PMID- 32320656
OWN - NLM
STAT- MEDLINE
DCOM- 20210514
LR  - 20240328
IS  - 2211-1247 (Electronic)
VI  - 31
IP  - 3
DP  - 2020 Apr 21
TI  - CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization 
      in Lymphoid Tissues.
PG  - 107523
LID - S2211-1247(20)30423-X [pii]
LID - 10.1016/j.celrep.2020.107523 [doi]
AB  - Recently developed approaches for highly multiplexed imaging have revealed 
      complex patterns of cellular positioning and cell-cell interactions with 
      important roles in both cellular- and tissue-level physiology. However, tools to 
      quantitatively study cellular patterning and tissue architecture are currently 
      lacking. Here, we develop a spatial analysis toolbox, the histo-cytometric 
      multidimensional analysis pipeline (CytoMAP), which incorporates data clustering, 
      positional correlation, dimensionality reduction, and 2D/3D region reconstruction 
      to identify localized cellular networks and reveal features of tissue 
      organization. We apply CytoMAP to study the microanatomy of innate immune subsets 
      in murine lymph nodes (LNs) and reveal mutually exclusive segregation of 
      migratory dendritic cells (DCs), regionalized compartmentalization of SIRPalpha(-) 
      dermal DCs, and preferential association of resident DCs with select LN 
      vasculature. The findings provide insights into the organization of myeloid cells 
      in LNs and demonstrate that CytoMAP is a comprehensive analytics toolbox for 
      revealing features of tissue organization in imaging datasets.
CI  - Copyright (c) 2020 The Author(s). Published by Elsevier Inc. All rights reserved.
FAU - Stoltzfus, Caleb R
AU  - Stoltzfus CR
AD  - Department of Immunology, University of Washington, Seattle, WA 98109, USA.
FAU - Filipek, Jakub
AU  - Filipek J
AD  - Department of Immunology, University of Washington, Seattle, WA 98109, USA.
FAU - Gern, Benjamin H
AU  - Gern BH
AD  - Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of 
      Pediatrics, University of Washington, Seattle, WA 98195, USA.
FAU - Olin, Brandy E
AU  - Olin BE
AD  - Department of Immunology, University of Washington, Seattle, WA 98109, USA.
FAU - Leal, Joseph M
AU  - Leal JM
AD  - Department of Immunology, University of Washington, Seattle, WA 98109, USA.
FAU - Wu, Yajun
AU  - Wu Y
AD  - Department of Immunology, University of Washington, Seattle, WA 98109, USA.
FAU - Lyons-Cohen, Miranda R
AU  - Lyons-Cohen MR
AD  - Department of Immunology, University of Washington, Seattle, WA 98109, USA.
FAU - Huang, Jessica Y
AU  - Huang JY
AD  - Department of Immunology, University of Washington, Seattle, WA 98109, USA.
FAU - Paz-Stoltzfus, Clarissa L
AU  - Paz-Stoltzfus CL
AD  - School of Medicine, University of Washington, Seattle, WA 98195, USA.
FAU - Plumlee, Courtney R
AU  - Plumlee CR
AD  - Seattle Children's Research Institute, Seattle, WA 98109, USA.
FAU - Poschinger, Thomas
AU  - Poschinger T
AD  - Roche Innovation Center Munich, Pharmaceutical Research & Early Development 
      (pRED), Discovery Pharmacology, Nonnenwald 2, 82377 Penzberg, Germany.
FAU - Urdahl, Kevin B
AU  - Urdahl KB
AD  - Department of Immunology, University of Washington, Seattle, WA 98109, USA; 
      Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of 
      Pediatrics, University of Washington, Seattle, WA 98195, USA.
FAU - Perro, Mario
AU  - Perro M
AD  - Roche Innovation Center Zurich, Pharmaceutical Research & Early Development 
      (pRED), Wagistrasse 10, 8952 Schlieren, Switzerland.
FAU - Gerner, Michael Y
AU  - Gerner MY
AD  - Department of Immunology, University of Washington, Seattle, WA 98109, USA. 
      Electronic address: gernermy@uw.edu.
LA  - eng
GR  - T32 AI106677/AI/NIAID NIH HHS/United States
GR  - R01 AI134246/AI/NIAID NIH HHS/United States
GR  - T32 GM007270/GM/NIGMS NIH HHS/United States
GR  - T32 HD007233/HD/NICHD NIH HHS/United States
GR  - U19 AI135976/AI/NIAID NIH HHS/United States
GR  - R21 AI142667/AI/NIAID NIH HHS/United States
GR  - R01 AI134713/AI/NIAID NIH HHS/United States
GR  - R01 AI076327/AI/NIAID NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
PL  - United States
TA  - Cell Rep
JT  - Cell reports
JID - 101573691
SB  - IM
MH  - Animals
MH  - Lymphoid Tissue/*metabolism
MH  - Mice
MH  - Myeloid Cells/*metabolism
MH  - Spatial Analysis
PMC - PMC7233132
MID - NIHMS1586767
OTO - NOTNLM
OT  - cellular organization
OT  - dendritic cell positioning
OT  - lymphoid tissue anatomy
OT  - machine learning
OT  - quantitative image analysis
OT  - quantitative microscopy
OT  - spatial analysis
OT  - tissue microanatomy
OT  - tissue organization
OT  - tumor microenvironments
COIS- Declaration of Interests M.P. and T.P. are employees of Roche. All other authors 
      declare no competing interests.
EDAT- 2020/04/23 06:00
MHDA- 2021/05/15 06:00
PMCR- 2020/05/18
CRDT- 2020/04/23 06:00
PHST- 2019/11/07 00:00 [received]
PHST- 2020/02/10 00:00 [revised]
PHST- 2020/03/26 00:00 [accepted]
PHST- 2020/04/23 06:00 [entrez]
PHST- 2020/04/23 06:00 [pubmed]
PHST- 2021/05/15 06:00 [medline]
PHST- 2020/05/18 00:00 [pmc-release]
AID - S2211-1247(20)30423-X [pii]
AID - 10.1016/j.celrep.2020.107523 [doi]
PST - ppublish
SO  - Cell Rep. 2020 Apr 21;31(3):107523. doi: 10.1016/j.celrep.2020.107523.