TY - JOUR
T1 - Mapping the physical network of cellular interactions
AU - Boisset, Jean Charles
AU - Vivié, Judith
AU - Grün, Dominic
AU - Muraro, Mauro J.
AU - Lyubimova, Anna
AU - Van Oudenaarden, Alexander
N1 - Funding Information:
We thank J. Korving for help with the microdissection microscope; the animal facility; A. de Graaf and the microscope facility; the sequencing facility; K. Wiebrands for suggesting a name for the method and assistance in intestinal crypt dissociation; N. Battich and B. De Barbanson for help with machine learning; L. Kester for help with the Monte Carlo simulations; and R. van der Linden for help with the sorting experiments. This work was supported by the European Research Council (advanced grant ERC-AdG 742225-IntScOmics to A.v.O.) and a Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) OPEN award (NWO-ALWOP189 to A.v.O.). This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. In addition, we thank the Hubrecht Sorting Facility and the Utrecht Sequencing Facility, subsidized by the University Medical Center Utrecht, Hubrecht Institute, and Utrecht University.
Publisher Copyright:
© 2018 The Author(s).
PY - 2018/7/1
Y1 - 2018/7/1
N2 - A cell's function is influenced by the environment, or niche, in which it resides. Studies of niches usually require assumptions about the cell types present, which impedes the discovery of new cell types or interactions. Here we describe ProximID, an approach for building a cellular network based on physical cell interaction and single-cell mRNA sequencing, and show that it can be used to discover new preferential cellular interactions without prior knowledge of component cell types. ProximID found specific interactions between megakaryocytes and mature neutrophils and between plasma cells and myeloblasts and/or promyelocytes (precursors of neutrophils) in mouse bone marrow, and it identified a Tac1+ enteroendocrine cell-Lgr5+ stem cell interaction in small intestine crypts. This strategy can be used to discover new niches or preferential interactions in a variety of organs.
AB - A cell's function is influenced by the environment, or niche, in which it resides. Studies of niches usually require assumptions about the cell types present, which impedes the discovery of new cell types or interactions. Here we describe ProximID, an approach for building a cellular network based on physical cell interaction and single-cell mRNA sequencing, and show that it can be used to discover new preferential cellular interactions without prior knowledge of component cell types. ProximID found specific interactions between megakaryocytes and mature neutrophils and between plasma cells and myeloblasts and/or promyelocytes (precursors of neutrophils) in mouse bone marrow, and it identified a Tac1+ enteroendocrine cell-Lgr5+ stem cell interaction in small intestine crypts. This strategy can be used to discover new niches or preferential interactions in a variety of organs.
UR - http://www.scopus.com/inward/record.url?scp=85047186828&partnerID=8YFLogxK
U2 - 10.1038/s41592-018-0009-z
DO - 10.1038/s41592-018-0009-z
M3 - Article
AN - SCOPUS:85047186828
SN - 1548-7091
VL - 15
SP - 547
EP - 553
JO - Nature Methods
JF - Nature Methods
IS - 7
ER -