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Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales AE, Ahmed AW, Kontopoulos DG, Hilgers L, Lindblad-Toh K, Karlsson EK, Hiller M, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Integrating gene annotation with orthology inference at scale. Science 2023; 380:eabn3107. [PMID: 37104600 DOI: 10.1126/science.abn3107] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.
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Affiliation(s)
- Bogdan M Kirilenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Chetan Munegowda
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - David Jebb
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Moritz Blumer
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Ariadna E Morales
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Alexis-Walid Ahmed
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Dimitrios-Georgios Kontopoulos
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Leon Hilgers
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 32 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Elinor K Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
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Colman K, Andrews RN, Atkins H, Boulineau T, Bradley A, Braendli-Baiocco A, Capobianco R, Caudell D, Cline M, Doi T, Ernst R, van Esch E, Everitt J, Fant P, Gruebbel MM, Mecklenburg L, Miller AD, Nikula KJ, Satake S, Schwartz J, Sharma A, Shimoi A, Sobry C, Taylor I, Vemireddi V, Vidal J, Wood C, Vahle JL. International Harmonization of Nomenclature and Diagnostic Criteria (INHAND): Non-proliferative and Proliferative Lesions of the Non-human Primate ( M. fascicularis). J Toxicol Pathol 2021; 34:1S-182S. [PMID: 34712008 PMCID: PMC8544165 DOI: 10.1293/tox.34.1s] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The INHAND (International Harmonization of Nomenclature and Diagnostic Criteria for
Lesions Project (www.toxpath.org/inhand.asp) is a joint initiative of the Societies of
Toxicologic Pathology from Europe (ESTP), Great Britain (BSTP), Japan (JSTP) and North
America (STP) to develop an internationally accepted nomenclature for proliferative and
nonproliferative lesions in laboratory animals. The purpose of this publication is to
provide a standardized nomenclature for classifying microscopic lesions observed in most
tissues and organs from the nonhuman primate used in nonclinical safety studies. Some of
the lesions are illustrated by color photomicrographs. The standardized nomenclature
presented in this document is also available electronically on the internet
(http://www.goreni.org/). Sources of material included histopathology databases from
government, academia, and industrial laboratories throughout the world. Content includes
spontaneous lesions as well as lesions induced by exposure to test materials. Relevant
infectious and parasitic lesions are included as well. A widely accepted and utilized
international harmonization of nomenclature for lesions in laboratory animals will provide
a common language among regulatory and scientific research organizations in different
countries and increase and enrich international exchanges of information among
toxicologists and pathologists.
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Affiliation(s)
- Karyn Colman
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Rachel N Andrews
- Wake Forest School of Medicine, Department of Radiation Oncology, Winston-Salem, NC, USA
| | - Hannah Atkins
- Penn State College of Medicine, Department of Comparative Medicine, Hershey, PA, USA
| | | | - Alys Bradley
- Charles River Laboratories Edinburgh Ltd., Tranent, Scotland, UK
| | - Annamaria Braendli-Baiocco
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Switzerland
| | - Raffaella Capobianco
- Janssen Research & Development, a Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - David Caudell
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Mark Cline
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Takuya Doi
- LSIM Safety Institute Corporation, Ibaraki, Japan
| | | | | | - Jeffrey Everitt
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | | | | | | | - Andew D Miller
- Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | | | - Shigeru Satake
- Shin Nippon Biomedical Laboratories, Ltd., Kagoshima and Tokyo, Japan
| | | | - Alok Sharma
- Covance Laboratories, Inc., Madison, WI, USA
| | | | | | | | | | | | - Charles Wood
- Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
| | - John L Vahle
- Lilly Research Laboratories, Indianapolis IN, USA
