251
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Behjati S, Lindsay S, Teichmann SA, Haniffa M. Mapping human development at single-cell resolution. Development 2018; 145:145/3/dev152561. [PMID: 29439135 DOI: 10.1242/dev.152561] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Human development is regulated by spatiotemporally restricted molecular programmes and is pertinent to many areas of basic biology and human medicine, such as stem cell biology, reproductive medicine and childhood cancer. Mapping human development has presented significant technological, logistical and ethical challenges. The availability of established human developmental biorepositories and the advent of cutting-edge single-cell technologies provide new opportunities to study human development. Here, we present a working framework for the establishment of a human developmental cell atlas exploiting single-cell genomics and spatial analysis. We discuss how the development atlas will benefit the scientific and clinical communities to advance our understanding of basic biology, health and disease.
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Affiliation(s)
- Sam Behjati
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK .,Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Susan Lindsay
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK .,Theory of Condensed Matter, Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK .,Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
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252
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Lu YC, Zheng Z, Robbins PF, Tran E, Prickett TD, Gartner JJ, Li YF, Ray S, Franco Z, Bliskovsky V, Fitzgerald PC, Rosenberg SA. An Efficient Single-Cell RNA-Seq Approach to Identify Neoantigen-Specific T Cell Receptors. Mol Ther 2018; 26:379-389. [PMID: 29174843 PMCID: PMC5835023 DOI: 10.1016/j.ymthe.2017.10.018] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/24/2017] [Accepted: 10/24/2017] [Indexed: 12/20/2022] Open
Abstract
The adoptive transfer of neoantigen-reactive tumor-infiltrating lymphocytes (TILs) can result in tumor regression in patients with metastatic cancer. To improve the efficacy of adoptive T cell therapy targeting these tumor-specific mutations, we have proposed a new therapeutic strategy, which involves the genetic modification of autologous T cells with neoantigen-specific T cell receptors (TCRs) and the transfer of these modified T cells back to cancer patients. However, the current techniques to isolate neoantigen-specific TCRs are labor intensive, time consuming, and technically challenging, not suitable for clinical applications. To facilitate this process, a new approach was developed, which included the co-culture of TILs with tandem minigene (TMG)-transfected or peptide-pulsed autologous antigen-presenting cells (APCs) and the single-cell RNA sequencing (RNA-seq) analysis of T cells to identify paired TCR sequences associated with cells expressing high levels of interferon-γ (IFN-γ) and interleukin-2 (IL-2). Following this new approach, multiple TCRs were identified, synthesized, cloned into a retroviral vector, and then transduced into donor T cells. These transduced T cells were shown to specifically recognize the neoantigens presented by autologous APCs. In conclusion, this approach provides an efficient procedure to isolate neoantigen-specific TCRs for clinical applications, as well as for basic and translational research.
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Affiliation(s)
- Yong-Chen Lu
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Zhili Zheng
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul F Robbins
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric Tran
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Todd D Prickett
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jared J Gartner
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yong F Li
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Satyajit Ray
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zulmarie Franco
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Valery Bliskovsky
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter C Fitzgerald
- Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven A Rosenberg
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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253
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Microfluidic single-cell technology in immunology and antibody screening. Mol Aspects Med 2018; 59:47-61. [DOI: 10.1016/j.mam.2017.09.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 09/06/2017] [Accepted: 09/13/2017] [Indexed: 11/20/2022]
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254
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255
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Patil VS, Madrigal A, Schmiedel BJ, Clarke J, O'Rourke P, de Silva AD, Harris E, Peters B, Seumois G, Weiskopf D, Sette A, Vijayanand P. Precursors of human CD4 + cytotoxic T lymphocytes identified by single-cell transcriptome analysis. Sci Immunol 2018; 3:eaan8664. [PMID: 29352091 PMCID: PMC5931334 DOI: 10.1126/sciimmunol.aan8664] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/27/2017] [Accepted: 11/30/2017] [Indexed: 01/03/2023]
Abstract
CD4+ cytotoxic T lymphocytes (CD4-CTLs) have been reported to play a protective role in several viral infections. However, little is known in humans about the biology of CD4-CTL generation, their functional properties, and heterogeneity, especially in relation to other well-described CD4+ memory T cell subsets. We performed single-cell RNA sequencing in more than 9000 cells to unravel CD4-CTL heterogeneity, transcriptional profile, and clonality in humans. Single-cell differential gene expression analysis revealed a spectrum of known transcripts, including several linked to cytotoxic and costimulatory function that are expressed at higher levels in the TEMRA (effector memory T cells expressing CD45RA) subset, which is highly enriched for CD4-CTLs, compared with CD4+ T cells in the central memory (TCM) and effector memory (TEM) subsets. Simultaneous T cell antigen receptor (TCR) analysis in single cells and bulk subsets revealed that CD4-TEMRA cells show marked clonal expansion compared with TCM and TEM cells and that most of CD4-TEMRA were dengue virus (DENV)-specific in donors with previous DENV infection. The profile of CD4-TEMRA was highly heterogeneous across donors, with four distinct clusters identified by the single-cell analysis. We identified distinct clusters of CD4-CTL effector and precursor cells in the TEMRA subset; the precursor cells shared TCR clonotypes with CD4-CTL effectors and were distinguished by high expression of the interleukin-7 receptor. Our identification of a CD4-CTL precursor population may allow further investigation of how CD4-CTLs arise in humans and, thus, could provide insights into the mechanisms that may be used to generate durable and effective CD4-CTL immunity.
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Affiliation(s)
- Veena S Patil
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Ariel Madrigal
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Benjamin J Schmiedel
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - James Clarke
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Patrick O'Rourke
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Aruna D de Silva
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
- Genetech Research Institute, Colombo, Sri Lanka
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
- Department of Medicine, University of California San Diego, 9500 Gilman Drive #0656, La Jolla, CA 92093, USA
| | - Gregory Seumois
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
- Department of Medicine, University of California San Diego, 9500 Gilman Drive #0656, La Jolla, CA 92093, USA
| | - Pandurangan Vijayanand
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
- Department of Medicine, University of California San Diego, 9500 Gilman Drive #0656, La Jolla, CA 92093, USA
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine University of Southampton, Southampton, UK
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256
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Dendrou CA, Petersen J, Rossjohn J, Fugger L. HLA variation and disease. Nat Rev Immunol 2018; 18:325-339. [PMID: 29292391 DOI: 10.1038/nri.2017.143] [Citation(s) in RCA: 419] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fifty years since the first description of an association between HLA and human disease, HLA molecules have proven to be central to physiology, protective immunity and deleterious, disease-causing autoimmune reactivity. Technological advances have enabled pivotal progress in the determination of the molecular mechanisms that underpin the association between HLA genetics and functional outcome. Here, we review our current understanding of HLA molecules as the fundamental platform for immune surveillance and responsiveness in health and disease. We evaluate the scope for personalized antigen-specific disease prevention, whereby harnessing HLA-ligand interactions for clinical benefit is becoming a realistic prospect.
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Affiliation(s)
- Calliope A Dendrou
- Nuffield Department of Medicine, The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jan Petersen
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Infection and Immunity Programme and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Infection and Immunity Programme and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Division of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Lars Fugger
- Danish National Research Foundation Centre PERSIMUNE, Rigshospitalet, University of Copenhagen, Copenhagen DK-2100, Denmark.,Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK
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257
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Gong H, Do D, Ramakrishnan R. Single-Cell mRNA-Seq Using the Fluidigm C1 System and Integrated Fluidics Circuits. Methods Mol Biol 2018; 1783:193-207. [PMID: 29767364 DOI: 10.1007/978-1-4939-7834-2_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-cell mRNA-seq is a valuable tool to dissect expression profiles and to understand the regulatory network of genes. Microfluidics is well suited for single-cell analysis owing both to the small volume of the reaction chambers and easiness of automation. Here we describe the workflow of single-cell mRNA-seq using C1 IFC, which can isolate and process up to 96 cells. Both on-chip procedure (lysis, reverse transcription, and preamplification PCR) and off-chip sequencing library preparation protocols are described. The workflow generates full-length mRNA information, which is more valuable compared to 3' end counting method for many applications.
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Affiliation(s)
- Haibiao Gong
- Fluidigm Corporation, South San Francisco, CA, USA
| | - Devin Do
- Fluidigm Corporation, South San Francisco, CA, USA
| | - Ramesh Ramakrishnan
- Fluidigm Corporation, South San Francisco, CA, USA.
- Dovetail Genomics LLC, Santa Cruz, CA, USA.
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258
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Abstract
Single-cell RNA sequencing has evolved into a benchmark application to study cellular heterogeneity, advancing our understanding of cellular differentiation, disease progression, and gene regulation in a multitude of research areas. The generation of high-quality cDNA, an important step in the experimental workflow when generating sequence-ready libraries, is critical to maximizing data quality. Here we describe a strategy that uses a microfluidic device (i.e., the C1™ IFC) to synthesize full-length cDNA from single cells in a fully automated, nanoliter-scale format. The device also facilitates confirmation of the presence of a single, viable cell and recording of phenotypic information, quality control measures that are crucial for streamlining downstream data processing and enhancing overall data validity.
