Journal Article
. 2017 Dec; 358(6370):1622-1626.
doi: 10.1126/science.aao4277.

Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq

Chiara Medaglia 1 Amir Giladi 1 Liat Stoler-Barak 1 Marco De Giovanni 2 Tomer Meir Salame 3 Adi Biram 1 Eyal David 1 Hanjie Li 1 Matteo Iannacone 4 Ziv Shulman 5 Ido Amit 5 
  • PMID: 29217582
  •     18 References
  •     74 citations


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.

Dynamic signaling by T follicular helper cells during germinal center B cell selection.
Ziv Shulman, Alexander D Gitlin, +5 authors, Michel C Nussenzweig.
Science, 2014 Aug 30; 345(6200). PMID: 25170154    Free PMC article.
Highly Cited.
Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
Patrik L Ståhl, Fredrik Salmén, +18 authors, Jonas Frisén.
Science, 2016 Jul 02; 353(6294). PMID: 27365449
Highly Cited.
Immunosurveillance of the liver by intravascular effector CD8(+) T cells.
Luca G Guidotti, Donato Inverso, +17 authors, Matteo Iannacone.
Cell, 2015 Apr 22; 161(3). PMID: 25892224
Highly Cited.
Computational and analytical challenges in single-cell transcriptomics.
Oliver Stegle, Sarah A Teichmann, John C Marioni.
Nat Rev Genet, 2015 Jan 30; 16(3). PMID: 25628217
Highly Cited. Review.
Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.
Alex A Pollen, Tomasz J Nowakowski, +27 authors, Jay A A West.
Nat Biotechnol, 2014 Aug 05; 32(10). PMID: 25086649    Free PMC article.
Highly Cited.
Single-molecule approaches to stochastic gene expression.
Arjun Raj, Alexander van Oudenaarden.
Annu Rev Biophys, 2009 May 07; 38. PMID: 19416069    Free PMC article.
Highly Cited. Review.
Spatiotemporal basis of innate and adaptive immunity in secondary lymphoid tissue.
Hai Qi, Wolfgang Kastenmüller, Ronald N Germain.
Annu Rev Cell Dev Biol, 2014 Aug 26; 30. PMID: 25150013
Inflammatory monocytes hinder antiviral B cell responses.
Stefano Sammicheli, Mirela Kuka, +15 authors, Matteo Iannacone.
Sci Immunol, 2016 Nov 22; 1(4). PMID: 27868108    Free PMC article.
Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors.
Franziska Paul, Ya'ara Arkin, +19 authors, Ido Amit.
Cell, 2015 Dec 03; 163(7). PMID: 26627738
Highly Cited.
Computational assignment of cell-cycle stage from single-cell transcriptome data.
Antonio Scialdone, Kedar N Natarajan, +5 authors, Florian Buettner.
Methods, 2015 Jul 06; 85. PMID: 26142758
Highly Cited.
Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue.
Ditte Lovatt, Brittani K Ruble, +15 authors, James Eberwine.
Nat Methods, 2014 Jan 15; 11(2). PMID: 24412976    Free PMC article.
Highly Cited.
Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance.
Sydney M Shaffer, Margaret C Dunagin, +14 authors, Arjun Raj.
Nature, 2017 Jun 14; 546(7658). PMID: 28607484    Free PMC article.
Highly Cited.
Robust Anti-viral Immunity Requires Multiple Distinct T Cell-Dendritic Cell Interactions.
Sarah Eickhoff, Anna Brewitz, +7 authors, Wolfgang Kastenmüller.
Cell, 2015 Aug 25; 162(6). PMID: 26296422    Free PMC article.
Highly Cited.
Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment.
Yonit Lavin, Deborah Winter, +5 authors, Ido Amit.
Cell, 2014 Dec 07; 159(6). PMID: 25480296    Free PMC article.
Highly Cited.
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.
Diego Adhemar Jaitin, Ephraim Kenigsberg, +8 authors, Ido Amit.
Science, 2014 Feb 18; 343(6172). PMID: 24531970    Free PMC article.
Highly Cited.
seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus.
Sheel Shah, Eric Lubeck, Wen Zhou, Long Cai.
Neuron, 2017 May 19; 94(4). PMID: 28521130
Germinal center dynamics revealed by multiphoton microscopy with a photoactivatable fluorescent reporter.
Gabriel D Victora, Tanja A Schwickert, +4 authors, Michel C Nussenzweig.
Cell, 2010 Nov 16; 143(4). PMID: 21074050    Free PMC article.
Highly Cited.
Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, +2 authors, Aviv Regev.
