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Single-cell transcriptomics to explore the immune system in health and disease
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TLDR
In this article, the authors provide an overview of the state of single-cell genomics methods and an outlook on the use of singlecell techniques to decipher the adaptive and innate components of immunity.Abstract:
The immune system varies in cell types, states, and locations. The complex networks, interactions, and responses of immune cells produce diverse cellular ecosystems composed of multiple cell types, accompanied by genetic diversity in antigen receptors. Within this ecosystem, innate and adaptive immune cells maintain and protect tissue function, integrity, and homeostasis upon changes in functional demands and diverse insults. Characterizing this inherent complexity requires studies at single-cell resolution. Recent advances such as massively parallel single-cell RNA sequencing and sophisticated computational methods are catalyzing a revolution in our understanding of immunology. Here we provide an overview of the state of single-cell genomics methods and an outlook on the use of single-cell techniques to decipher the adaptive and innate components of immunity.read more
Citations
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Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
Itay Tirosh,Benjamin Izar,Daniel J. Treacy,John J. Trombetta,Asaf Rotem,Christopher Rodman,Christine G. Lian,George F. Murphy,Mohammad Fallahi-Sichani,Ken Dutton-Regester,Jia-Ren Lin,Ofir Cohen,Parin Shah,Diana Lu,Alexandra-Chloé Villani,Aleksandr Andreev,E.M. Van Allen,Monica M. Bertagnolli,Peter K. Sorger,Ryan J. Sullivan,Keith T. Flaherty,Dennie T. Frederick,Judit Jané-Valbuena,Orit Rozenblatt-Rosen,Sanjay M. Prakadan,Marc H. Wadsworth,Alex S. Genshaft,Travis K. Hughes,Carly G. K. Ziegler,Samuel W. Kazer,Alethe Gaillard de Saint Germain,Kellie E. Kolb,Cory M. Johannessen,Clifford H. Yoon,Alex K. Shalek,Aviv Regev,Levi A. Garraway +36 more
TL;DR: Tirosh et al. as discussed by the authors applied single-cell RNA sequencing (RNA-seq) to 4645 single cells isolated from 19 patients, profiling malignant, immune, stromal, and endothelial cells.
Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens
Atray Dixit,Atray Dixit,Oren Parnas,Biyu Li,Jenny Chen,Jenny Chen,Charles P. Fulco,Charles P. Fulco,Livnat Jerby-Arnon,Nemanja D. Marjanovic,Nemanja D. Marjanovic,Danielle Dionne,Tyler Burks,Raktima Raychowdhury,Britt Adamson,Thomas M. Norman,Eric S. Lander,Eric S. Lander,Eric S. Lander,Jonathan S. Weissman,Jonathan S. Weissman,Nir Friedman,Nir Friedman,Aviv Regev,Aviv Regev,Aviv Regev +25 more
TL;DR: Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions, and posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation.
Revealing the vectors of cellular identity with single-cell genomics
TL;DR: Single-cell genomics has now made it possible to create a comprehensive atlas of human cells and has reopened definitions of a cell's identity and of the ways in which identity is regulated by the cell's molecular circuitry.
CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity
Chao Wang,Nir Yosef,Nir Yosef,Jellert T. Gaublomme,Jellert T. Gaublomme,Chuan Wu,Youjin Lee,Clary B. Clish,James Kaminski,Sheng Xiao,Gerd Meyer zu Hörste,Mathias Pawlak,Yasuhiro Kishi,Yasuhiro Kishi,Nicole Joller,Katarzyna Karwacz,Chen Zhu,Maria Ordovas-Montanes,Asaf Madi,Asaf Madi,Ivo Wortman,Toru Miyazaki,Raymond A. Sobel,Hongkun Park,Hongkun Park,Aviv Regev,Aviv Regev,Vijay K. Kuchroo,Vijay K. Kuchroo +28 more
TL;DR: In this article, the authors used single-cell RNA-seq to identify CD5L/AIM as a regulator expressed in non-pathogenic, but not in pathogenic Th17 cells.
