title: Unsupervised High-Dimensional Analysis Aligns Dendritic Cells across Tissues and Species.
abstract: Dendritic cells (DCs) are professional antigen-presenting cells that hold great therapeutic potential. Multiple DC subsets have been described, and it remains challenging to align them across tissues and species to analyze their function in the absence of macrophage contamination. Here, we provide and validate a universal toolbox for the automated identification of DCs through unsupervised analysis of conventional flow cytometry and mass cytometry data obtained from multiple mouse, macaque, and human tissues. The use of a minimal set of lineage-imprinted markers was sufficient to subdivide DCs into conventional type 1 (cDC1s), conventional type 2 (cDC2s), and plasmacytoid DCs (pDCs) across tissues and species. This way, a large number of additional markers can still be used to further characterize the heterogeneity of DCs across tissues and during inflammation. This framework represents the way forward to a universal, high-throughput, and standardized analysis of DC populations from mutant mice and human patients.
authors.affiliation: Unit of Immunoregulation and Mucosal Immunology, VIB Inflammation Research Center, Ghent 9052, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent 9000, Belgium; Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, Inserm, CNRS, 13288 Marseille, France. Electronic address: martin.guilliams@irc.vib-ugent.be.
authors.forename: Martin
authors.initials: M
authors.lastname: Guilliams
authors.affiliation: Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, IMMUNOS Building #3-4, BIOPOLIS, Singapore 138648, Singapore; Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Charles-Antoine
authors.initials: CA
authors.lastname: Dutertre
authors.affiliation: Unit of Immunoregulation and Mucosal Immunology, VIB Inflammation Research Center, Ghent 9052, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent 9000, Belgium.
authors.forename: Charlotte L
authors.initials: CL
authors.lastname: Scott
authors.affiliation: Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, IMMUNOS Building #3-4, BIOPOLIS, Singapore 138648, Singapore.
authors.forename: Naomi
authors.initials: N
authors.lastname: McGovern
authors.affiliation: Unit of Immunoregulation and Mucosal Immunology, VIB Inflammation Research Center, Ghent 9052, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent 9000, Belgium.
authors.forename: Dorine
authors.initials: D
authors.lastname: Sichien
authors.affiliation: Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, IMMUNOS Building #3-4, BIOPOLIS, Singapore 138648, Singapore.
authors.forename: Svetoslav
authors.initials: S
authors.lastname: Chakarov
authors.affiliation: Department of Information Technology, iMinds, Ghent University, Ghent 9000, Belgium; Data Mining and Modeling for Biomedicine, VIB Inflammation Research Center, Ghent 9052, Belgium.
authors.forename: Sofie
authors.initials: S
authors.lastname: Van Gassen
authors.affiliation: Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, IMMUNOS Building #3-4, BIOPOLIS, Singapore 138648, Singapore.
authors.forename: Jinmiao
authors.initials: J
authors.lastname: Chen
authors.affiliation: Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, IMMUNOS Building #3-4, BIOPOLIS, Singapore 138648, Singapore.
authors.forename: Michael
authors.initials: M
authors.lastname: Poidinger
authors.affiliation: Unit of Immunoregulation and Mucosal Immunology, VIB Inflammation Research Center, Ghent 9052, Belgium; Department of Internal Medicine, Ghent University, Ghent 9000, Belgium.
authors.forename: Sofie
authors.initials: S
authors.lastname: De Prijck
authors.affiliation: Unit of Immunoregulation and Mucosal Immunology, VIB Inflammation Research Center, Ghent 9052, Belgium; Department of Internal Medicine, Ghent University, Ghent 9000, Belgium.
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Tavernier
authors.affiliation: Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, IMMUNOS Building #3-4, BIOPOLIS, Singapore 138648, Singapore.
authors.forename: Ivy
authors.initials: I
authors.lastname: Low
authors.affiliation: Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Sergio Erdal
authors.initials: SE
authors.lastname: Irac
authors.affiliation: Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore.
authors.forename: Citra Nurfarah
authors.initials: CN
authors.lastname: Mattar
authors.affiliation: Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, IMMUNOS Building #3-4, BIOPOLIS, Singapore 138648, Singapore.
authors.forename: Hermi Rizal
authors.initials: HR
authors.lastname: Sumatoh
authors.affiliation: Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, IMMUNOS Building #3-4, BIOPOLIS, Singapore 138648, Singapore.
