and differences among diverse GPCRs. We identify a external and internal environments. One of the largest and most diverse consensus structural scaffold of GPCRs that is constituted by a network membrane protein families is the GPCRs, which are encoded by more of non-covalent contacts between residues on the transmembrane (TM) than 800 genes in the human genome1. GPCRs function by detecting a helices. -
CD74 Targeted Nanoparticles As Dexamethasone Delivery System for B Lymphoid Malignancies
CD74 targeted nanoparticles as Dexamethasone Delivery System for B lymphoid malignancies DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Georgia Triantafillou, MPH Integrated Biomedical Sciences Graduate Program The Ohio State University 2011 Dissertation Committee John C. Byrd, MD, advisor Natarajan Muthusamy, PhD co-advisor Robert J.Lee, PhD, co-advisor Mitch A.Phelps, PhD, co-advisor Guido Marcucci, MD committee member Susheela Tridandapani, PhD committee member Copyright page Georgia Triantafillou 2011 ABSTRACT Chronic Lymphocytic Leukemia (CLL) is the most common adult leukemia and is not curable with standard therapy. In CLL the B lymphocytes appear morphologically mature but immunologically express less mature B cell makers. Specifically, the CLL B cells co-express surface antigens including CD19, CD20, CD5, CD23. Due to nonspecific delivery of the drugs to malignant as well as normal cells, patients experience numerous side effects. Targeted drug delivery to cancer cells is a desirable goal for all anti cancer strategies. Corticosteroids have been proven to be a beneficial and well established part of CLL treatment. Dexamethasone(DEX) is frequently used in CLL therapies as well as other malignancies and antiinflammatory diseases. However, DEX nonspecifically enters all tissues inducing various toxicities to patients. Therefore, DEX treatment is often discontinued or not administered to certain patients. We aimed to deliver this efficient clinical agent via a targeted delivery vehicle and examine its effect on its target B-CLL cells. The main scope of the work presented is the creation of a sterically stable nanoparticle, an ii immunoliposome (ILP), that has DEX encapsulated in its interior and a monoclonal antibody(Mab) in its exterior targeting CLL B cells expressing the surface antigen that is recognized by the Mab. -
Complementary DNA Microarray Analysis of Chemokines and Their Receptors in Allergic Rhinitis RX Zhang,1 SQ Yu,2 JZ Jiang,3 GJ Liu3
RX Zhang, et al ORIGINAL ARTICLE Complementary DNA Microarray Analysis of Chemokines and Their Receptors in Allergic Rhinitis RX Zhang,1 SQ Yu,2 JZ Jiang,3 GJ Liu3 1 Department of Otolaryngology, Huadong Hospital, Fudan University, Shanghai, China 2 Department of Otolaryngology , Jinan General Hospital of PLA, Shandong, China 3 Department of Otolaryngology, Changhai Hospital, Second Military Medical University, Shanghai, China ■ Abstract Objective: To analyze the roles of chemokines and their receptors in the pathogenesis of allergic rhinitis by observing the complementary DNA (cDNA) expression of the chemokines and their receptors in the nasal mucosa of patients with and without allergic rhinitis, using gene chips. Methods: The total RNAs were isolated from the nasal mucosa of 20 allergic rhinitis patients and purifi ed to messenger RNAs, and then reversely transcribed to cDNAs and incorporated with samples of fl uorescence-labeled with Cy5-dUPT (rhinitis patient samples) or Cy3- dUTP (control samples of nonallergic nasal mucosa). Thirty-nine cDNAs of chemokines and their receptors were latticed into expression profi le chips, which were hybridized with probes and then scanned with the computer to study gene expression according to the different fl uorescence intensities. Results: The cDNAs of the following chemokines were upregulated: CCL1, CCL2, CCL5, CCL7, CCL8, CCL11, CCL13, CCL14, CCL17, CCL18, CCL19, CCL24, and CX3CL1 in most of the allergic rhinitis sample chips. CCR2, CCR3, CCR4, CCR5, CCR8 and CX3CR1 were the highly expressed receptor genes. Low expression of CXCL4 was found in these tissues. Conclusion: The T helper cell (TH) immune system is not well regulated in allergic rhinitis. -
Anti-CCL13 / MCP4 Antibody (Biotin) (ARG65993)