Nat Biotechnol, 2015 Apr 14; 33(5). PMID: 25867923    Free PMC article.
Highly Cited.
Technique: Single-cell transcriptomes in space.
Linda Koch.
Nat Rev Genet, 2017 Dec 28; 19(2). PMID: 29279607
The Peripheral and Intratumoral Immune Cell Landscape in Cancer Patients: A Proxy for Tumor Biology and a Tool for Outcome Prediction.
Annette Schnell, Christian Schmidl, Wolfgang Herr, Peter J Siska.
Biomedicines, 2018 Mar 03; 6(1). PMID: 29495308    Free PMC article.
Quantitative single-cell transcriptomics.
Christoph Ziegenhain, Beate Vieth, +2 authors, Wolfgang Enard.
Brief Funct Genomics, 2018 Mar 27; 17(4). PMID: 29579145    Free PMC article.
Visualizing Viral Infection In Vivo by Multi-Photon Intravital Microscopy.
Xaver Sewald.
Viruses, 2018 Jun 22; 10(6). PMID: 29925766    Free PMC article.
Local exchange of metabolites shapes immunity.
Felix Clemens Richter, Sandrine Obba, Anna Katharina Simon.
Immunology, 2018 Jul 05; 155(3). PMID: 29972686    Free PMC article.
Single Cell RNA Sequencing of Rare Immune Cell Populations.
Akira Nguyen, Weng Hua Khoo, +2 authors, Tri Giang Phan.
Front Immunol, 2018 Jul 20; 9. PMID: 30022984    Free PMC article.
Neonatally imprinted stromal cell subsets induce tolerogenic dendritic cells in mesenteric lymph nodes.
Joern Pezoldt, Maria Pasztoi, +21 authors, Jochen Huehn.
Nat Commun, 2018 Sep 27; 9(1). PMID: 30254319    Free PMC article.
Understanding tumor ecosystems by single-cell sequencing: promises and limitations.
Xianwen Ren, Boxi Kang, Zemin Zhang.
Genome Biol, 2018 Dec 05; 19(1). PMID: 30509292    Free PMC article.
Genomics-Guided Immunotherapy for Precision Medicine in Cancer.
Shradha Mukherjee.
Cancer Biother Radiopharm, 2019 Jul 18; 34(8). PMID: 31314580    Free PMC article.
B cell dissemination patterns during the germinal center reaction revealed by whole-organ imaging.
Liat Stoler-Barak, Adi Biram, +3 authors, Ziv Shulman.
J Exp Med, 2019 Sep 08; 216(11). PMID: 31492809    Free PMC article.
Studying interactions between dendritic cells and T cells in vivo.
Aleksey Chudnovskiy, Giulia Pasqual, Gabriel D Victora.
Curr Opin Immunol, 2019 Mar 19; 58. PMID: 30884422    Free PMC article.
Eleven grand challenges in single-cell data science.
David Lähnemann, Johannes Köster, +48 authors, Alexander Schönhuth.
Genome Biol, 2020 Feb 09; 21(1). PMID: 32033589    Free PMC article.
Live-animal imaging of native haematopoietic stem and progenitor cells.
Constantina Christodoulou, Joel A Spencer, +16 authors, Fernando D Camargo.
Nature, 2020 Feb 07; 578(7794). PMID: 32025033    Free PMC article.
Brain Parenchymal and Extraparenchymal Macrophages in Development, Homeostasis, and Disease.
Simone Brioschi, Yingyue Zhou, Marco Colonna.
J Immunol, 2020 Jan 08; 204(2). PMID: 31907272    Free PMC article.
Spatiotemporal regulation of type I interferon expression determines the antiviral polarization of CD4+ T cells.
Marco De Giovanni, Valeria Cutillo, +14 authors, Matteo Iannacone.
Nat Immunol, 2020 Feb 19; 21(3). PMID: 32066949    Free PMC article.
Atherosclerosis in the single-cell era.
Holger Winkels, Erik Ehinger, +2 authors, Klaus Ley.
Curr Opin Lipidol, 2018 Jul 19; 29(5). PMID: 30020199    Free PMC article.
Revolutionizing Cancer Immunology: The Power of Next-Generation Sequencing Technologies.
Meromit Singer, Ana C Anderson.
Cancer Immunol Res, 2019 Feb 03; 7(2). PMID: 30709909    Free PMC article.
Mutually assured destruction: the cold war between viruses and natural killer cells.
Ayad Ali, Ivayla E Gyurova, Stephen N Waggoner.
Curr Opin Virol, 2019 Mar 17; 34. PMID: 30877885    Free PMC article.