authors.forename: Gillian Hui Ling
authors.initials: GHL
authors.lastname: Low
authors.affiliation: Department of Surgery, Yong Loo Lin School of Medicine, National University Singapore, Singapore 119077, Singapore.
authors.forename: Tam John Kit
authors.initials: TJK
authors.lastname: Chung
authors.affiliation: Department of Surgery, Yong Loo Lin School of Medicine, National University Singapore, Singapore 119077, Singapore.
authors.forename: Dedrick Kok Hong
authors.initials: DKH
authors.lastname: Chan
authors.affiliation: Department of Surgery, Yong Loo Lin School of Medicine, National University Singapore, Singapore 119077, Singapore.
authors.forename: Ker Kan
authors.initials: KK
authors.lastname: Tan
authors.affiliation: Department of Pathology, National University of Singapore, Singapore 119077, Singapore.
authors.forename: Tony Lim Kiat
authors.initials: TLK
authors.lastname: Hon
authors.affiliation: K.G. Jebsen Centre for Influenza Vaccine Research, Oslo University Hospital, University of Oslo, 0027 Oslo, Norway.
authors.forename: Even
authors.initials: E
authors.lastname: Fossum
authors.affiliation: K.G. Jebsen Centre for Influenza Vaccine Research, Oslo University Hospital, University of Oslo, 0027 Oslo, Norway; Center for Immune Regulation, Institute of Immunology, Oslo University Hospital Rikshospitalet, University of Oslo, 0424 Oslo, Norway.
authors.forename: Bjarne
authors.initials: B
authors.lastname: Bogen
authors.affiliation: Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore.
authors.forename: Mahesh
authors.initials: M
authors.lastname: Choolani
authors.affiliation: Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, IMMUNOS Building #3-4, BIOPOLIS, Singapore 138648, Singapore; Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore; Department of Reproductive Medicine, Division of Obstetrics and Gynaecology, KK Women's and Children's Hospital, Singapore 229899, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore 119077, Singapore.
authors.forename: Jerry Kok Yen
authors.initials: JKY
authors.lastname: Chan
authors.affiliation: Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, IMMUNOS Building #3-4, BIOPOLIS, Singapore 138648, Singapore.
authors.forename: Anis
authors.initials: A
authors.lastname: Larbi
authors.affiliation: Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, Inserm, CNRS, 13288 Marseille, France; Centre d'Immunophénomique, Aix Marseille Université, Inserm, CNRS, 13288 Marseille, France.
authors.forename: Hervé
authors.initials: H
authors.lastname: Luche
authors.affiliation: Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, Inserm, CNRS, 13288 Marseille, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Henri
authors.affiliation: Data Mining and Modeling for Biomedicine, VIB Inflammation Research Center, Ghent 9052, Belgium; Department of Internal Medicine, Ghent University, Ghent 9000, Belgium.
authors.forename: Yvan
authors.initials: Y
authors.lastname: Saeys
authors.affiliation: Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, IMMUNOS Building #3-4, BIOPOLIS, Singapore 138648, Singapore.
authors.forename: Evan William
authors.initials: EW
authors.lastname: Newell
authors.affiliation: Unit of Immunoregulation and Mucosal Immunology, VIB Inflammation Research Center, Ghent 9052, Belgium; Department of Internal Medicine, Ghent University, Ghent 9000, Belgium; Department of Pulmonary Medicine, Erasmus MC Rotterdam, Dr Molewaterplein 50, Rotterdam 3015 GE, The Netherlands. Electronic address: bart.lambrecht@irc.vib-ugent.be.
authors.forename: Bart N
authors.initials: BN
authors.lastname: Lambrecht
authors.affiliation: Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, Inserm, CNRS, 13288 Marseille, France; Centre d'Immunophénomique, Aix Marseille Université, Inserm, CNRS, 13288 Marseille, France. Electronic address: bernardm@ciml.univ-mrs.fr.
authors.forename: Bernard
authors.initials: B
authors.lastname: Malissen
authors.affiliation: Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, IMMUNOS Building #3-4, BIOPOLIS, Singapore 138648, Singapore. Electronic address: florent_ginhoux@immunol.a-star.edu.sg.
authors.forename: Florent
authors.initials: F
authors.lastname: Ginhoux
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000502:physiology; D003713:Dendritic Cells / Q000502:physiology*; D005434:Flow Cytometry; D006801:Humans; D007249:Inflammation / Q000473:pathology; D008251:Macaca; D051379:Mice; D008810:Mice, Inbred C57BL