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Existence of Conventional Dendritic Cells in Gallus gallus Revealed by Comparative Gene Expression Profiling This information is current as Thien-Phong Vu Manh, Hélène Marty, Pierre Sibille, Yves of October 1, 2021. Le Vern, Bernd Kaspers, Marc Dalod, Isabelle Schwartz-Cornil and Pascale Quéré J Immunol 2014; 192:4510-4517; Prepublished online 16 April 2014; doi: 10.4049/jimmunol.1303405 http://www.jimmunol.org/content/192/10/4510 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2014/04/16/jimmunol.130340 Material 5.DCSupplemental http://www.jimmunol.org/ References This article cites 34 articles, 13 of which you can access for free at: http://www.jimmunol.org/content/192/10/4510.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on October 1, 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 © 2014 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Existence of Conventional Dendritic Cells in Gallus gallus Revealed by Comparative Gene Expression Profiling Thien-Phong Vu Manh,*,†,‡,1 He´le`ne Marty,†,x,{,1 Pierre Sibille,‖ Yves Le Vern,x,{ Bernd Kaspers,# Marc Dalod,*,†,‡,2 Isabelle Schwartz-Cornil,‖,2 and Pascale Que´re´x,{,2 The existence of conventional dendritic cells (cDCs) has not yet been demonstrated outside mammals. In this article, we identified bona fide cDCs in chicken spleen. Comparative profiling of global and of immune response gene expression, morphology, and T cell activation properties show that cDCs and macrophages (MPs) exist as distinct mononuclear phagocytes in the chicken, resembling their human and mouse cell counterparts. With computational analysis, core gene expression signatures for cDCs, MPs, and T and B cells across the chicken, human, and mouse were established, which will facilitate the identification of these subsets in other vertebrates. Overall, this study, by extending the newly uncovered cDC and MP paradigm to the chicken, suggests that these two phagocyte lineages were already in place in the common ancestor of reptiles (including birds) and mammals in evolution. Downloaded from It opens avenues for the design of new vaccines and nutraceuticals that are mandatory for the sustained supply of poultry products in the expanding human population. The Journal of Immunology, 2014, 192: 4510–4517. onventional dendritic cells (cDCs) are functionally char- cDCs derive from a clonogenic common DC progenitor in the acterized by their exquisite capacities to present Ags bone marrow and are ontogenetically distinct from other mono- to naive T cells, having a key role in maintenance of nuclear phagocytes, such as macrophages (MPs), monocyte -de- C http://www.jimmunol.org/ tolerance and induction of immune effectors against invading rived dendritic cells and yolk sac– and fetal liver–derived skin pathogens (1). cDCs constitute a unique immune cell lineage, as Langerhans cells (LCs) (1, 5–7). Compared with other mononu- recently revealed in mice by genetic cell fate mapping (2) and the clear phagocytes, cDCs are endowed with a much higher efficacy precursor–progeny relationship at the single-cell level (3) and in in patrolling virtually all peripheral tissues and in migrating to humans by comparative gene expression profiling (4). Mouse lymph nodes both at steady state and upon stimulation. Further- more, cDCs and the other types of mononuclear phagocytes are differentially involved in setting and tuning specific arms of im- *Centre d’Immunologie de Marseille-Luminy, Aix-Marseille University, UM2, 13288 Marseille Cedex 9, France; †INSERM, U1104, 13288 Marseille, France; munity, depending on tissue location, inflammatory response, and ‡Centre National de la Recherche Scientifique, Unite´ Mixte de Recherche 7280, pathogens (1). Finally, cDCs include two subsets, the CD8a+ and x by guest on October 1, 2021 13288 Marseille, France; Institut National de la Recherche Agronomique, Unite´ CD11b+ types in the mouse and their homologous BDCA3+ Mixte de Recherche 1282 Infectiologie et Sante´ Publique, 37380 Nouzilly, France; + {Universite´ Franc¸ois Rabelais de Tours, Unite´ Mixte de Recherche 1282, 37000 and BDCA1 types in humans, respectively, that display distinct ‖ Tours, France; Institut National de la Recherche Agronomique, Unite´ de Recherche gene expression programs, surface phenotypes, and functional 892 Virologie et Immunologie Mole´culaires, Domaine de Vilvert, 78352 Jouy-en- + Josas Cedex, France; and #Department of Veterinary Sciences, University of Munich, specialization (4, 8, 9). In particular, the mouse CD8a type, and, + 80539 Munich, Germany to some extent, the human BDCA3 type cDCs, are specialized in + 1T.-P.V.M. and H.M. contributed equally to this work. cross-presentation of endocytosed Ags to CD8 T cells (8, 10–15). 