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259
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Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. eLife 2017; 6:e27041. [PMID: 29206104 DOI: 10.1101/121202] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/30/2017] [Indexed: 05/28/2023] Open
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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Affiliation(s)
- Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Ewan Birney
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Bernd Bodenmiller
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Piero Carninci
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Hans Clevers
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Ian Dunham
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Wolfgang Enard
- Department of Biology II, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Andrew Farmer
- Takara Bio United States, Inc., Mountain View, United States
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, United States
- Massachusetts General Hospital Cancer Center, Boston, United States
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Seung Kim
- Departments of Developmental Biology and of Medicine, Stanford University School of Medicine, Stanford, United States
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Arnold Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, United States
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, United States
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Genetics, Stanford University, Stanford, United States
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Musa Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Martijn Nawijn
- Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mihai Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Garry Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, United States
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, United States
| | | | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen Quake
- Department of Applied Physics and Department of Bioengineering, Stanford University, Stanford, United States
- Chan Zuckerberg Biohub, San Francisco, United States
| | - Wolf Reik
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | | | - Joshua Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Rahul Satija
- Department of Biology, New York University, New York, United States
- New York Genome Center, New York University, New York, United States
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alex Shalek
- Broad Institute of MIT and Harvard, Cambridge, United States
- Institute for Medical Engineering & Science (IMES) and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Ehud Shapiro
- Department of Computer Science and Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer Center, University of Texas, Houston, United States
| | - Jay W Shin
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Oliver Stegle
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Michael Stratton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | - Fabian J Theis
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Matthias Uhlen
- Science for Life Laboratory and Department of Proteomics, KTH Royal Institute of Technology, Stockholm, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | | | - Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, United States
| | - Fiona Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Jonathan Weissman
- Howard Hughes Medical Institute, Chevy Chase, United States
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, United States
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, United States
| | - Nir Yosef
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, United States
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260
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Cao Y, Zhu J, Jia P, Zhao Z. scRNASeqDB: A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells. Genes (Basel) 2017; 8:genes8120368. [PMID: 29206167 PMCID: PMC5748686 DOI: 10.3390/genes8120368] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 11/30/2017] [Accepted: 11/30/2017] [Indexed: 12/14/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-Seq) is rapidly becoming a powerful tool for high-throughput transcriptomic analysis of cell states and dynamics at the single cell level. Both the number and quality of scRNA-Seq datasets have dramatically increased recently. A database that can comprehensively collect, curate, and compare expression features of scRNA-Seq data in humans has not yet been built. Here, we present scRNASeqDB, a database that includes almost all the currently available human single cell transcriptome datasets (n = 38) covering 200 human cell lines or cell types and 13,440 samples. Our online web interface allows users to rank the expression profiles of the genes of interest across different cell types. It also provides tools to query and visualize data, including Gene Ontology and pathway annotations for differentially expressed genes between cell types or groups. The scRNASeqDB is a useful resource for single cell transcriptional studies. This database is publicly available at https://bioinfo.uth.edu/scrnaseqdb/.
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Affiliation(s)
- Yuan Cao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Junjie Zhu
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA.
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA.
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261
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Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. eLife 2017; 6:e27041. [PMID: 29206104 PMCID: PMC5762154 DOI: 10.7554/elife.27041] [Citation(s) in RCA: 1247] [Impact Index Per Article: 178.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/30/2017] [Indexed: 12/12/2022] Open
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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Affiliation(s)
- Aviv Regev
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
| | - Eric S Lander
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | - Ido Amit
- Department of ImmunologyWeizmann Institute of ScienceRehovotIsrael
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUnited States
| | - Ewan Birney
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - Bernd Bodenmiller
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Institute of Molecular Life SciencesUniversity of ZürichZürichSwitzerland
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Piero Carninci
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Hans Clevers
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center UtrechtUtrechtThe Netherlands
| | - Bart Deplancke
- Institute of Bioengineering, School of Life SciencesSwiss Federal Institute of Technology (EPFL)LausanneSwitzerland
| | - Ian Dunham
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - James Eberwine
- Department of Systems Pharmacology and Translational TherapeuticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuantHeidelberg UniversityHeidelbergGermany
| | - Wolfgang Enard
- Department of Biology IILudwig Maximilian University MunichMartinsriedGermany
| | - Andrew Farmer
- Takara Bio United States, Inc.Mountain ViewUnited States
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineJohn Radcliffe Hospital, University of OxfordOxfordUnited Kingdom
| | - Berthold Göttgens
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Nir Hacohen
- Broad Institute of MIT and HarvardCambridgeUnited States
- Massachusetts General Hospital Cancer CenterBostonUnited States
| | - Muzlifah Haniffa
- Institute of Cellular MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Seung Kim
- Departments of Developmental Biology and of MedicineStanford University School of MedicineStanfordUnited States
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
| | - Arnold Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUniversity of California, San FranciscoSan FranciscoUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Emma Lundberg
- Science for Life Laboratory, School of BiotechnologyKTH Royal Institute of TechnologyStockholmSweden
- Department of GeneticsStanford UniversityStanfordUnited States
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologyStockholmSweden
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Miriam Merad
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Musa Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Martijn Nawijn
- Department of Pathology and Medical Biology, GRIAC Research InstituteUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Mihai Netea
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
| | - Garry Nolan
- Department of Microbiology and ImmunologyStanford UniversityStanfordUnited States
| | - Dana Pe'er
- Computational and Systems Biology ProgramSloan Kettering InstituteNew YorkUnited States
| | | | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Stephen Quake
- Department of Applied Physics and Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Wolf Reik
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Joshua Sanes
- Center for Brain Science and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
| | - Rahul Satija
- Department of BiologyNew York UniversityNew YorkUnited States
- New York Genome CenterNew York UniversityNew YorkUnited States
| | - Ton N Schumacher
- Division of ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Alex Shalek
- Broad Institute of MIT and HarvardCambridgeUnited States
- Institute for Medical Engineering & Science (IMES) and Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | - Ehud Shapiro
- Department of Computer Science and Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Jay W Shin
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Oliver Stegle
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - Michael Stratton
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | | | - Fabian J Theis
- Institute of Computational BiologyGerman Research Center for Environmental Health, Helmholtz Center MunichNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
| | - Matthias Uhlen
- Science for Life Laboratory and Department of ProteomicsKTH Royal Institute of TechnologyStockholmSweden
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityLyngbyDenmark
| | | | - Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Fiona Watt
- Centre for Stem Cells and Regenerative MedicineKing's College LondonLondonUnited Kingdom
| | - Jonathan Weissman
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Department of Cellular & Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biomedical ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Center for RNA Systems BiologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Barbara Wold
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
| | - Ramnik Xavier
- Broad Institute of MIT and HarvardCambridgeUnited States
- Center for Computational and Integrative BiologyMassachusetts General HospitalBostonUnited States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonUnited States
- Center for Microbiome Informatics and TherapeuticsMassachusetts Institute of TechnologyCambridgeUnited States
| | - Nir Yosef
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Human Cell Atlas Meeting Participants
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
- Department of ImmunologyWeizmann Institute of ScienceRehovotIsrael
- Division of Immunology, Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUnited States
- Institute of Molecular Life SciencesUniversity of ZürichZürichSwitzerland
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUnited Kingdom
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center UtrechtUtrechtThe Netherlands
- Institute of Bioengineering, School of Life SciencesSwiss Federal Institute of Technology (EPFL)LausanneSwitzerland
- Department of Systems Pharmacology and Translational TherapeuticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Division of Theoretical Bioinformatics (B080)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuantHeidelberg UniversityHeidelbergGermany
- Department of Biology IILudwig Maximilian University MunichMartinsriedGermany
- Takara Bio United States, Inc.Mountain ViewUnited States
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineJohn Radcliffe Hospital, University of OxfordOxfordUnited Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Massachusetts General Hospital Cancer CenterBostonUnited States
- Institute of Cellular MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
- Departments of Developmental Biology and of MedicineStanford University School of MedicineStanfordUnited States
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Allen Institute for Brain ScienceSeattleUnited States
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
- Science for Life Laboratory, School of BiotechnologyKTH Royal Institute of TechnologyStockholmSweden
- Department of GeneticsStanford UniversityStanfordUnited States
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologyStockholmSweden
- National Institute of Biomedical GenomicsKalyaniIndia
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
- Department of Pathology and Medical Biology, GRIAC Research InstituteUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
- Department of Microbiology and ImmunologyStanford UniversityStanfordUnited States
- Computational and Systems Biology ProgramSloan Kettering InstituteNew YorkUnited States
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
- Department of Applied Physics and Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUnited Kingdom
- Center for Brain Science and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
- Department of BiologyNew York UniversityNew YorkUnited States
- New York Genome CenterNew York UniversityNew YorkUnited States
- Division of ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Institute for Medical Engineering & Science (IMES) and Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Computer Science and Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
- Institute of Computational BiologyGerman Research Center for Environmental Health, Helmholtz Center MunichNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
- Science for Life Laboratory and Department of ProteomicsKTH Royal Institute of TechnologyStockholmSweden
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityLyngbyDenmark
- Hubrecht Institute and University Medical Center UtrechtUtrechtThe Netherlands
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Centre for Stem Cells and Regenerative MedicineKing's College LondonLondonUnited Kingdom
- Department of Cellular & Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biomedical ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Center for RNA Systems BiologyUniversity of California, San FranciscoSan FranciscoUnited States
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
- Center for Computational and Integrative BiologyMassachusetts General HospitalBostonUnited States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonUnited States
- Center for Microbiome Informatics and TherapeuticsMassachusetts Institute of TechnologyCambridgeUnited States
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263
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Afik S, Yates KB, Bi K, Darko S, Godec J, Gerdemann U, Swadling L, Douek DC, Klenerman P, Barnes EJ, Sharpe AH, Haining WN, Yosef N. Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state. Nucleic Acids Res 2017; 45:e148. [PMID: 28934479 PMCID: PMC5766189 DOI: 10.1093/nar/gkx615] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/12/2017] [Indexed: 12/19/2022] Open
Abstract
The T cell compartment must contain diversity in both T cell receptor (TCR) repertoire and cell state to provide effective immunity against pathogens. However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell state. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current methods for TCR inference from scRNA-seq are limited in their sensitivity and require long sequencing reads, thus increasing the cost and decreasing the number of cells that can be feasibly analyzed. Here we present TRAPeS, a publicly available tool that can efficiently extract TCR sequence information from short-read scRNA-seq libraries. We apply it to investigate heterogeneity in the CD8+ T cell response in humans and mice, and show that it is accurate and more sensitive than existing approaches. Coupling TRAPeS with transcriptome analysis of CD8+ T cells specific for a single epitope from Yellow Fever Virus (YFV), we show that the recently described ‘naive-like’ memory population have significantly longer CDR3 regions and greater divergence from germline sequence than do effector-memory phenotype cells. This suggests that TCR usage is associated with the differentiation state of the CD8+ T cell response to YFV.