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SnapshotDx Quiz: December 2020. J Invest Dermatol 2020. [DOI: 10.1016/j.jid.2020.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Jandke A, Melandri D, Monin L, Ushakov DS, Laing AG, Vantourout P, East P, Nitta T, Narita T, Takayanagi H, Feederle R, Hayday A. Butyrophilin-like proteins display combinatorial diversity in selecting and maintaining signature intraepithelial γδ T cell compartments. Nat Commun 2020; 11:3769. [PMID: 32724083 PMCID: PMC7387338 DOI: 10.1038/s41467-020-17557-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 06/26/2020] [Indexed: 12/14/2022] Open
Abstract
Butyrophilin-like (Btnl) genes are emerging as major epithelial determinants of tissue-associated γδ T cell compartments. Thus, the development of signature, murine TCRγδ+ intraepithelial lymphocytes (IEL) in gut and skin depends on Btnl family members, Btnl1 and Skint1, respectively. In seeking mechanisms underlying these profound effects, we now show that normal gut and skin γδ IEL development additionally requires Btnl6 and Skint2, respectively, and furthermore that different Btnl heteromers can seemingly shape different intestinal γδ+ IEL repertoires. This formal genetic evidence for the importance of Btnl heteromers also applied to the steady-state, since sustained Btnl expression is required to maintain the signature TCR.Vγ7+ IEL phenotype, including specific responsiveness to Btnl proteins. In sum, Btnl proteins are required to select and to maintain the phenotypes of tissue-protective γδ IEL compartments, with combinatorially diverse heteromers having differential impacts on different IEL subsets.
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Affiliation(s)
- Anett Jandke
- Immunosurveillance Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW11AT, UK
| | - Daisy Melandri
- Immunosurveillance Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW11AT, UK.,Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, Great Maze Pond, London Bridge, London, SE19RT, UK
| | - Leticia Monin
- Immunosurveillance Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW11AT, UK
| | - Dmitry S Ushakov
- Immunosurveillance Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW11AT, UK.,Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, Great Maze Pond, London Bridge, London, SE19RT, UK
| | - Adam G Laing
- Immunosurveillance Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW11AT, UK.,Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, Great Maze Pond, London Bridge, London, SE19RT, UK
| | - Pierre Vantourout
- Immunosurveillance Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW11AT, UK.,Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, Great Maze Pond, London Bridge, London, SE19RT, UK
| | - Philip East
- Bioinformatics and Biostatistics Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW11AT, UK
| | - Takeshi Nitta
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tomoya Narita
- Department of Pharmacotherapy, Research Institute of Pharmaceutical Sciences, Musashino University, Nishitokyo, Tokyo, 202-8585, Japan
| | - Hiroshi Takayanagi
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum, München, German Research Centre for Environmental Health, 85764, Neuherberg, Germany
| | - Adrian Hayday
- Immunosurveillance Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW11AT, UK. .,Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, Great Maze Pond, London Bridge, London, SE19RT, UK.
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Nussbaumer O, Thurnher M. Functional Phenotypes of Human Vγ9Vδ2 T Cells in Lymphoid Stress Surveillance. Cells 2020; 9:E772. [PMID: 32235722 PMCID: PMC7140623 DOI: 10.3390/cells9030772] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 12/15/2022] Open
Abstract
Butyrophilin and butyrophilin-like proteins select γδ T cells and direct the migration of γδ T cell subsets to distinct anatomical sites. γδ T cells expressing Vδ2 paired with Vγ9 (Vγ9Vδ2 T cells) are the predominant γδ T cell type in human peripheral blood. Vγ9Vδ2 T cells, which cannot be studied easily in vivo because they do not exist in rodents, are often referred to as innate-like T cells. The genetically recombined γδ T cell receptor (TCR) that responds to isoprenoid-derived pyrophosphates (phosphoantigens) produced by infected and malignant cells in a butyrophilin-dependent manner qualifies them as therapeutically relevant components of the adaptive immune system. On the other hand, cell-surface proteins such as the C-type lectin CD161 mark a functional phenotype of Vγ9Vδ2 T cells that mediates TCR-independent innate-like responses. Moreover, CD56 (neural cell adhesion molecule, NCAM) and the G protein-coupled receptor GPR56 define Vγ9Vδ2 T cells with increased cytolytic potential and, like CD161, may also be expressed by dendritic cells, principally facilitating the generation of an innate-like immunological synapse. In this review, we summarise current knowledge of Vγ9Vδ2 T cell functional phenotypes that are critical to lymphoid stress surveillance.