Posted Content
Evidence of innate lymphoid cell redundancy in humans
Frédéric Vély,Vincent Barlogis,Blandine Vallentin,Bénédicte Neven,Christelle Piperoglou,Thibaut Perchet,Maxime Petit,Nadia Yessaad,Fabien Touzot,Julie Bruneau,Nizar Mahlaoui,Nicolas Zucchini,Catherine Farnarier,Gérard Michel,Despina Moshous,Stéphane Blanche,Arnaud Dujardin,Hergen Spits,Joerg H. W. Distler,Andreas Ramming,Capucine Picard,Rachel Golub,Alain Fischer,Eric Vivier +23 more
TL;DR: In this article, the authors investigated the presence of ILCs in a cohort of patients with severe combined a immunodeficiency (SCID) and found that ILC subsets were absent in patients with a SCID who had mutation of the gene encoding the common gamma-chain a cytokine receptor subunit IL-2R gamma or the tyrosine a kinase JAK3.
References
More filters
Posted ContentDOI
Integrated analysis of multimodal single-cell data
Yuhan Hao,Stephanie Hao,Erica Andersen-Nissen,William M. Mauck,Shiwei Zheng,Andrew Butler,Maddie Jane Lee,Aaron J. Wilk,Charlotte A. Darby,Michael Zagar,Paul Hoffman,Marlon Stoeckius,Efthymia Papalexi,Eleni P. Mimitou,Jaison Jain,Avi Srivastava,Tim Stuart,Lamar Ballweber Fleming,Bertrand Z. Yeung,Angela J. Rogers,Juliana M. McElrath,Catherine A. Blish,Raphael Gottardo,Peter Smibert,Rahul Satija +24 more
TL;DR: ‘weighted-nearest neighbor’ analysis is introduced, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities.
Journal ArticleDOI
A Unique Microglia Type Associated with Restricting Development of Alzheimer’s Disease
Hadas Keren-Shaul,Amit Spinrad,Assaf Weiner,Assaf Weiner,Orit Matcovitch-Natan,Raz Dvir-Szternfeld,Tyler K. Ulland,Eyal David,Kuti Baruch,David Lara-Astaiso,Beáta Tóth,Shalev Itzkovitz,Marco Colonna,Michal Schwartz,Ido Amit +14 more
TL;DR: A novel microglia type associated with neurodegenerative diseases (DAM) is described and it is revealed that the DAM program is activated in a two-step process that involves downregulation of microglian checkpoints, followed by activation of a Trem2-dependent program.
Journal ArticleDOI
The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge.
TL;DR: The current status of TCGA Research Network structure, purpose, and achievements are discussed, to provide publicly available datasets to help improve diagnostic methods, treatment standards, and finally to prevent cancer.
Journal ArticleDOI
Simultaneous epitope and transcriptome measurement in single cells.
Marlon Stoeckius,Christoph Hafemeister,William Stephenson,Brian Houck-Loomis,Pratip K. Chattopadhyay,Harold Swerdlow,Rahul Satija,Peter Smibert +7 more
TL;DR: In this article, a method called cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) is proposed, in which oligonucleotide-labeled antibodies are used to integrate cellular protein and transcriptome measurements into an efficient, single-cell readout.
Journal ArticleDOI
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.
Alexandra-Chloé Villani,Alexandra-Chloé Villani,Rahul Satija,Rahul Satija,Gary Reynolds,Siranush Sarkizova,Karthik Shekhar,James Fletcher,Morgane Griesbeck,Andrew Butler,Shiwei Zheng,Suzan Lazo,Laura Jardine,David Dixon,Emily Stephenson,Emil Nilsson,Ida Grundberg,David McDonald,Andrew Filby,Weibo Li,Weibo Li,Philip L. De Jager,Philip L. De Jager,Orit Rozenblatt-Rosen,Andrew A. Lane,Andrew A. Lane,Muzlifah Haniffa,Muzlifah Haniffa,Aviv Regev,Aviv Regev,Aviv Regev,Nir Hacohen,Nir Hacohen +32 more
TL;DR: This refined analysis has identified, among others, a previously unknown dendritic cell population that potently activates T cells and reclassify pDCs as the originally described “natural interferon-producing cells (IPCs)” with weaker T cell proliferation induction ability.