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Affiliation(s)
- Shaked Afik
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Kathleen B Yates
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kevin Bi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Samuel Darko
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Jernej Godec
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Ulrike Gerdemann
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Leo Swadling
- Translational Gastroenterology Unit, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Paul Klenerman
- Translational Gastroenterology Unit, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Eleanor J Barnes
- Translational Gastroenterology Unit, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Arlene H Sharpe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - W Nicholas Haining
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Hematology/Oncology, Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.,Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, MA, USA.,Chan Zuckerberg Biohub
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264
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Oakes T, Heather JM, Best K, Byng-Maddick R, Husovsky C, Ismail M, Joshi K, Maxwell G, Noursadeghi M, Riddell N, Ruehl T, Turner CT, Uddin I, Chain B. Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile. Front Immunol 2017; 8:1267. [PMID: 29075258 PMCID: PMC5643411 DOI: 10.3389/fimmu.2017.01267] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/22/2017] [Indexed: 11/13/2022] Open
Abstract
The T cell receptor (TCR) repertoire can provide a personalized biomarker for infectious and non-infectious diseases. We describe a protocol for amplifying, sequencing, and analyzing TCRs which is robust, sensitive, and versatile. The key experimental step is ligation of a single-stranded oligonucleotide to the 3' end of the TCR cDNA. This allows amplification of all possible rearrangements using a single set of primers per locus. It also introduces a unique molecular identifier to label each starting cDNA molecule. This molecular identifier is used to correct for sequence errors and for effects of differential PCR amplification efficiency, thus producing more accurate measures of the true TCR frequency within the sample. This integrated experimental and computational pipeline is applied to the analysis of human memory and naive subpopulations, and results in consistent measures of diversity and inequality. After error correction, the distribution of TCR sequence abundance in all subpopulations followed a power law over a wide range of values. The power law exponent differed between naïve and memory populations, but was consistent between individuals. The integrated experimental and analysis pipeline we describe is appropriate to studies of T cell responses in a broad range of physiological and pathological contexts.
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Affiliation(s)
- Theres Oakes
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - James M. Heather
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Katharine Best
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Rachel Byng-Maddick
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Connor Husovsky
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Kroopa Joshi
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Gavin Maxwell
- Unilever Safety and Environmental Assurance Centre, Unilever, Sharnbrook, United Kingdom
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Natalie Riddell
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Tabea Ruehl
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Carolin T. Turner
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
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265
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Bolotin DA, Poslavsky S, Davydov AN, Frenkel FE, Fanchi L, Zolotareva OI, Hemmers S, Putintseva EV, Obraztsova AS, Shugay M, Ataullakhanov RI, Rudensky AY, Schumacher TN, Chudakov DM. Antigen receptor repertoire profiling from RNA-seq data. Nat Biotechnol 2017; 35:908-911. [PMID: 29020005 PMCID: PMC6169298 DOI: 10.1038/nbt.3979] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Dmitriy A Bolotin
- MiLaboratory LLC, Skolkovo Innovation Center, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Stanislav Poslavsky
- MiLaboratory LLC, Skolkovo Innovation Center, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | | | | | - Lorenzo Fanchi
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Saskia Hemmers
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Ekaterina V Putintseva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Anna S Obraztsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail Shugay
- MiLaboratory LLC, Skolkovo Innovation Center, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ravshan I Ataullakhanov
- BostonGene LLC, Lincoln, Massachusetts, USA
- Institute of Immunology FMBA, Moscow, Russia
- Faculties for Physics and Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
- Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Dmitriy M Chudakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Brno, Czech Republic
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
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266
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Abstract
PURPOSE OF REVIEW The genetic susceptibility and dominant protection for type 1 diabetes (T1D) associated with human leukocyte antigen (HLA) haplotypes, along with minor risk variants, have long been thought to shape the T cell receptor (TCR) repertoire and eventual phenotype of autoreactive T cells that mediate β-cell destruction. While autoantibodies provide robust markers of disease progression, early studies tracking autoreactive T cells largely failed to achieve clinical utility. RECENT FINDINGS Advances in acquisition of pancreata and islets from T1D organ donors have facilitated studies of T cells isolated from the target tissues. Immunosequencing of TCR α/β-chain complementarity determining regions, along with transcriptional profiling, offers the potential to transform biomarker discovery. Herein, we review recent studies characterizing the autoreactive TCR signature in T1D, emerging technologies, and the challenges and opportunities associated with tracking TCR molecular profiles during the natural history of T1D.
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Affiliation(s)
- Laura M Jacobsen
- Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Amanda Posgai
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Howard R Seay
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Michael J Haller
- Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA.
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267
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Rizzetto S, Eltahla AA, Lin P, Bull R, Lloyd AR, Ho JWK, Venturi V, Luciani F. Impact of sequencing depth and read length on single cell RNA sequencing data of T cells. Sci Rep 2017; 7:12781. [PMID: 28986563 PMCID: PMC5630586 DOI: 10.1038/s41598-017-12989-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/14/2017] [Indexed: 11/12/2022] Open
Abstract
Single cell RNA sequencing (scRNA-seq) provides great potential in measuring the gene expression profiles of heterogeneous cell populations. In immunology, scRNA-seq allowed the characterisation of transcript sequence diversity of functionally relevant T cell subsets, and the identification of the full length T cell receptor (TCRαβ), which defines the specificity against cognate antigens. Several factors, e.g. RNA library capture, cell quality, and sequencing output affect the quality of scRNA-seq data. We studied the effects of read length and sequencing depth on the quality of gene expression profiles, cell type identification, and TCRαβ reconstruction, utilising 1,305 single cells from 8 publically available scRNA-seq datasets, and simulation-based analyses. Gene expression was characterised by an increased number of unique genes identified with short read lengths (<50 bp), but these featured higher technical variability compared to profiles from longer reads. Successful TCRαβ reconstruction was achieved for 6 datasets (81% − 100%) with at least 0.25 millions (PE) reads of length >50 bp, while it failed for datasets with <30 bp reads. Sufficient read length and sequencing depth can control technical noise to enable accurate identification of TCRαβ and gene expression profiles from scRNA-seq data of T cells.
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Affiliation(s)
- Simone Rizzetto
- School of Medical Sciences, UNSW, Sydney, Australia.,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Auda A Eltahla
- School of Medical Sciences, UNSW, Sydney, Australia.,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Peijie Lin
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, UNSW, Sydney, Australia
| | - Rowena Bull
- School of Medical Sciences, UNSW, Sydney, Australia.,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Andrew R Lloyd
- School of Medical Sciences, UNSW, Sydney, Australia.,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Joshua W K Ho
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, UNSW, Sydney, Australia
| | - Vanessa Venturi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Fabio Luciani
- School of Medical Sciences, UNSW, Sydney, Australia. .,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia.