Multimodal single-cell approaches shed light on T cell heterogeneity.
Aparna Nathan, Yuriy Baglaenko, +2 authors, Soumya Raychaudhuri.
Curr Opin Immunol, 2019 Aug 21; 61. PMID: 31430664    Free PMC article.
SpatialDB: a database for spatially resolved transcriptomes.
Zhen Fan, Runsheng Chen, Xiaowei Chen.
Nucleic Acids Res, 2019 Nov 13; 48(D1). PMID: 31713629    Free PMC article.
The Mononuclear Phagocytic System. Generation of Diversity.
Siamon Gordon, Annette Plüddemann.
Front Immunol, 2019 Aug 27; 10. PMID: 31447860    Free PMC article.
Single-Cell High-Throughput Technologies in Cerebrospinal Fluid Research and Diagnostics.
Tobias V Lanz, Anne-Katrin Pröbstel, +2 authors, Lucas Schirmer.
Front Immunol, 2019 Jun 28; 10. PMID: 31244848    Free PMC article.
Add on the next level-the time point of the type I IFN response orchestrates the immune response.
Angela Wedekind, David Fritzsch, Andrea Kröger.
Cell Mol Immunol, 2020 Apr 30; 17(8). PMID: 32346100    Free PMC article.
The Spatial and Genomic Hierarchy of Tumor Ecosystems Revealed by Single-Cell Technologies.
Eric A Smith, H Courtney Hodges.
Trends Cancer, 2019 Jul 18; 5(7). PMID: 31311656    Free PMC article.
In vivo imaging of adaptive immune responses to viruses.
Marco De Giovanni, Matteo Iannacone.
Curr Opin Virol, 2017 Dec 30; 28. PMID: 29287222    Free PMC article.
Tools and Concepts for Interrogating and Defining Cellular Identity.
Kara L McKinley, David Castillo-Azofeifa, Ophir D Klein.
Cell Stem Cell, 2020 May 11; 26(5). PMID: 32386555    Free PMC article.
Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients.
Pierre Bost, Amir Giladi, +12 authors, Ido Amit.
Cell, 2020 Jun 02; 181(7). PMID: 32479746    Free PMC article.
High-throughput, microscope-based sorting to dissect cellular heterogeneity.
Nicholas Hasle, Anthony Cooke, +10 authors, Douglas M Fowler.
Mol Syst Biol, 2020 Jun 06; 16(6). PMID: 32500953    Free PMC article.
Dual-Activatable Cell Tracker for Controlled and Prolonged Single-Cell Labeling.
Elias A Halabi, Jorge Arasa, +3 authors, Pablo Rivera-Fuentes.
ACS Chem Biol, 2020 Apr 17; 15(6). PMID: 32298071    Free PMC article.
A hybrid deep clustering approach for robust cell type profiling using single-cell RNA-seq data.
Suhas Srinivasan, Anastasia Leshchyk, Nathan T Johnson, Dmitry Korkin.
RNA, 2020 Jun 14; 26(10). PMID: 32532794    Free PMC article.
Studying immune to non-immune cell cross-talk using single-cell technologies.
R Elmentaite, S A Teichmann, E Madissoon.
Curr Opin Syst Biol, 2020 Sep 29; 18. PMID: 32984660    Free PMC article.
Prognostic significance of spatial immune profiles in human solid cancers.
Takahiro Tsujikawa, Junichi Mitsuda, +4 authors, Shigeru Hirano.
Cancer Sci, 2020 Jul 30; 111(10). PMID: 32726495    Free PMC article.
Live Imaging of Innate and Adaptive Immune Responses in the Liver.
Lu Li, Zhutian Zeng.
Front Immunol, 2020 Oct 13; 11. PMID: 33042143    Free PMC article.
Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly.
Xianwen Ren, Guojie Zhong, +3 authors, Zemin Zhang.
Cell Res, 2020 Jun 17; 30(9). PMID: 32541867    Free PMC article.
LifeTime and improving European healthcare through cell-based interceptive medicine.
Nikolaus Rajewsky, Geneviève Almouzni, +48 authors, LifeTime Community Working Groups.
Nature, 2020 Sep 08; 587(7834). PMID: 32894860    Free PMC article.
Versatile phenotype-activated cell sorting.
Jihwan Lee, Zhuohe Liu, +5 authors, François St-Pierre.
Sci Adv, 2020 Oct 25; 6(43). PMID: 33097540    Free PMC article.
Iterative point set registration for aligning scRNA-seq data.
Amir Alavi, Ziv Bar-Joseph.