2M.D., I.S.-C., and P.Q. are senior authors. The cDCs have been described only in mammals. Nonmamma- Received for publication December 23, 2013. Accepted for publication March 14, lian vertebrates, such as fishes and birds, have the same basic 2014. principles of adaptive immunity as mammals, but they present This work was supported by institutional funding from the Agence Nationale de la many evolutionary particularities, with different repertoires of Recherche PhyloGenDC, ANR-09-BLAN-0073-02; the PhyloGenDC ANR grant and genes, cells, and lymphoid organs, including absence of lymph the European Research Council (T.-P.V.M.); and European Research Council Frame Program 2007-2013 Grant Agreement 281225 for the SystemsDendritic project nodes (16). In these species, cells with dendritic morphology that (M.D.). seem to be distinct from MPs have been described (16–18). In I.S.-C. orchestrated the research program; M.D., I.S.-C., and P.Q. designed experi- chicken in vitro, DC-like cells have been obtained upon differ- ments and directed research; I.S.-C. wrote the paper with input from M.D., T.-P.V.M., entiation of bone marrow cells in GM-CSF and IL-4 cultures (19). H.M., P.S., and P.Q.; H.M., P.S., Y.L.V., I.S.-C., and P.Q. performed experiments and analyzed data; T.-P.V.M. and M.D. carried out bioinformatics analyses; and B.K. In vivo, LCs have been identified in skin (20); in spleen and bursa, + provided reagents and array annotations. which is the primary B cell lymphoid organ in birds, CD83 cells + The microarray data presented in this article have been submitted to the Gene Ex- and CD205 cells have been described, the later corresponding to pression Omnibus (http://www.ncbi.nlm.nih.gov/geo/info/) under accession number both putative DCs and MPs (21, 22). A subset of lung phagocytes GSE55642. presenting higher endosomal pH compared with resident MPs has Address correspondence and reprint requests to Dr. Isabelle Schwartz-Cornil, Institut also been identified in chicken (23). Although birds seem equipped National de la Recherche Agronomique, Unite´ de Recherche 892 Virologie et Im- munologie Mole´culaires, Domaine de Vilvert, 78352 Jouy-en-Josas, France. E-mail with LCs and can develop DC-type cells from bone marrow ex vivo, address: [email protected] it is not known whether they dispose of the cDC lineage homolo- The online version of this article contains supplemental material. gous to that of mammals (23). In addition, whether the biological Abbreviations used in this article: cDC, conventional dendritic cell; GSEA, gene set differences between cDCs and MPs recently unraveled in mammals enrichment analysis; LC, Langerhans cell; MGG, May–Grunwald–Giemsa€ (stain); pertain to distant vertebrate species such as birds is not known. MP, macrophage; pDC, plasmacytoid DC; qPCR, qualitative PCR. Gene expression profiling has proved to be a very efficient an- Copyright Ó 2014 by The American Association of Immunologists, Inc. 0022-1767/14/$16.00 alytical approach to delineate homologies between mononuclear www.jimmunol.org/cgi/doi/10.4049/jimmunol.1303405 The Journal of Immunology 4511 phagocyte subsets of mice, sheep, and humans (4, 24, 25). In this Bioinformatics analyses article, a comparative gene expression analysis between chicken The bioinformatics analyses were adapted from previous reports (4, 24). (Gallus gallus), human and mouse immune cell subsets shows the Raw gene expression data were background corrected using the “normexp” existence in chicken of MPs and of bona fide cDCs that are ca- method and quantile normalized with the limma package through Bio- pable of T cell activation. These data suggest that the establish- conductor in the R statistical environment (version 2.15.0). Independent ment of the cDC lineage occurred before the common bird/mammal biological triplicates (B cells) and quadruplicates (cDCs, MPs, and T cells) were performed using cells isolated from four different animals. Quality ancestor, and is likely to apply to amniotes in general. control of the expression data was assessed by boxplots of raw expression data, density plots of normalized data, scatter plots, and calculation of the Materials and Methods Pearson correlation coefficients between arrays, using the Ringo package. Animals The microarray data have been assigned the Gene Expression Omnibus number GSE55642 (www.ncbi.nlm.nih.gov/geo/info/), and they are pub- Highly inbred white Leghorn chickens that originate from the GB1 Athens licly available. line and are homozygous for the B13 histocompatibility B complex were To statistically test whether mouse and human cell transcriptional fin- used for the cDCs, MPs, and T and B cell characterization.