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268
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Stubbington MJT, Rozenblatt-Rosen O, Regev A, Teichmann SA. Single-cell transcriptomics to explore the immune system in health and disease. Science 2017; 358:58-63. [PMID: 28983043 PMCID: PMC5654495 DOI: 10.1126/science.aan6828] [Citation(s) in RCA: 337] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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.
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Affiliation(s)
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
- Howard Hughes Medical Institute, Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
- Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, UK
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269
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Miragaia RJ, Teichmann SA, Hagai T. Single-cell insights into transcriptomic diversity in immunity. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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270
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Wang L, Livak KJ, Wu CJ. High-dimension single-cell analysis applied to cancer. Mol Aspects Med 2017; 59:70-84. [PMID: 28823596 DOI: 10.1016/j.mam.2017.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/10/2017] [Accepted: 08/16/2017] [Indexed: 12/14/2022]
Abstract
High-dimension single-cell technology is transforming our ability to study and understand cancer. Numerous studies and reviews have reported advances in technology development. The biological insights gleaned from single-cell technology about cancer biology are less reviewed. Here we focus on research studies that illustrate novel aspects of cancer biology that bulk analysis could not achieve, and discuss the fresh insights gained from the application of single-cell technology across basic and clinical cancer studies.
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Affiliation(s)
- Lili Wang
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
| | - Kenneth J Livak
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
| | - Catherine J Wu
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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271
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Abstract
Systems-biology approaches in immunology take various forms, but here we review strategies for measuring a broad swath of immunological functions as a means of discovering previously unknown relationships and phenomena and as a powerful way of understanding the immune system as a whole. This approach has rejuvenated the field of vaccine development and has fostered hope that new ways will be found to combat infectious diseases that have proven refractory to classical approaches. Systems immunology also presents an important new strategy for understanding human immunity directly, taking advantage of the many ways the immune system of humans can be manipulated.
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272
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Haque A, Engel J, Teichmann SA, Lönnberg T. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Med 2017; 9:75. [PMID: 28821273 PMCID: PMC5561556 DOI: 10.1186/s13073-017-0467-4] [Citation(s) in RCA: 561] [Impact Index Per Article: 80.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing (RNA-seq) is a genomic approach for the detection and quantitative analysis of messenger RNA molecules in a biological sample and is useful for studying cellular responses. RNA-seq has fueled much discovery and innovation in medicine over recent years. For practical reasons, the technique is usually conducted on samples comprising thousands to millions of cells. However, this has hindered direct assessment of the fundamental unit of biology-the cell. Since the first single-cell RNA-sequencing (scRNA-seq) study was published in 2009, many more have been conducted, mostly by specialist laboratories with unique skills in wet-lab single-cell genomics, bioinformatics, and computation. However, with the increasing commercial availability of scRNA-seq platforms, and the rapid ongoing maturation of bioinformatics approaches, a point has been reached where any biomedical researcher or clinician can use scRNA-seq to make exciting discoveries. In this review, we present a practical guide to help researchers design their first scRNA-seq studies, including introductory information on experimental hardware, protocol choice, quality control, data analysis and biological interpretation.
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Affiliation(s)
- Ashraful Haque
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, 4006, Australia.
| | - Jessica Engel
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, 4006, Australia
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tapio Lönnberg
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland.
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273
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Schober K, Busch DH. TIL 2.0: More effective and predictive T-cell products by enrichment for defined antigen specificities. Eur J Immunol 2017; 46:1335-9. [PMID: 27280482 DOI: 10.1002/eji.201646436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 04/17/2016] [Accepted: 04/21/2016] [Indexed: 12/21/2022]
Abstract
Adoptive transfer of in vitro-expanded T cells derived from tumor-infiltrating lymphocytes (TILs) in melanoma patients started the era of tumor immunotherapy three decades ago. The approach has demonstrated remarkable clinical responses in several studies since. Reinfusion of TIL-derived T cells represents a highly personalized form of immunotherapy, taking into account the enormous interindividual tumor heterogeneity. However, despite its successes, TIL therapy does not lead to objective clinical responses in all cases. It is thus crucial to find out which tumor antigens are particularly valuable targets and to develop strategies to enhance the reactivity of T-cell products toward them. In this issue of the European Journal of Immunology, Kelderman et al. [Eur. J. Immunol. 2016. 46: 1351-1360] present a platform for the generation of antigen-specific TIL therapy. Combining recently developed technologies for clinical identification and enrichment of antigen-specific CD8(+) T cells, such as MHC Streptamers and UV-mediated peptide exchange, the authors could enrich T-cell populations with defined antigen specificities from melanoma-derived TILs. This T-cell product showed higher reactivity against autologous tumor cell lines than bulk TIL-derived T cells. The novel platform might enable the generation of more effective and predictable TIL-derived T-cell products for future clinical applications.
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Affiliation(s)
- Kilian Schober
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany.,DZIF - National Centre for Infection Research, Munich, Germany.,Focus Group "Clinical Cell Processing and Purification,", Institute for Advanced Study, Technische Universität München, Munich, Germany
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274
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Li Y, Jang JH, Wang C, He B, Zhang K, Zhang P, Vu T, Qin L. Microfluidics Cell Loading-Dock System: Ordered Cellular Array for Dynamic Lymphocyte-Communication Study. ACTA ACUST UNITED AC 2017; 1:e1700085. [PMID: 32646193 DOI: 10.1002/adbi.201700085] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/12/2017] [Indexed: 12/26/2022]
Abstract
It remains a great challenge to establish a high-throughput platform that can explore the interactions among multiple lymphocytes (>2 cells) and retrieve the interested cells for downstream analysis. This study demonstrates a microfluidics cell loading-dock system (Cell-Dock) to enclose multiple cells in 1D, 2D, and 3D chambers with high throughput and efficiency and single-cell accuracy. The loading efficiencies of 95%, 85%, and 74% for one-, three-, and five-cell systems are achieved, respectively. The Cell-Dock system provides precise and dynamic cell packing models to facilitate lymphocyte-interaction studies. The results demonstrate that individual natural killer (NK) cells may function independently rather than cooperate to lyse target cells in the defined microenvironment. Furthermore, the strong/weak NK cells are retrieved based on their on-chip cytotoxicity and mRNA sequencing is conducted to find the possible mechanisms for "serial killing," an important but unsolved issue. This study finds that the stronger NK cells overexpress multiple genes involved in cytotoxicity and adhesion molecules (including the well-known ICAM1 and seldom reported B4GALT1) might play important roles in the regulation of NK cytolysis.
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Affiliation(s)
- Ying Li
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX, 77030, USA.,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Joon Hee Jang
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX, 77030, USA.,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Crystal Wang
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX, 77030, USA.,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Bangshun He
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX, 77030, USA.,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA.,Central Laboratory, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China
| | - Kai Zhang
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX, 77030, USA.,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Pengchao Zhang
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX, 77030, USA.,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Timothy Vu
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX, 77030, USA.,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA.,Department of Bioengineering, Rice University, Houston, TX, 77005, USA
| | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX, 77030, USA.,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA
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275
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Papalexi E, Satija R. Single-cell RNA sequencing to explore immune cell heterogeneity. Nat Rev Immunol 2017; 18:35-45. [DOI: 10.1038/nri.2017.76] [Citation(s) in RCA: 692] [Impact Index Per Article: 98.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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276
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Zheng C, Zheng L, Yoo JK, Guo H, Zhang Y, Guo X, Kang B, Hu R, Huang JY, Zhang Q, Liu Z, Dong M, Hu X, Ouyang W, Peng J, Zhang Z. Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing. Cell 2017. [PMID: 28622514 DOI: 10.1016/j.cell.2017.05.035] [Citation(s) in RCA: 1349] [Impact Index Per Article: 192.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. Here, we perform deep single-cell RNA sequencing on 5,063 single T cells isolated from peripheral blood, tumor, and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional profiles of these individual cells, coupled with assembled T cell receptor (TCR) sequences, enable us to identify 11 T cell subsets based on their molecular and functional properties and delineate their developmental trajectory. Specific subsets such as exhausted CD8+ T cells and Tregs are preferentially enriched and potentially clonally expanded in hepatocellular carcinoma (HCC), and we identified signature genes for each subset. One of the genes, layilin, is upregulated on activated CD8+ T cells and Tregs and represses the CD8+ T cell functions in vitro. This compendium of transcriptome data provides valuable insights and a rich resource for understanding the immune landscape in cancers.