PLoS Comput Biol, 2020 Oct 28; 16(10). PMID: 33108369    Free PMC article.
Technical Advancements for Studying Immune Regulation of Disseminated Dormant Cancer Cells.
Luigi Ombrato, Marco Montagner.
Front Oncol, 2020 Dec 01; 10. PMID: 33251149    Free PMC article.
Systems Immunology: Learning the Rules of the Immune System.
Alexandra-Chloé Villani, Siranush Sarkizova, Nir Hacohen.
Annu Rev Immunol, 2018 Apr 21; 36. PMID: 29677477    Free PMC article.
Recording the wild lives of immune cells.
Mikael J Pittet, Christopher S Garris, Sean P Arlauckas, Ralph Weissleder.
Sci Immunol, 2018 Sep 09; 3(27). PMID: 30194240    Free PMC article.
NicheNet: modeling intercellular communication by linking ligands to target genes.
Robin Browaeys, Wouter Saelens, Yvan Saeys.
Nat Methods, 2019 Dec 11; 17(2). PMID: 31819264
Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization.
Chiara Baccin, Jude Al-Sabah, +7 authors, Simon Haas.
Nat Cell Biol, 2019 Dec 25; 22(1). PMID: 31871321    Free PMC article.
T Cell Dysfunction in Cancer.
Daniela S Thommen, Ton N Schumacher.
Cancer Cell, 2018 Apr 11; 33(4). PMID: 29634943    Free PMC article.
Highly Cited. Review.
Macrophage imaging and subset analysis using single-cell RNA sequencing.
Sean Arlauckas, Nuri Oh, +2 authors, Miles A Miller.
Nanotheranostics, 2021 Jan 05; 5(1). PMID: 33391974    Free PMC article.
Immune cell infiltration features and related marker genes in lung cancer based on single-cell RNA-seq.
R Zhong, D Chen, +3 authors, H Zhong.
Clin Transl Oncol, 2020 Jul 14; 23(2). PMID: 32656582
Turning Nature's own processes into design strategies for living bone implant biomanufacturing: a decade of Developmental Engineering.
Ioannis Papantoniou, Gabriella Nilsson Hall, +4 authors, Liesbet Geris.
Adv Drug Deliv Rev, 2020 Dec 09; 169. PMID: 33290762    Free PMC article.
Location, location, location: how the tissue microenvironment affects inflammation in RA.
Christopher D Buckley, Caroline Ospelt, Steffen Gay, Kim S Midwood.
Nat Rev Rheumatol, 2021 Feb 03; 17(4). PMID: 33526927
Dissecting cellular crosstalk by sequencing physically interacting cells.
Amir Giladi, Merav Cohen, +11 authors, Ido Amit.
Nat Biotechnol, 2020 Mar 11; 38(5). PMID: 32152598
ZipSeq: barcoding for real-time mapping of single cell transcriptomes.
Kenneth H Hu, John P Eichorst, +7 authors, Matthew F Krummel.
Nat Methods, 2020 Jul 08; 17(8). PMID: 32632238    Free PMC article.
Next Generation Imaging Techniques to Define Immune Topographies in Solid Tumors.
Violena Pietrobon, Alessandra Cesano, Francesco Marincola, Jakob Nikolas Kather.
Front Immunol, 2021 Feb 16; 11. PMID: 33584676    Free PMC article.
Imaging-based screens of pool-synthesized cell libraries.
Michael Lawson, Johan Elf.
Nat Methods, 2021 Feb 17; 18(4). PMID: 33589838
Cross-species RNA-seq for deciphering host-microbe interactions.
Alexander J Westermann, Jörg Vogel.
Nat Rev Genet, 2021 Feb 19; 22(6). PMID: 33597744
Identification of resistance pathways and therapeutic targets in relapsed multiple myeloma patients through single-cell sequencing.
Yael C Cohen, Mor Zada, +25 authors, Ido Amit.
Nat Med, 2021 Feb 24; 27(3). PMID: 33619369
Dissecting phenotypic transitions in metastatic disease via photoconversion-based isolation.
Yogev Sela, Jinyang Li, +5 authors, Ben Z Stanger.
Elife, 2021 Feb 24; 10. PMID: 33620315    Free PMC article.
Characterization of Immunological Niches within Peyer's Patches by ex vivo Photoactivation and Flow Cytometry Analysis.
Adi Biram, Ziv Shulman.
Bio Protoc, 2021 Mar 05; 10(6). PMID: 33659533    Free PMC article.
Conversations that count: Cellular interactions that drive T cell fate.
Brigette C Duckworth, Joanna R Groom.