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Affiliation(s)
- Oliver Nussbaumer
- GammaDelta Therapeutics Ltd., The Westworks, 195 Wood Lane, London W12 7FQ, UK
- Peter Gorer Department of Immunobiology, Kings College, London SE1 9RT, UK
| | - Martin Thurnher
- Immunotherapy Unit, Department of Urology, Medical University of Innsbruck, 6020 Innsbruck, Austria
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Hahn AM, Winkler TH. Resolving the mystery-How TCR transgenic mouse models shed light on the elusive case of gamma delta T cells. J Leukoc Biol 2020; 107:993-1007. [PMID: 32068302 DOI: 10.1002/jlb.1mr0120-237r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/08/2020] [Accepted: 01/20/2020] [Indexed: 12/22/2022] Open
Abstract
Cutting-edge questions in αβ T cell biology were addressed by investigating a range of different genetically modified mouse models. In comparison, the γδ T cell field lacks behind on the availability of such models. Nevertheless, transgenic mouse models proved useful for the investigation of γδ T cell biology and their stepwise development in the thymus. In general, animal models and especially mouse models give access to a wide range of opportunities of modulating γδ T cells, which is unachievable in human beings. Because of their complex biology and specific tissue tropism, it is especially challenging to investigate γδ T cells in in vitro experiments since they might not reliably reflect their behavior and phenotype under physiologic conditions. This review aims to provide a comprehensive historical overview about how different transgenic mouse models contributed in regards of the understanding of γδ T cell biology, whereby a special focus is set on studies including the elusive role of the γδTCR. Furthermore, evolutionary and translational remarks are discussed under the aspect of future implications for the field. The ultimate full understanding of γδ T cells will pave the way for their usage as a powerful new tool in immunotherapy.
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MESH Headings
- Animals
- Cell Differentiation
- Cell Lineage/genetics
- Cell Lineage/immunology
- Cell Movement
- Founder Effect
- Gene Expression
- Humans
- Immunotherapy/methods
- Mice
- Mice, Transgenic/genetics
- Mice, Transgenic/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Signal Transduction
- Species Specificity
- T-Lymphocytes/classification
- T-Lymphocytes/cytology
- T-Lymphocytes/immunology
- Thymus Gland/cytology
- Thymus Gland/immunology
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Affiliation(s)
- Anne M Hahn
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen, Germany
| | - Thomas H Winkler
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen, Germany
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Narita T, Nitta T, Nitta S, Okamura T, Takayanagi H. Mice lacking all of the Skint family genes. Int Immunol 2019; 30:301-309. [PMID: 29718261 DOI: 10.1093/intimm/dxy030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 04/25/2018] [Indexed: 11/14/2022] Open
Abstract
γδT cells develop in the thymus and play important roles in protection against infection and tumor development, but the mechanisms by which the thymic microenvironment supports γδT cell differentiation remain largely unclear. Skint1, a B7-related protein expressed in thymic epithelial cells, was shown to be essential for the development of mouse Vγ5Vδ1 γδT cells. The Skint family in mouse consists of 11 members, Skint1-11. Here we generated mutant mice lacking the entire genomic region that contains all of the Skint genes. These mice exhibited a marked reduction of Vγ5Vδ1 γδT cells in the thymus and skin, but surprisingly, had normal development of other γδT cell subsets and leukocytes including αβT, B and myeloid cells. This phenotype is essentially identical to that of Skint1-deficient mice. These results indicate that the Skint family exerts an exclusive function in regulating the development of Vγ5Vδ1 γδT cells and is dispensable for development of other leukocytes.