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Affiliation(s)
- Chunhong Zheng
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Liangtao Zheng
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jae-Kwang Yoo
- Department of Inflammation and Oncology, Amgen Inc., South San Francisco, CA 94080, USA
| | - Huahu Guo
- Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China; Ninth School of Clinical Medicine, Peking University, Beijing 100038, China; School of Oncology, Capital Medical University, Beijing 100038, China
| | - Yuanyuan Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xinyi Guo
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Boxi Kang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Ruozhen Hu
- Department of Inflammation and Oncology, Amgen Inc., South San Francisco, CA 94080, USA
| | - Julie Y Huang
- Department of Inflammation and Oncology, Amgen Inc., South San Francisco, CA 94080, USA
| | - Qiming Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhouzerui Liu
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Minghui Dong
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueda Hu
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenjun Ouyang
- Department of Inflammation and Oncology, Amgen Inc., South San Francisco, CA 94080, USA.
| | - Jirun Peng
- Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China; Ninth School of Clinical Medicine, Peking University, Beijing 100038, China; School of Oncology, Capital Medical University, Beijing 100038, China.
| | - Zemin Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
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277
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Rosati E, Dowds CM, Liaskou E, Henriksen EKK, Karlsen TH, Franke A. Overview of methodologies for T-cell receptor repertoire analysis. BMC Biotechnol 2017; 17:61. [PMID: 28693542 PMCID: PMC5504616 DOI: 10.1186/s12896-017-0379-9] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/26/2017] [Indexed: 12/13/2022] Open
Abstract
Background The T-cell receptor (TCR), located on the surface of T cells, is responsible for the recognition of the antigen-major histocompatibility complex, leading to the initiation of an inflammatory response. Analysing the TCR repertoire may help to gain a better understanding of the immune system features and of the aetiology and progression of diseases, in particular those with unknown antigenic triggers. The extreme diversity of the TCR repertoire represents a major analytical challenge; this has led to the development of specialized methods which aim to characterize the TCR repertoire in-depth. Currently, next generation sequencing based technologies are most widely employed for the high-throughput analysis of the immune cell repertoire. Results Here, we report on the latest methodological advancements in the field by describing and comparing the available tools; from the choice of the starting material and library preparation method, to the sequencing technologies and data analysis. Finally, we provide a practical example and our own experience by reporting some exemplary results from a small internal benchmark study, where current approaches from the literature and the market are employed and compared. Conclusions Several valid methods for clonotype identification and TCR repertoire analysis exist, however, a gold standard method for the field has not yet been identified. Depending on the purpose of the scientific study, some approaches may be more suitable than others. Finally, due to possible method specific biases, scientists must be careful when comparing results obtained using different methods. Electronic supplementary material The online version of this article (doi:10.1186/s12896-017-0379-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Rosati
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany
| | - C Marie Dowds
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany
| | - Evaggelia Liaskou
- Centre for Liver Research and NIHR Birmingham Liver Biomedical Research Unit, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Eva Kristine Klemsdal Henriksen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Tom H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany.
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278
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Behnam Sani K, Sawitzki B. Immune monitoring as prerequisite for transplantation tolerance trials. Clin Exp Immunol 2017; 189:158-170. [PMID: 28518214 DOI: 10.1111/cei.12988] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2017] [Indexed: 02/06/2023] Open
Abstract
Ever since its first application in clinical medicine, scientists have been urged to induce tolerance towards foreign allogeneic transplants and thus avoid rejection by the recipient's immune system. This would circumvent chronic use of immunosuppressive drugs (IS) and thus avoid development of IS-induced side effects, which are contributing to the still unsatisfactory long-term graft and patient survival after solid organ transplantation. Although manifold strategies of tolerance induction have been described in preclinical models, only three therapeutic approaches have been utilized successfully in a still small number of patients. These approaches are based on (i) IS withdrawal in spontaneous operational tolerant (SOT) patients, (ii) induction of a mixed chimerism and (iii) adoptive transfer of regulatory cells. Results of clinical trials utilizing these approaches show that tolerance induction does not work in all patients. Thus, there is a need for reliable biomarkers, which can be used for patient selection and post-therapeutic immune monitoring of safety, success and failure. In this review, we summarize recent achievements in the identification and validation of such immunological assays and biomarkers, focusing mainly on kidney and liver transplantation. From the published findings so far, it has become clear that indicative biomarkers may vary between different therapeutic approaches applied and organs transplanted. Also, patient numbers studied so far are very small. This is the main reason why nearly all described parameters lack validation and reproducibility testing in large clinical trials, and are therefore not yet suitable for clinical practice.
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Affiliation(s)
- K Behnam Sani
- Institute of Medical Immunology, Charité Universitaetsmedizin Berlin, Berlin, Germany
| | - B Sawitzki
- Institute of Medical Immunology, Charité Universitaetsmedizin Berlin, Berlin, Germany
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279
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Wagner A, Regev A, Yosef N. Revealing the vectors of cellular identity with single-cell genomics. Nat Biotechnol 2017; 34:1145-1160. [PMID: 27824854 DOI: 10.1038/nbt.3711] [Citation(s) in RCA: 375] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Single-cell genomics has now made it possible to create a comprehensive atlas of human cells. At the same time, it has reopened definitions of a cell's identity and of the ways in which identity is regulated by the cell's molecular circuitry. Emerging computational analysis methods, especially in single-cell RNA sequencing (scRNA-seq), have already begun to reveal, in a data-driven way, the diverse simultaneous facets of a cell's identity, from discrete cell types to continuous dynamic transitions and spatial locations. These developments will eventually allow a cell to be represented as a superposition of 'basis vectors', each determining a different (but possibly dependent) aspect of cellular organization and function. However, computational methods must also overcome considerable challenges-from handling technical noise and data scale to forming new abstractions of biology. As the scale of single-cell experiments continues to increase, new computational approaches will be essential for constructing and characterizing a reference map of cell identities.
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Affiliation(s)
- Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, California, USA
| | - Aviv Regev
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, California, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, Massachusetts, USA
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280
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Burkholder WF, Newell EW, Poidinger M, Chen S, Fink K. Deep Sequencing in Infectious Diseases: Immune and Pathogen Repertoires for the Improvement of Patient Outcomes. Front Immunol 2017; 8:593. [PMID: 28620372 PMCID: PMC5451494 DOI: 10.3389/fimmu.2017.00593] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/04/2017] [Indexed: 12/17/2022] Open
Abstract
The inaugural workshop “Deep Sequencing in Infectious Diseases: Immune and Pathogen Repertoires for the Improvement of Patient Outcomes” was held in Singapore on 13–14 October 2016. The aim of the workshop was to discuss the latest trends in using high-throughput sequencing, bioinformatics, and allied technologies to analyze immune and pathogen repertoires and their interplay within the host, bringing together key international players in the field and Singapore-based researchers and clinician-scientists. The focus was in particular on the application of these technologies for the improvement of patient diagnosis, prognosis and treatment, and for other broad public health outcomes. The presentations by scientists and clinicians showed the potential of deep sequencing technology to capture the coevolution of adaptive immunity and pathogens. For clinical applications, some key challenges remain, such as the long turnaround time and relatively high cost of deep sequencing for pathogen identification and characterization and the lack of international standardization in immune repertoire analysis.
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Affiliation(s)
- William F Burkholder
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Evan W Newell
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Michael Poidinger
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Swaine Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Katja Fink
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
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281
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Cerosaletti K, Barahmand-Pour-Whitman F, Yang J, DeBerg HA, Dufort MJ, Murray SA, Israelsson E, Speake C, Gersuk VH, Eddy JA, Reijonen H, Greenbaum CJ, Kwok WW, Wambre E, Prlic M, Gottardo R, Nepom GT, Linsley PS. Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4 + T Cells in Peripheral Blood of Subjects with Type 1 Diabetes. THE JOURNAL OF IMMUNOLOGY 2017; 199:323-335. [PMID: 28566371 DOI: 10.4049/jimmunol.1700172] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/25/2017] [Indexed: 12/20/2022]
Abstract
The significance of islet Ag-reactive T cells found in peripheral blood of type 1 diabetes (T1D) subjects is unclear, partly because similar cells are also found in healthy control (HC) subjects. We hypothesized that key disease-associated cells would show evidence of prior Ag exposure, inferred from expanded TCR clonotypes, and essential phenotypic properties in their transcriptomes. To test this, we developed single-cell RNA sequencing procedures for identifying TCR clonotypes and transcript phenotypes in individual T cells. We applied these procedures to analysis of islet Ag-reactive CD4+ memory T cells from the blood of T1D and HC individuals after activation with pooled immunodominant islet peptides. We found extensive TCR clonotype sharing in Ag-activated cells, especially from individual T1D subjects, consistent with in vivo T cell expansion during disease progression. The expanded clonotype from one T1D subject was detected at repeat visits spanning >15 mo, demonstrating clonotype stability. Notably, we found no clonotype sharing between subjects, indicating a predominance of "private" TCR specificities. Expanded clones from two T1D subjects recognized distinct IGRP peptides, implicating this molecule as a trigger for CD4+ T cell expansion. Although overall transcript profiles of cells from HC and T1D subjects were similar, profiles from the most expanded clones were distinctive. Our findings demonstrate that islet Ag-reactive CD4+ memory T cells with unique Ag specificities and phenotypes are expanded during disease progression and can be detected by single-cell analysis of peripheral blood.