Immunol Rev, 2021 Feb 16; 300(1). PMID: 33586207    Free PMC article.
Single-Cell Transcriptomics: Current Methods and Challenges in Data Acquisition and Analysis.
Asif Adil, Vijay Kumar, Arif Tasleem Jan, Mohammed Asger.
Front Neurosci, 2021 May 11; 15. PMID: 33967674    Free PMC article.
Advances and Opportunities in Single-Cell Transcriptomics for Plant Research.
Carolin Seyfferth, Jim Renema, +8 authors, Bert De Rybel.
Annu Rev Plant Biol, 2021 Mar 18; 72. PMID: 33730513    Free PMC article.
Single-cell and spatial analyses of cancer cells: toward elucidating the molecular mechanisms of clonal evolution and drug resistance acquisition.
Satoi Nagasawa, Yukie Kashima, Ayako Suzuki, Yutaka Suzuki.
Inflamm Regen, 2021 Jul 18; 41(1). PMID: 34271973    Free PMC article.
Spatial omics and multiplexed imaging to explore cancer biology.
Sabrina M Lewis, Marie-Liesse Asselin-Labat, +6 authors, Shalin H Naik.
Nat Methods, 2021 Aug 04; 18(9). PMID: 34341583
Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes.
Alex S Genshaft, Carly G K Ziegler, +12 authors, Alex K Shalek.
Nat Commun, 2021 Aug 19; 12(1). PMID: 34404785    Free PMC article.
Single-cell analysis of regions of interest (SCARI) using a photosensitive tag.
Anne M van der Leun, Mirjam E Hoekstra, +14 authors, Ton N Schumacher.
Nat Chem Biol, 2021 Sep 11; 17(11). PMID: 34504322    Free PMC article.
CD177 modulates the function and homeostasis of tumor-infiltrating regulatory T cells.
Myung-Chul Kim, Nicholas Borcherding, +32 authors, Weizhou Zhang.
Nat Commun, 2021 Oct 03; 12(1). PMID: 34599187    Free PMC article.
A Multi-Modal Toolkit for Studying Neutrophils in Cancer and Beyond.
Diana Changirwa, Jared Schlechte, Braedon McDonald.
Cancers (Basel), 2021 Nov 14; 13(21). PMID: 34771495    Free PMC article.
Automatic cell type identification methods for single-cell RNA sequencing.
Bingbing Xie, Qin Jiang, Antonio Mora, Xuri Li.
Comput Struct Biotechnol J, 2021 Nov 25; 19. PMID: 34815832    Free PMC article.
Aging of the Hematopoietic Stem Cell Niche: New Tools to Answer an Old Question.
Francesca Matteini, Medhanie A Mulaw, M Carolina Florian.
Front Immunol, 2021 Dec 04; 12. PMID: 34858399    Free PMC article.
scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network.
Xin Shao, Haihong Yang, +6 authors, Xiaohui Fan.
Nucleic Acids Res, 2021 Sep 10; 49(21). PMID: 34500471    Free PMC article.
Human placental biology at single-cell resolution: a contemporaneous review.
E R Barrozo, K M Aagaard.
BJOG, 2021 Oct 16; 129(2). PMID: 34651399    Free PMC article.
Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis.
Tam Vu, Alexander Vallmitjana, +13 authors, Weian Zhao.
Nat Commun, 2022 Jan 12; 13(1). PMID: 35013281    Free PMC article.
Spatial components of molecular tissue biology.
Giovanni Palla, David S Fischer, Aviv Regev, Fabian J Theis.
Nat Biotechnol, 2022 Feb 09; 40(3). PMID: 35132261
Single-Cell Technologies to Decipher the Immune Microenvironment in Myeloid Neoplasms: Perspectives and Opportunities.
Chiara Caprioli, Iman Nazari, Sara Milovanovic, Pier Giuseppe Pelicci.
Front Oncol, 2022 Feb 22; 11. PMID: 35186713    Free PMC article.
Fate-mapping mice: new tools and technology for immune discovery.
Scarlett E Lee, Brian D Rudd, Norah L Smith.
Trends Immunol, 2022 Feb 01; 43(3). PMID: 35094945    Free PMC article.
Museum of spatial transcriptomics.
Lambda Moses, Lior Pachter.
Nat Methods, 2022 Mar 12; 19(5). PMID: 35273392
Clinical and translational values of spatial transcriptomics.
Linlin Zhang, Dongsheng Chen, +4 authors, Xiangdong Wang.
Signal Transduct Target Ther, 2022 Apr 03; 7(1). PMID: 35365599    Free PMC article.