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Affiliation(s)
- Tomoya Narita
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Takeshi Nitta
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Sachiko Nitta
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine, Toyama, Shinjuku-ku, Tokyo, Japan.,Section of Animal Models, Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Toyama, Shinjuku-ku, Tokyo, Japan
| | - Hiroshi Takayanagi
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
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Abstract
The recent successes of chimeric antigen receptor T cells in the treatment of hematological malignancies have clearly led to an explosion in the field of adoptive cell therapy for cancer. Current efforts are focused on the translation of this exciting technology to the treatment of solid tumors and the development of allogeneic ‘off-the-shelf’ therapies. γδ T cells are currently gaining considerable attention in this field as their unique biology and established role in cancer immunosurveillance place them in a unique position to potentially overcome these challenges in adoptive cell therapy. Here, we review the relevant aspects of the function of γδ T cells in cancer immunity, and summarize clinical observations and clinical trial results that highlight their emerging role as a platform for the development of safe and effective cancer immunotherapies. γδ T cells are a unique subset of T cells combining innate and adaptive features. Tissue-resident γδ T cells have important functions in tissue and cancer immunosurveillance. γδ T cells are being exploited increasingly for cancer immunotherapy.
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Sutoh Y, Mohamed RH, Kasahara M. Origin and Evolution of Dendritic Epidermal T Cells. Front Immunol 2018; 9:1059. [PMID: 29868019 PMCID: PMC5960712 DOI: 10.3389/fimmu.2018.01059] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/27/2018] [Indexed: 01/01/2023] Open
Abstract
Dendritic epidermal T cells (DETCs) expressing invariant Vγ5Vδ1 T-cell receptors (TCRs) play a crucial role in maintaining skin homeostasis in mice. When activated, they secrete cytokines, which recruit various immune cells to sites of infection and promote wound healing. Recently, a member of the butyrophilin family, Skint1, expressed specifically in the skin and thymus was identified as a gene required for DETC development in mice. Skint1 is a gene that arose by rodent-specific gene duplication. Consequently, a gene orthologs to mouse Skint1 exists only in rodents, indicating that Skint1-dependent DETCs are unique to rodents. However, dendritic-shaped epidermal γδ T cells with limited antigen receptor diversity appear to occur in other mammals. Even lampreys, a member of the most primitive class of vertebrates that even lacks TCRs, have γδ T-like lymphocytes that resemble DETCs. This indicates that species as divergent as mice and lampreys share the needs to have innate-like T cells at their body surface, and that the origin of DETC-like cells is as ancient as that of lymphocytes.
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Affiliation(s)
- Yoichi Sutoh
- Division of Biobank and Data Management, Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa-gun, Japan
| | - Rania Hassan Mohamed
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Masanori Kasahara
- Department of Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
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Keyes BE, Liu S, Asare A, Naik S, Levorse J, Polak L, Lu CP, Nikolova M, Pasolli HA, Fuchs E. Impaired Epidermal to Dendritic T Cell Signaling Slows Wound Repair in Aged Skin. Cell 2016; 167:1323-1338.e14. [PMID: 27863246 PMCID: PMC5364946 DOI: 10.1016/j.cell.2016.10.052] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 09/14/2016] [Accepted: 10/28/2016] [Indexed: 01/07/2023]
Abstract
Aged skin heals wounds poorly, increasing susceptibility to infections. Restoring homeostasis after wounding requires the coordinated actions of epidermal and immune cells. Here we find that both intrinsic defects and communication with immune cells are impaired in aged keratinocytes, diminishing their efficiency in restoring the skin barrier after wounding. At the wound-edge, aged keratinocytes display reduced proliferation and migration. They also exhibit a dampened ability to transcriptionally activate epithelial-immune crosstalk regulators, including a failure to properly activate/maintain dendritic epithelial T cells (DETCs), which promote re-epithelialization following injury. Probing mechanism, we find that aged keratinocytes near the wound edge don't efficiently upregulate Skints or activate STAT3. Notably, when epidermal Stat3, Skints, or DETCs are silenced in young skin, re-epithelialization following wounding is perturbed. These findings underscore epithelial-immune crosstalk perturbations in general, and Skints in particular, as critical mediators in the age-related decline in wound-repair.