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Affiliation(s)
- Karen Cerosaletti
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101;
| | | | - Junbao Yang
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Hannah A DeBerg
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Matthew J Dufort
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Sara A Murray
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Elisabeth Israelsson
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Cate Speake
- Diabetes Clinical Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Vivian H Gersuk
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - James A Eddy
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Helena Reijonen
- Diabetes Clinical Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Carla J Greenbaum
- Diabetes Clinical Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - William W Kwok
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Erik Wambre
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Martin Prlic
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and
| | | | - Peter S Linsley
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101;
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282
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Novel Approaches to Analyze Immunoglobulin Repertoires. Trends Immunol 2017; 38:471-482. [PMID: 28566130 DOI: 10.1016/j.it.2017.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/25/2017] [Accepted: 05/04/2017] [Indexed: 11/21/2022]
Abstract
Analysis of immunoglobulin (Ig) repertoires aims to comprehend Ig diversity with the goal of predicting humoral immune responses in the context of infection, vaccination, autoimmunity, and malignancies. The first next-generation sequencing (NGS) analyses of bulk B cell populations dramatically advanced sampling depth over previous low-throughput single-cell-based protocols, albeit at the expense of accuracy and loss of chain-pairing information. In recent years the field has substantially differentiated, with bulk analyses becoming more accurate while single-cell approaches have gained in throughput. Additionally, new platforms striving to combine high throughput and chain pairing have been developed as well as various computational tools for analysis. Here we review the developments of the past 4-5 years and discuss the open challenges.
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283
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Zhu S, Qing T, Zheng Y, Jin L, Shi L. Advances in single-cell RNA sequencing and its applications in cancer research. Oncotarget 2017; 8:53763-53779. [PMID: 28881849 PMCID: PMC5581148 DOI: 10.18632/oncotarget.17893] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/24/2017] [Indexed: 12/13/2022] Open
Abstract
Unlike population-level approaches, single-cell RNA sequencing enables transcriptomic analysis of an individual cell. Through the combination of high-throughput sequencing and bioinformatic tools, single-cell RNA-seq can detect more than 10,000 transcripts in one cell to distinguish cell subsets and dynamic cellular changes. After several years’ development, single-cell RNA-seq can now achieve massively parallel, full-length mRNA sequencing as well as in situ sequencing and even has potential for multi-omic detection. One appealing area of single-cell RNA-seq is cancer research, and it is regarded as a promising way to enhance prognosis and provide more precise target therapy by identifying druggable subclones. Indeed, progresses have been made regarding solid tumor analysis to reveal intratumoral heterogeneity, correlations between signaling pathways, stemness, drug resistance, and tumor architecture shaping the microenvironment. Furthermore, through investigation into circulating tumor cells, many genes have been shown to promote a propensity toward stemness and the epithelial-mesenchymal transition, to enhance anchoring and adhesion, and to be involved in mechanisms of anoikis resistance and drug resistance. This review focuses on advances and progresses of single-cell RNA-seq with regard to the following aspects: 1. Methodologies of single-cell RNA-seq 2. Single-cell isolation techniques 3. Single-cell RNA-seq in solid tumor research 4. Single-cell RNA-seq in circulating tumor cell research 5. Perspectives
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Affiliation(s)
- Sibo Zhu
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Tao Qing
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Yuanting Zheng
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Li Jin
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Leming Shi
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200438, China
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284
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Scaling single-cell genomics from phenomenology to mechanism. Nature 2017; 541:331-338. [PMID: 28102262 DOI: 10.1038/nature21350] [Citation(s) in RCA: 484] [Impact Index Per Article: 69.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/14/2016] [Indexed: 02/08/2023]
Abstract
Three of the most fundamental questions in biology are how individual cells differentiate to form tissues, how tissues function in a coordinated and flexible fashion and which gene regulatory mechanisms support these processes. Single-cell genomics is opening up new ways to tackle these questions by combining the comprehensive nature of genomics with the microscopic resolution that is required to describe complex multicellular systems. Initial single-cell genomic studies provided a remarkably rich phenomenology of heterogeneous cellular states, but transforming observational studies into models of dynamics and causal mechanisms in tissues poses fresh challenges and requires stronger integration of theoretical, computational and experimental frameworks.
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285
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Prakadan SM, Shalek AK, Weitz DA. Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices. Nat Rev Genet 2017; 18:345-361. [PMID: 28392571 DOI: 10.1038/nrg.2017.15] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent advances in cellular profiling have demonstrated substantial heterogeneity in the behaviour of cells once deemed 'identical', challenging fundamental notions of cell 'type' and 'state'. Not surprisingly, these findings have elicited substantial interest in deeply characterizing the diversity, interrelationships and plasticity among cellular phenotypes. To explore these questions, experimental platforms are needed that can extensively and controllably profile many individual cells. Here, microfluidic structures - whether valve-, droplet- or nanowell-based - have an important role because they can facilitate easy capture and processing of single cells and their components, reducing labour and costs relative to conventional plate-based methods while also improving consistency. In this article, we review the current state-of-the-art methodologies with respect to microfluidics for mammalian single-cell 'omics' and discuss challenges and future opportunities.
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Affiliation(s)
- Sanjay M Prakadan
- Institute for Medical Engineering &Science (IMES) and Department of Chemistry, MIT, Cambridge, Massachusetts 02139, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Alex K Shalek
- Institute for Medical Engineering &Science (IMES) and Department of Chemistry, MIT, Cambridge, Massachusetts 02139, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David A Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
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286
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Lane K, Van Valen D, DeFelice MM, Macklin DN, Kudo T, Jaimovich A, Carr A, Meyer T, Pe'er D, Boutet SC, Covert MW. Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation. Cell Syst 2017; 4:458-469.e5. [PMID: 28396000 DOI: 10.1016/j.cels.2017.03.010] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/16/2016] [Accepted: 03/15/2017] [Indexed: 02/02/2023]
Abstract
Signaling proteins display remarkable cell-to-cell heterogeneity in their dynamic responses to stimuli, but the consequences of this heterogeneity remain largely unknown. For instance, the contribution of the dynamics of the innate immune transcription factor nuclear factor κB (NF-κB) to gene expression output is disputed. Here we explore these questions by integrating live-cell imaging approaches with single-cell sequencing technologies. We used this approach to measure both the dynamics of lipopolysaccharide-induced NF-κB activation and the global transcriptional response in the same individual cell. Our results identify multiple, distinct cytokine expression patterns that are correlated with NF-κB activation dynamics, establishing a functional role for NF-κB dynamics in determining cellular phenotypes. Applications of this approach to other model systems and single-cell sequencing technologies have significant potential for discovery, as it is now possible to trace cellular behavior from the initial stimulus, through the signaling pathways, down to genome-wide changes in gene expression, all inside of a single cell.
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Affiliation(s)
- Keara Lane
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - David Van Valen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Mialy M DeFelice
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Derek N Macklin
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Takamasa Kudo
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Ariel Jaimovich
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Ambrose Carr
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Dana Pe'er
- Program in Computational and Systems Biology, Sloan Kettering Institute, New York, NY 10065, USA
| | - Stéphane C Boutet
- R&D Department, Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA 94080, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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287
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Martinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA, Connor F, Stojic L, Rayner TF, Stubbington MJT, Teichmann SA, de la Roche M, Marioni JC, Odom DT. Aging increases cell-to-cell transcriptional variability upon immune stimulation. Science 2017; 355:1433-1436. [PMID: 28360329 PMCID: PMC5405862 DOI: 10.1126/science.aah4115] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 12/07/2016] [Accepted: 02/23/2017] [Indexed: 12/24/2022]
Abstract
Aging is characterized by progressive loss of physiological and cellular functions, but the molecular basis of this decline remains unclear. We explored how aging affects transcriptional dynamics using single-cell RNA sequencing of unstimulated and stimulated naïve and effector memory CD4+ T cells from young and old mice from two divergent species. In young animals, immunological activation drives a conserved transcriptomic switch, resulting in tightly controlled gene expression characterized by a strong up-regulation of a core activation program, coupled with a decrease in cell-to-cell variability. Aging perturbed the activation of this core program and increased expression heterogeneity across populations of cells in both species. These discoveries suggest that increased cell-to-cell transcriptional variability will be a hallmark feature of aging across most, if not all, mammalian tissues.
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Affiliation(s)
- Celia Pilar Martinez-Jimenez
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Nils Eling
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Hung-Chang Chen
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Catalina A Vallejos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- MRC Biostatistics Unit, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK
| | - Aleksandra A Kolodziejczyk
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Frances Connor
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Lovorka Stojic
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Timothy F Rayner
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Michael J T Stubbington
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Maike de la Roche
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - John C Marioni
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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288
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Vieira Braga FA, Teichmann SA, Stubbington MJT. Are cells from a snowman realistic? Cryopreserved tissues as a source for single-cell RNA-sequencing experiments. Genome Biol 2017; 18:54. [PMID: 28340618 PMCID: PMC5364640 DOI: 10.1186/s13059-017-1192-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A recently published study in Genome Biology shows that cells isolated from cryopreserved tissues are a reliable source of genetic material for single-cell RNA-sequencing experiments.Please see related Method article: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1171-9.