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    This document is downloaded from DR‑NTU (https://dr.ntu.edu.sg) Nanyang Technological University, Singapore. Transcriptome alterations of vascular smooth muscle cells in aortic wall of myocardial infarction patients Wongsurawat, Thidathip; Woo, Chin Cheng; Giannakakis, Antonis; Lin, Xiao Yun; Cheow, Esther Sok Hwee; Lee, Chuen Neng; Richards, Mark; Sze, Siu Kwan; Nookaew, Intawat; Sorokin, Vitaly; Kuznetsov, Vladimir Andreevich 2018 Wongsurawat, T., Woo, C. C., Giannakakis, A., Lin, X. Y., Cheow, E. S. H., Lee, C. N., et al. (2018). Transcriptome alterations of vascular smooth muscle cells in aortic wall of myocardial infarction patients. Data in Brief, 17, 1112‑1135. https://hdl.handle.net/10356/85590 https://doi.org/10.1016/j.dib.2018.01.108 © 2018 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Downloaded on 09 Oct 2021 06:21:01 SGT Data in Brief 17 (2018) 1112–1135 Contents lists available at ScienceDirect Data in Brief journal homepage: www.elsevier.com/locate/dib Data Article Transcriptome alterations of vascular smooth muscle cells in aortic wall of myocardial infarction patients Thidathip Wongsurawat a,b, Chin Cheng Woo c, Antonis Giannakakis a, Xiao Yun Lin d, Esther Sok Hwee Cheow e, Chuen Neng Lee c,d, Mark Richards f,g, Siu Kwan Sze e, Intawat Nookaew b, Vladimir A. Kuznetsov a,h, Vitaly Sorokin c,d,⁎ a Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR),
  • Characterization of Transcription Factor Networks Involved in Umbilical Cord Blood CD34+ Stem Cells-Derived Erythropoiesis

    Characterization of Transcription Factor Networks Involved in Umbilical Cord Blood CD34+ Stem Cells-Derived Erythropoiesis

    Characterization of Transcription Factor Networks Involved in Umbilical Cord Blood CD34+ Stem Cells-Derived Erythropoiesis Biaoru Li1, Lianghao Ding2, Chinrang Yang2, Baolin Kang1, Li Liu3, Michael D. Story2, Betty S. Pace1* 1 Department of Pediatrics, Hematology/Oncology Division, Georgia Regents University, Augusta, Georgia, United States of America, 2 Department of Radiation Oncology and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America, 3 Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas, United States of America Abstract Fetal stem cells isolated from umbilical cord blood (UCB) possess a great capacity for proliferation and differentiation and serve as a valuable model system to study gene regulation. Expanded knowledge of the molecular control of hemoglobin synthesis will provide a basis for rational design of therapies for b-hemoglobinopathies. Transcriptome data are available for erythroid progenitors derived from adult stem cells, however studies to define molecular mechanisms controlling globin gene regulation during fetal erythropoiesis are limited. Here, we utilize UCB-CD34+ stem cells induced to undergo erythroid differentiation to characterize the transcriptome and transcription factor networks (TFNs) associated with the c/b-globin switch during fetal erythropoiesis. UCB-CD34+ stem cells grown in the one-phase liquid culture system displayed a higher proliferative capacity than adult CD34+ stem cells. The c/b-globin switch was observed after day 42 during fetal erythropoiesis in contrast to adult progenitors where the switch occurred around day 21. To gain insights into transcription factors involved in globin gene regulation, microarray analysis was performed on RNA isolated from UCB-CD34+ cell-derived erythroid progenitors harvested on day 21, 42, 49 and 56 using the HumanHT-12 Expression BeadChip.