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Affiliation(s)
| | - Siqi Liu
- The Rockefeller University, New York, NY 10065, USA
| | - Amma Asare
- The Rockefeller University, New York, NY 10065, USA
| | - Shruti Naik
- The Rockefeller University, New York, NY 10065, USA
| | - John Levorse
- The Rockefeller University, New York, NY 10065, USA
| | - Lisa Polak
- The Rockefeller University, New York, NY 10065, USA
| | | | | | | | - Elaine Fuchs
- The Rockefeller University, New York, NY 10065, USA.
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Salim M, Knowles TJ, Hart R, Mohammed F, Woodward MJ, Willcox CR, Overduin M, Hayday AC, Willcox BE. Characterization of a Putative Receptor Binding Surface on Skint-1, a Critical Determinant of Dendritic Epidermal T Cell Selection. J Biol Chem 2016; 291:9310-21. [PMID: 26917727 PMCID: PMC4861494 DOI: 10.1074/jbc.m116.722066] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Indexed: 12/21/2022] Open
Abstract
Dendritic epidermal T cells (DETC) form a skin-resident γδ T cell population that makes key contributions to cutaneous immune stress surveillance, including non-redundant contributions to protection from cutaneous carcinogens. How DETC become uniquely associated with the epidermis was in large part solved by the identification of Skint-1, the prototypic member of a novel B7-related multigene family. Expressed only by thymic epithelial cells and epidermal keratinocytes, Skint-1 drives specifically the development of DETC progenitors, making it the first clear candidate for a selecting ligand for non-MHC/CD1-restricted T cells. However, the molecular mechanisms underpinning Skint-1 activity are unresolved. Here, we provide evidence that DETC selection requires Skint-1 expression on the surface of thymic epithelial cells, and depends upon specific residues on the CDR3-like loop within the membrane-distal variable domain of Skint-1 (Skint-1 DV). Nuclear magnetic resonance of Skint-1 DV revealed a core tertiary structure conserved across the Skint family, but a highly distinct surface charge distribution, possibly explaining its unique function. Crucially, the CDR3-like loop formed an electrostatically distinct surface, featuring key charged and hydrophobic solvent-exposed residues, at the membrane-distal tip of DV. These results provide the first structural insights into the Skint family, identifying a putative receptor binding surface that directly implicates Skint-1 in receptor-ligand interactions crucial for DETC selection.
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Affiliation(s)
- Mahboob Salim
- From the Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT
| | - Timothy J Knowles
- the School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT
| | - Rosie Hart
- the Francis Crick Institute, Lincoln's Inn Fields Research Laboratories, London WC2A 3LY, the Peter Gorer Department of Immunobiology, King's College London, London SE1 9RT, United Kingdom
| | - Fiyaz Mohammed
- From the Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT
| | - Martin J Woodward
- the Francis Crick Institute, Lincoln's Inn Fields Research Laboratories, London WC2A 3LY, the Peter Gorer Department of Immunobiology, King's College London, London SE1 9RT, United Kingdom
| | - Carrie R Willcox
- From the Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT
| | - Michael Overduin
- the School of Cancer Sciences, University of Birmingham, Henry Wellcome Building for Biomolecular NMR, Edgbaston, Birmingham B15 2TT, and
| | - Adrian C Hayday
- the Francis Crick Institute, Lincoln's Inn Fields Research Laboratories, London WC2A 3LY, the Peter Gorer Department of Immunobiology, King's College London, London SE1 9RT, United Kingdom
| | - Benjamin E Willcox
- From the Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT,
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