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Affiliation(s)
- Felipe A Vieira Braga
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Cavendish Laboratory, Cambridge University, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
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289
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Yosef N, Regev A. Writ large: Genomic dissection of the effect of cellular environment on immune response. Science 2017; 354:64-68. [PMID: 27846493 DOI: 10.1126/science.aaf5453] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cells of the immune system routinely respond to cues from their local environment and feed back to their surroundings through transient responses, choice of differentiation trajectories, plastic changes in cell state, and malleable adaptation to their tissue of residence. Genomic approaches have opened the way for comprehensive interrogation of such orchestrated responses. Focusing on genomic profiling of transcriptional and epigenetic cell states, we discuss how they are applied to investigate immune cells faced with various environmental cues. We highlight some of the emerging principles on the role of dense regulatory circuitry, epigenetic memory, cell type fluidity, and reuse of regulatory modules in achieving and maintaining appropriate responses to a changing environment. These provide a first step toward a systematic understanding of molecular circuits in complex tissues.
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Affiliation(s)
- Nir Yosef
- Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720, USA. .,Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. .,Howard Hughes Medical Institute and Koch Institute of Integrative Cancer Biology, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
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290
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Gonçalves P, Ferrarini M, Molina-Paris C, Lythe G, Vasseur F, Lim A, Rocha B, Azogui O. A new mechanism shapes the naïve CD8 + T cell repertoire: the selection for full diversity. Mol Immunol 2017; 85:66-80. [PMID: 28212502 DOI: 10.1016/j.molimm.2017.01.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 01/16/2017] [Accepted: 01/28/2017] [Indexed: 12/17/2022]
Abstract
During thymic T cell differentiation, TCR repertoires are shaped by negative, positive and agonist selection. In the thymus and in the periphery, repertoires are also shaped by strong inter-clonal and intra-clonal competition to survive death by neglect. Understanding the impact of these events on the T cell repertoire requires direct evaluation of TCR expression in peripheral naïve T cells. Several studies have evaluated TCR diversity, with contradictory results. Some of these studies had intrinsic technical limitations since they used material obtained from T cell pools, preventing the direct evaluation of clonal sizes. Indeed with these approaches, identical TCRs may correspond to different cells expressing the same receptor, or to several amplicons from the same T cell. We here overcame this limitation by evaluating TCRB expression in individual naïve CD8+ T cells. Of the 2269 Tcrb sequences we obtained from 13 mice, 99% were unique. Mathematical analysis of the data showed that the average number of naïve peripheral CD8+ T cells expressing the same TCRB is 1.1 cell. Since TCRA co-expression studies could only increase repertoire diversity, these results reveal that the number of naïve T cells with unique TCRs approaches the number of naïve cells. Since thymocytes undergo multiple rounds of divisions after TCRB rearrangement and 3-5% of thymocytes survive thymic selection events the number of cells expressing the same TCRB was expected to be much higher. Thus, these results suggest a new repertoire selection mechanism, which strongly selects for full TCRB diversity.
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Affiliation(s)
- Pedro Gonçalves
- Lymphocyte Population Biology Unit, CNRS URA 196, Institut Pasteur, Paris, France; INSERM, U1151, CNRS, UMR8253, Faculté de Médecine Paris Descartes, Paris, France.
| | - Marco Ferrarini
- Department of Applied Mathematics, University of Leeds, Leeds LS29JT, UK
| | | | - Grant Lythe
- Department of Applied Mathematics, University of Leeds, Leeds LS29JT, UK
| | - Florence Vasseur
- Lymphocyte Population Biology Unit, CNRS URA 196, Institut Pasteur, Paris, France; INSERM, U1151, CNRS, UMR8253, Faculté de Médecine Paris Descartes, Paris, France
| | - Annik Lim
- Lymphocyte Population Biology Unit, CNRS URA 196, Institut Pasteur, Paris, France
| | - Benedita Rocha
- Lymphocyte Population Biology Unit, CNRS URA 196, Institut Pasteur, Paris, France; INSERM, U1151, CNRS, UMR8253, Faculté de Médecine Paris Descartes, Paris, France.
| | - Orly Azogui
- INSERM, U1151, CNRS, UMR8253, Faculté de Médecine Paris Descartes, Paris, France
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291
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Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MSF, Fogg LG, Nair AS, Liligeto U, Stubbington MJT, Ly LH, Bagger FO, Zwiessele M, Lawrence ND, Souza-Fonseca-Guimaraes F, Bunn PT, Engwerda CR, Heath WR, Billker O, Stegle O, Haque A, Teichmann SA. Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria. Sci Immunol 2017; 2:eaal2192. [PMID: 28345074 PMCID: PMC5365145 DOI: 10.1126/sciimmunol.aal2192] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Differentiation of naïve CD4+ T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to extensive heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissection in vivo. By using single-cell transcriptomics and computational analysis using a temporal mixtures of Gaussian processes model, termed GPfates, we reconstructed the developmental trajectories of Th1 and Tfh cells during blood-stage Plasmodium infection in mice. By tracking clonality using endogenous TCR sequences, we first demonstrated that Th1/Tfh bifurcation had occurred at both population and single-clone levels. Next, we identified genes whose expression was associated with Th1 or Tfh fates, and demonstrated a T-cell intrinsic role for Galectin-1 in supporting a Th1 differentiation. We also revealed the close molecular relationship between Th1 and IL-10-producing Tr1 cells in this infection. Th1 and Tfh fates emerged from a highly proliferative precursor that upregulated aerobic glycolysis and accelerated cell cycling as cytokine expression began. Dynamic gene expression of chemokine receptors around bifurcation predicted roles for cell-cell in driving Th1/Tfh fates. In particular, we found that precursor Th cells were coached towards a Th1 but not a Tfh fate by inflammatory monocytes. Thus, by integrating genomic and computational approaches, our study has provided two unique resources, a database www.PlasmoTH.org, which facilitates discovery of novel factors controlling Th1/Tfh fate commitment, and more generally, GPfates, a modelling framework for characterizing cell differentiation towards multiple fates.
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Affiliation(s)
- Tapio Lönnberg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Valentine Svensson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kylie R. James
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Daniel Fernandez-Ruiz
- Department of Microbiology and Immunology, The Peter Doherty Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Ismail Sebina
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Ruddy Montandon
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Megan S. F. Soon
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Lily G. Fogg
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Arya Sheela Nair
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Urijah Liligeto
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Michael J. T. Stubbington
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lam-Ha Ly
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Frederik Otzen Bagger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, UK
| | - Max Zwiessele
- Department of Computer Science, University of Sheffield, Sheffield, UK
| | - Neil D. Lawrence
- Department of Computer Science, University of Sheffield, Sheffield, UK
| | | | - Patrick T. Bunn
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | | | - William R. Heath
- Department of Microbiology and Immunology, The Peter Doherty Institute, University of Melbourne, Parkville, Victoria, Australia
- The Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Parkville, Victoria, Australia
| | - Oliver Billker
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ashraful Haque
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Sarah A. Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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292
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Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJT, Cvejic A, Gfeller D. Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types. Genome Res 2017; 27:451-461. [PMID: 28087841 PMCID: PMC5340972 DOI: 10.1101/gr.207704.116] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 01/12/2017] [Indexed: 12/30/2022]
Abstract
The immune system of vertebrate species consists of many different cell types that have distinct functional roles and are subject to different evolutionary pressures. Here, we first analyzed conservation of genes specific for all major immune cell types in human and mouse. Our results revealed higher gene turnover and faster evolution of trans-membrane proteins in NK cells compared with other immune cell types, and especially T cells, but similar conservation of nuclear and cytoplasmic protein coding genes. To validate these findings in a distant vertebrate species, we used single-cell RNA sequencing of lck:GFP cells in zebrafish and obtained the first transcriptome of specific immune cell types in a nonmammalian species. Unsupervised clustering and single-cell TCR locus reconstruction identified three cell populations, T cells, a novel type of NK-like cells, and a smaller population of myeloid-like cells. Differential expression analysis uncovered new immune-cell-specific genes, including novel immunoglobulin-like receptors, and neofunctionalization of recently duplicated paralogs. Evolutionary analyses confirmed the higher gene turnover of trans-membrane proteins in NK cells compared with T cells in fish species, suggesting that this is a general property of immune cell types across all vertebrates.
