title: IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system.
abstract: Immune cells function in an interacting hierarchy that coordinates the activities of various cell types according to genetic and environmental contexts. We developed graphical approaches to construct an extensible immune reference map from mass cytometry data of cells from different organs, incorporating landmark cell populations as flags on the map to compare cells from distinct samples. The maps recapitulated canonical cellular phenotypes and revealed reproducible, tissue-specific deviations. The approach revealed influences of genetic variation and circadian rhythms on immune system structure, enabled direct comparisons of murine and human blood cell phenotypes, and even enabled archival fluorescence-based flow cytometry data to be mapped onto the reference framework. This foundational reference map provides a working definition of systemic immune organization to which new data can be integrated to reveal deviations driven by genetics, environment, or pathology.
authors.affiliation: Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. Department of Pathology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA. gnolan@stanford.edu matthew.spitzer@stanford.edu.
authors.forename: Matthew H
authors.initials: MH
authors.lastname: Spitzer
authors.affiliation: Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Pier Federico
authors.initials: PF
authors.lastname: Gherardini
authors.affiliation: Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Gabriela K
authors.initials: GK
authors.lastname: Fragiadakis
authors.affiliation: Department of Pathology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Nupur
authors.initials: N
authors.lastname: Bhattacharya
authors.affiliation: Department of Pathology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Robert T
authors.initials: RT
authors.lastname: Yuan
authors.affiliation: Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Andrew N
authors.initials: AN
authors.lastname: Hotson
authors.affiliation: Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Rachel
authors.initials: R
authors.lastname: Finck
authors.affiliation: Department of Pathology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Yaron
authors.initials: Y
authors.lastname: Carmi
authors.affiliation: Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Eli R
authors.initials: ER
authors.lastname: Zunder
authors.affiliation: Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Wendy J
authors.initials: WJ
authors.lastname: Fantl
authors.affiliation: Department of Pathology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Sean C
authors.initials: SC
authors.lastname: Bendall
authors.affiliation: Department of Pathology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Edgar G
authors.initials: EG
authors.lastname: Engleman
authors.affiliation: Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA. gnolan@stanford.edu matthew.spitzer@stanford.edu.
authors.forename: Garry P
authors.initials: GP
authors.lastname: Nolan
mesh_terms: D000818:Animals; D001853:Bone Marrow / Q000276:immunology; D002940:Circadian Rhythm / Q000276:immunology; D005434:Flow Cytometry; D014644:Genetic Variation; D006801:Humans; D007107:Immune System / Q000166:cytology* / Q000276:immunology*; D051379:Mice; D008810:Mice, Inbred C57BL; D008954:Models, Biological; D010641:Phenotype; D012015:Reference Standards