Product datasheet [email protected] ARG65993 Package: 50 μg anti-CCL13 / MCP4 antibody (Biotin) Store at: 4°C Summary Product Description Biotin-conjugated Goat Polyclonal antibody recognizes CCL13 / MCP4 Tested Reactivity Hu Tested Application ELISA, WB Host Goat Clonality Polyclonal Isotype IgG Target Name CCL13 / MCP4 Antigen Species Human Immunogen E. coli derived recombinant Human CCL13 / MCP4. (QPDALNVPST CCFTFSSKKI SLQRLKSYVI TTSRCPQKAV IFRTKLGKEI CADPKEKWVQ NYMKHLGRKA HTLKT) Conjugation Biotin Alternate Names SCYA13; C-C motif chemokine 13; Monocyte chemotactic protein 4; Small-inducible cytokine A13; CKb10; SCYL1; Monocyte chemoattractant protein 4; MCP-4; NCC-1; NCC1; CK-beta-10 Application Instructions Application table Application Dilution ELISA Direct: 0.25 - 1.0 µg/ml Sandwich: 0.25 - 1.0 µg/ml with ARG65992 as a capture antibody WB 0.1 - 0.2 µg/ml Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Calculated Mw 11 kDa Properties Form Liquid Purification Purified by affinity chromatography. Buffer PBS (pH 7.2) Concentration 1 mg/ml Storage instruction Aliquot and store in the dark at 2-8°C. Keep protected from prolonged exposure to light. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. Note For laboratory research only, not for drug, diagnostic or other use. www.arigobio.com 1/2 Bioinformation Database links GeneID: 6357 Human Swiss-port # Q99616 Human Gene Symbol CCL13 Gene Full Name chemokine (C-C motif) ligand 13 Background This antimicrobial gene is one of several Cys-Cys (CC) cytokine genes clustered on the q-arm of chromosome 17. -
Single-Cell RNA Sequencing Identifies Candidate Renal
BASIC RESEARCH www.jasn.org Single-Cell RNA Sequencing Identifies Candidate Renal Resident Macrophage Gene Expression Signatures across Species Kurt A. Zimmerman,1 Melissa R. Bentley,1 Jeremie M. Lever ,2 Zhang Li,1 David K. Crossman,3 Cheng Jack Song,1 Shanrun Liu,4 Michael R. Crowley,3 James F. George,5 Michal Mrug,2,6 and Bradley K. Yoder1 1Department of Cell, Developmental, and Integrative Biology, 2Division of Nephrology, Department of Medicine, 3Department of Genetics, 4Department of Biochemistry and Molecular Genetics, and 5Division of Cardiothoracic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama; and 6Department of Veterans Affairs Medical Center, Birmingham, Alabama ABSTRACT Background Resident macrophages regulate homeostatic and disease processes in multiple tissues, in- cluding the kidney. Despite having well defined markers to identify these cells in mice, technical limita- tions have prevented identification of a similar cell type across species. The inability to identify resident macrophage populations across species hinders the translation of data obtained from animal model to human patients. Methods As an entry point to determine novel markers that could identify resident macrophages across species, we performed single-cell RNA sequencing (scRNAseq) analysis of all T and B cell–negative CD45+ innate immune cells in mouse, rat, pig, and human kidney tissue. Results We identified genes with enriched expression in mouse renal resident macrophages that were also present in candidate resident macrophage populations across species. Using the scRNAseq data, we defined a novel set of possible cell surface markers (Cd74 and Cd81) for these candidate kidney resident macrophages. We confirmed, using parabiosis and flow cytometry, that these proteins are indeed enriched in mouse resident macrophages. -
Edinburgh Research Explorer
Edinburgh Research Explorer International Union of Basic and Clinical Pharmacology. LXXXVIII. G protein-coupled receptor list Citation for published version: Davenport, AP, Alexander, SPH, Sharman, JL, Pawson, AJ, Benson, HE, Monaghan, AE, Liew, WC, Mpamhanga, CP, Bonner, TI, Neubig, RR, Pin, JP, Spedding, M & Harmar, AJ 2013, 'International Union of Basic and Clinical Pharmacology. LXXXVIII. G protein-coupled receptor list: recommendations for new pairings with cognate ligands', Pharmacological reviews, vol. 65, no. 3, pp. 967-86. https://doi.org/10.1124/pr.112.007179 Digital Object Identifier (DOI): 10.1124/pr.112.007179 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Pharmacological reviews Publisher Rights Statement: U.S. Government work not protected by U.S. copyright General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 02. Oct. 2021 1521-0081/65/3/967–986$25.00 http://dx.doi.org/10.1124/pr.112.007179 PHARMACOLOGICAL REVIEWS Pharmacol Rev 65:967–986, July 2013 U.S. -
General Discussion
UvA-DARE (Digital Academic Repository) EGF-TM7 receptors: A diverse and still evolving family of receptors on the leukocyte surface Matmati, M. Publication date 2008 Link to publication Citation for published version (APA): Matmati, M. (2008). EGF-TM7 receptors: A diverse and still evolving family of receptors on the leukocyte surface. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:23 Sep 2021 Chapter 6 General Discussion GENERAL DISCUSSION Since their identification, starting about 15 years ago, a growing amount of data has accumulated about the structure, the expression, the ligands and, more recently, also the functional implications of EGF-TM7 receptors. Studies with antibody treatment and gene targeting in mice and antibody treatment of human cells in vitro, led to the implication of EGF-TM7 receptors in the trafficking of granulocytes, the generation of efferent antigen specific regulatory T cells and the potentiation of different granulocyte effector functions [1-4].