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Affiliation(s)
- Santiago J Carmona
- Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Sarah A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Lauren Ferreira
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
- Wellcome Trust-Medical Research Council, Cambridge Stem Cell Institute, Cambridge CB2 1QR, United Kingdom
| | - Iain C Macaulay
- Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, United Kingdom
| | - Michael J T Stubbington
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Ana Cvejic
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
- Wellcome Trust-Medical Research Council, Cambridge Stem Cell Institute, Cambridge CB2 1QR, United Kingdom
| | - David Gfeller
- Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
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293
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Lindau P, Robins HS. Advances and applications of immune receptor sequencing in systems immunology. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2016.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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294
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Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing. PLoS Comput Biol 2017; 13:e1005313. [PMID: 28103239 PMCID: PMC5289640 DOI: 10.1371/journal.pcbi.1005313] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 02/02/2017] [Accepted: 12/15/2016] [Indexed: 12/20/2022] Open
Abstract
Characterisation of the T cell receptors (TCR) involved in immune responses is important for the design of vaccines and immunotherapies for cancer and autoimmune disease. The specificity of the interaction between the TCR heterodimer and its peptide-MHC ligand derives largely from the juxtaposed hypervariable CDR3 regions on the TCRα and TCRβ chains, and obtaining the paired sequences of these regions is a standard for functionally defining the TCR. A brute force approach to identifying the TCRs in a population of T cells is to use high-throughput single-cell sequencing, but currently this process remains costly and risks missing small clones. Alternatively, CDR3α and CDR3β sequences can be associated using their frequency of co-occurrence in independent samples, but this approach can be confounded by the sharing of CDR3α and CDR3β across clones, commonly observed within epitope-specific T cell populations. The accurate, exhaustive, and economical recovery of TCR sequences from such populations therefore remains a challenging problem. Here we describe an algorithm for performing frequency-based pairing (alphabetr) that accommodates CDR3α- and CDR3β-sharing, cells expressing two TCRα chains, and multiple forms of sequencing error. The algorithm also yields accurate estimates of clonal frequencies.
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295
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Neu KE, Tang Q, Wilson PC, Khan AA. Single-Cell Genomics: Approaches and Utility in Immunology. Trends Immunol 2017; 38:140-149. [PMID: 28094102 DOI: 10.1016/j.it.2016.12.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/03/2016] [Accepted: 12/05/2016] [Indexed: 12/27/2022]
Abstract
Single-cell genomics offers powerful tools for studying immune cells, which make it possible to observe rare and intermediate cell states that cannot be resolved at the population level. Advances in computer science and single-cell sequencing technology have created a data-driven revolution in immunology. The challenge for immunologists is to harness computing and turn an avalanche of quantitative data into meaningful discovery of immunological principles, predictive models, and strategies for therapeutics. Here, we review the current literature on computational analysis of single-cell RNA-sequencing data and discuss underlying assumptions, methods, and applications in immunology, and highlight important directions for future research.
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Affiliation(s)
- Karlynn E Neu
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Qingming Tang
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Patrick C Wilson
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Aly A Khan
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA.
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296
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Identification of Small-Molecule Inducers of FOXP3 in Human T Cells Using High-Throughput Flow Cytometry. SINGLE CELL ANALYSIS 2017. [DOI: 10.1007/978-981-10-4499-1_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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297
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Seay HR, Yusko E, Rothweiler SJ, Zhang L, Posgai AL, Campbell-Thompson M, Vignali M, Emerson RO, Kaddis JS, Ko D, Nakayama M, Smith MJ, Cambier JC, Pugliese A, Atkinson MA, Robins HS, Brusko TM. Tissue distribution and clonal diversity of the T and B cell repertoire in type 1 diabetes. JCI Insight 2016; 1:e88242. [PMID: 27942583 DOI: 10.1172/jci.insight.88242] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The adaptive immune repertoire plays a critical role in type 1 diabetes (T1D) pathogenesis. However, efforts to characterize B cell and T cell receptor (TCR) profiles in T1D subjects have been largely limited to peripheral blood sampling and restricted to known antigens. To address this, we collected pancreatic draining lymph nodes (pLN), "irrelevant" nonpancreatic draining lymph nodes, peripheral blood mononuclear cells (PBMC), and splenocytes from T1D subjects (n = 18) and control donors (n = 9) as well as pancreatic islets from 1 T1D patient; from these tissues, we collected purified CD4+ conventional T cells (Tconv), CD4+ Treg, CD8+ T cells, and B cells. By conducting high-throughput immunosequencing of the TCR β chain (TRB) and B cell receptor (BCR) immunoglobulin heavy chain (IGH) on these samples, we sought to analyze the molecular signature of the lymphocyte populations within these tissues and of T1D. Ultimately, we observed a highly tissue-restricted CD4+ repertoire, while up to 24% of CD8+ clones were shared among tissues. We surveyed our data set for previously described proinsulin- and glutamic acid decarboxylase 65-reactive (GAD65-reactive) receptors, and interestingly, we observed a TRB with homology to a known GAD65-reactive TCR (clone GAD4.13) present in 7 T1D donors (38.9%), representing >25% of all productive TRB within Tconv isolated from the pLN of 1 T1D subject. These data demonstrate diverse receptor signatures at the nucleotide level and enriched autoreactive clones at the amino acid level, supporting the utility of coupling immunosequencing data with knowledge of characterized autoreactive receptors.
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Affiliation(s)
- Howard R Seay
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA
| | - Erik Yusko
- Adaptive Biotechnologies Corporation, Seattle, Washington, USA
| | - Stephanie J Rothweiler
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA
| | - Lin Zhang
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA
| | - Amanda L Posgai
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA
| | - Marissa Vignali
- Adaptive Biotechnologies Corporation, Seattle, Washington, USA
| | - Ryan O Emerson
- Adaptive Biotechnologies Corporation, Seattle, Washington, USA
| | - John S Kaddis
- Department of Information Sciences, City of Hope National Medical Center, Duarte, California, USA
| | - Dave Ko
- Department of Information Sciences, City of Hope National Medical Center, Duarte, California, USA
| | | | - Mia J Smith
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - John C Cambier
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Alberto Pugliese
- Diabetes Research Institute and Departments of Medicine, Microbiology, and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA
| | - Harlan S Robins
- Adaptive Biotechnologies Corporation, Seattle, Washington, USA.,Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA
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298
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Zilionis R, Nainys J, Veres A, Savova V, Zemmour D, Klein AM, Mazutis L. Single-cell barcoding and sequencing using droplet microfluidics. Nat Protoc 2016; 12:44-73. [PMID: 27929523 DOI: 10.1038/nprot.2016.154] [Citation(s) in RCA: 434] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Single-cell RNA sequencing has recently emerged as a powerful tool for mapping cellular heterogeneity in diseased and healthy tissues, yet high-throughput methods are needed for capturing the unbiased diversity of cells. Droplet microfluidics is among the most promising candidates for capturing and processing thousands of individual cells for whole-transcriptome or genomic analysis in a massively parallel manner with minimal reagent use. We recently established a method called inDrops, which has the capability to index >15,000 cells in an hour. A suspension of cells is first encapsulated into nanoliter droplets with hydrogel beads (HBs) bearing barcoding DNA primers. Cells are then lysed and mRNA is barcoded (indexed) by a reverse transcription (RT) reaction. Here we provide details for (i) establishing an inDrops platform (1 d); (ii) performing hydrogel bead synthesis (4 d); (iii) encapsulating and barcoding cells (1 d); and (iv) RNA-seq library preparation (2 d). inDrops is a robust and scalable platform, and it is unique in its ability to capture and profile >75% of cells in even very small samples, on a scale of thousands or tens of thousands of cells.
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Affiliation(s)
- Rapolas Zilionis
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Juozas Nainys
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Adrian Veres
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Virginia Savova
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - David Zemmour
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Linas Mazutis
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
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299
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Abstract
The human immune system is highly variable between individuals but relatively stable over time within a given person. Recent conceptual and technological advances have enabled systems immunology analyses, which reveal the composition of immune cells and proteins in populations of healthy individuals. The range of variation and some specific influences that shape an individual's immune system is now becoming clearer. Human immune systems vary as a consequence of heritable and non-heritable influences, but symbiotic and pathogenic microbes and other non-heritable influences explain most of this variation. Understanding when and how such influences shape the human immune system is key for defining metrics of immunological health and understanding the risk of immune-mediated and infectious diseases.
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Affiliation(s)
- Petter Brodin
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institutet, Stockholm 17165, Sweden.,Department of Neonatology, Karolinska University Hospital, Stockholm 14186, Sweden
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine.,Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine.,Howard Hughes Medical Institute, Stanford University School of Medicine, California 94304, USA
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300
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Exploring viral infection using single-cell sequencing. Virus Res 2016; 239:55-68. [PMID: 27816430 DOI: 10.1016/j.virusres.2016.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/31/2022]
Abstract
Single-cell sequencing (SCS) has emerged as a valuable tool to study cellular heterogeneity in diverse fields, including virology. By studying the viral and cellular genome and/or transcriptome, the dynamics of viral infection can be investigated at single cell level. Most studies have explored the impact of cell-to-cell variation on the viral life cycle from the point of view of the virus, by analyzing viral sequences, and from the point of view of the cell, mainly by analyzing the cellular host transcriptome. In this review, we will focus on recent studies that use single-cell sequencing to explore viral diversity and cell variability in response to viral replication.
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