Mapping the physical network of cellular interactions

被引：124

作者：

Boisset, Jean-Charles ^{[1
,2
]}

Vivie, Judith ^{[1
,2
]}

Gruen, Dominic ^{[1
,2
,3
]}

Muraro, Mauro J. ^{[1
,2
]}

Lyubimova, Anna ^{[1
,2
]}

van Oudenaarden, Alexander ^{[1
,2
]}

机构：

[1] Royal Netherlands Acad Arts & Sci, Hubrecht Inst KNAW, Oncode Inst, Utrecht, Netherlands

[2] Univ Med Ctr Utrecht, Canc Genom Netherlands, Utrecht, Netherlands

[3] Max Planck Inst Immunobiol & Epigenet, Freiburg, Germany

来源：

NATURE METHODS | 2018年 / 15卷 / 07期

基金：

欧洲研究理事会;

关键词：

RNA-SEQ DATA; IN-SITU; COMPLEX NETWORKS; GENE-EXPRESSION; SINGLE CELLS; TISSUE; DIFFERENTIATION; NICHE; ERYTHROPOIESIS; HIPPOCAMPUS;

D O I：

10.1038/s41592-018-0009-z

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

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.

引用

页码：547 / +

页数：9

共 40 条

[1]

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin [J].