@article{ed1dab85c4c844f894fb46854055271c,
title = "Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq",
abstract = "Cellular functions are strongly dependent on surrounding cells and environmental factors. Current technologies are limited in their ability to characterize the spatial location and gene programs of cells in poorly structured and dynamic niches. We developed a method, NICHE-seq, that combines photoactivatable fluorescent reporters, two-photon microscopy, and single-cell RNA sequencing (scRNA-seq) to infer the cellular and molecular composition of niches. We applied NICHE-seq to examine the high-order assembly of immune cell networks. NICHE-seq is highly reproducible in spatial tissue reconstruction, enabling identification of rare niche-specific immune subpopulations and gene programs, including natural killer cells within infected B cell follicles and distinct myeloid states in the spleen and tumor. This study establishes NICHE-seq as a broadly applicable method for elucidating high-order spatial organization of cell types and their molecular pathways.",
author = "Chiara Medaglia and Amir Giladi and Liat Stoler-Barak and {De Giovanni}, Marco and Salame, {Tomer Meir} and Adi Biram and Eyal David and Hanjie Li and Matteo Iannacone and Ziv Shulman and Ido Amit",
note = "I.A. is supported by the Chan Zuckerberg Initiative; the Howard Hughes Medical Institute International Scholar Award; European Research Council Consolidator Grant 724471-HemTree2.0; a Melanoma Research Alliance Established Investigator Award (509044); the Israel Science Foundation (703/15); the Ernest and Bonnie Beutler Research Program of Excellence in Genomic Medicine; the Helen and Martin Kimmel Award for Innovative Investigation; a Minerva Stiftung research grant; the Israeli Ministry of Science, Technology, and Space; the David and Fela Shapell Family Foundation; the NeuroMac DFG (German Research Foundation)/Transregional Collaborative Research Center Grant; and the Abramson Family Center for Young Scientists. Z.S. is supported by European Research Council grant 677713, the Morris Kahn Institute for Human Immunology and Human Frontiers of Science Program (CDA-00023/2016), the Azrieli Foundation, the Rising Tide Foundation, grants from the Benoziyo Endowment Fund for the Advancement of Science, the Sir Charles Clore Research Prize, the Comisaroff Family Trust, the Irma and Jacques Ber-Lehmsdorf Foundation, the Gerald O. Mann Charitable Foundation, and the David M. Polen Charitable Trust. M.I. is supported by European Research Council Consolidator Grant 725038, Italian Association for Cancer Research grant 15350, Italian Ministry of Health grant GR-2011-02347925, Fondazione Regionale per la Ricerca Biomedica grant 2015-0010, the European Molecular Biology Organization Young Investigator Program, and a Career Development Award from the Giovanni Armenise-Harvard Foundation. A.G. is a recipient of the Clore Fellowship. H.L. is funded by a Marie Curie Individual Fellowship (European Union project 746382, SCALTIE). The data reported in this manuscript are presented in the main paper and the supplementary materials. Raw and processed scRNA-seq data have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus with accession number GSE104054.",
year = "2017",
month = dec,
day = "22",
doi = "10.1126/science.aao4277",
language = "الإنجليزيّة",
volume = "358",
pages = "1622--1626",
journal = "Science",
issn = "0036-8075",
publisher = "American Association for the Advancement of Science",
number = "6370",
}