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Hirabayashi Y, Lewis TL, Du Y, Virga DM, Decker AM, Coceano G, Alvelid J, Paul MA, Hamilton S, Kneis P, Takahashi Y, Gaublomme JT, Testa I, Polleux F. Most axonal mitochondria in cortical pyramidal neurons lack mitochondrial DNA and consume ATP. bioRxiv 2024:2024.02.12.579972. [PMID: 38405915 PMCID: PMC10888904 DOI: 10.1101/2024.02.12.579972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
In neurons of the mammalian central nervous system (CNS), axonal mitochondria are thought to be indispensable for supplying ATP during energy-consuming processes such as neurotransmitter release. Here, we demonstrate using multiple, independent, in vitro and in vivo approaches that the majority (~80-90%) of axonal mitochondria in cortical pyramidal neurons (CPNs), lack mitochondrial DNA (mtDNA). Using dynamic, optical imaging analysis of genetically encoded sensors for mitochondrial matrix ATP and pH, we demonstrate that in axons of CPNs, but not in their dendrites, mitochondrial complex V (ATP synthase) functions in a reverse way, consuming ATP and protruding H+ out of the matrix to maintain mitochondrial membrane potential. Our results demonstrate that in mammalian CPNs, axonal mitochondria do not play a major role in ATP supply, despite playing other functions critical to regulating neurotransmission such as Ca2+ buffering.
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Affiliation(s)
- Yusuke Hirabayashi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo; Tokyo, 113-8656, Japan
| | - Tommy L. Lewis
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Yudan Du
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo; Tokyo, 113-8656, Japan
| | - Daniel M. Virga
- Department of Biological Sciences, Columbia University; New York, NY, 10027, USA
- Department of Neuroscience, Columbia University; New York, NY, 10027, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University; New York, NY, 10027, USA
| | - Aubrianna M. Decker
- Department of Biological Sciences, Columbia University; New York, NY, 10027, USA
| | - Giovanna Coceano
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jonatan Alvelid
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Biophysical Imaging, Leibniz Institute of Photonic Technology, Jena, Germany
| | - Maëla A. Paul
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University; New York, NY, 10027, USA
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL; Paris, France
| | - Stevie Hamilton
- Department of Neuroscience, Columbia University; New York, NY, 10027, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University; New York, NY, 10027, USA
| | - Parker Kneis
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Yasufumi Takahashi
- Department of Electronics, Graduate School of Engineering, Nagoya University, 464-8603, Nagoya, Japan
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920–1192 Japan
| | - Jellert T. Gaublomme
- Department of Biological Sciences, Columbia University; New York, NY, 10027, USA
| | - Ilaria Testa
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Franck Polleux
- Department of Neuroscience, Columbia University; New York, NY, 10027, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University; New York, NY, 10027, USA
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2
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Gu J, Iyer A, Wesley B, Taglialatela A, Leuzzi G, Hangai S, Decker A, Gu R, Klickstein N, Shuai Y, Jankovic K, Parker-Burns L, Jin Y, Zhang JY, Hong J, Niu S, Chou J, Landau DA, Azizi E, Chan EM, Ciccia A, Gaublomme JT. CRISPRmap: Sequencing-free optical pooled screens mapping multi-omic phenotypes in cells and tissue. bioRxiv 2023:2023.12.26.572587. [PMID: 38234835 PMCID: PMC10793456 DOI: 10.1101/2023.12.26.572587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Pooled genetic screens are powerful tools to study gene function in a high-throughput manner. Typically, sequencing-based screens require cell lysis, which limits the examination of critical phenotypes such as cell morphology, protein subcellular localization, and cell-cell/tissue interactions. In contrast, emerging optical pooled screening methods enable the investigation of these spatial phenotypes in response to targeted CRISPR perturbations. In this study, we report a multi-omic optical pooled CRISPR screening method, which we have named CRISPRmap. Our method combines a novel in situ CRISPR guide identifying barcode readout approach with concurrent multiplexed immunofluorescence and in situ RNA detection. CRISPRmap barcodes are detected and read out through combinatorial hybridization of DNA oligos, enhancing barcode detection efficiency, while reducing both dependency on third party proprietary sequencing reagents and assay cost. Notably, we conducted a multi-omic base-editing screen in a breast cancer cell line on core DNA damage repair genes involved in the homologous recombination and Fanconi anemia pathways investigating how nucleotide variants in those genes influence DNA damage signaling and cell cycle regulation following treatment with ionizing radiation or DNA damaging agents commonly used for cancer therapy. Approximately a million cells were profiled with our multi-omic approach, providing a comprehensive phenotypic assessment of the functional consequences of the studied variants. CRISPRmap enabled us to pinpoint likely-pathogenic patient-derived mutations that were previously classified as variants of unknown clinical significance. Furthermore, our approach effectively distinguished barcodes of a pooled library in tumor tissue, and we coupled it with cell-type and molecular phenotyping by cyclic immunofluorescence. Multi-omic spatial analysis of how CRISPR-perturbed cells respond to various environmental cues in the tissue context offers the potential to significantly expand our understanding of tissue biology in both health and disease.
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Affiliation(s)
- Jiacheng Gu
- Department of Biological Sciences, Columbia University, NY, USA
| | - Abhishek Iyer
- Department of Biological Sciences, Columbia University, NY, USA
| | - Ben Wesley
- Department of Biological Sciences, Columbia University, NY, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Columbia University Irving Medical Center, NY, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Columbia University Irving Medical Center, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
- Institute for Cancer Genetics, Columbia University Irving Medical Center, NY, USA
| | - Sho Hangai
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
| | | | - Ruoyu Gu
- Department of Biological Sciences, Columbia University, NY, USA
| | | | - Yuanlong Shuai
- Department of Biological Sciences, Columbia University, NY, USA
| | - Kristina Jankovic
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
| | - Lucy Parker-Burns
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
| | - Yinuo Jin
- Department of Biomedical Engineering, Columbia University, NY, USA
| | - Jia Yi Zhang
- Department of Biomedical Engineering, Columbia University, NY, USA
| | - Justin Hong
- Department of Computer Science, Columbia University, NY, USA
| | - Steve Niu
- Weill Cornell Medicine, NY, USA
- Genentech Research and Early Development, CA, USA
| | - Jacqueline Chou
- Department of Biological Sciences, Columbia University, NY, USA
- Weill Cornell Medicine, NY, USA
| | - Dan A. Landau
- Weill Cornell Medicine, NY, USA
- New York Genome Center, NY, USA
| | - Elham Azizi
- Department of Biomedical Engineering, Columbia University, NY, USA
- Department of Computer Science, Columbia University, NY, USA
- Irving Institute for Cancer Dynamics, Columbia University, NY, USA
| | - Edmond M. Chan
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
- New York Genome Center, NY, USA
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, NY, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
- Institute for Cancer Genetics, Columbia University Irving Medical Center, NY, USA
| | - Jellert T. Gaublomme
- Department of Biological Sciences, Columbia University, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
- New York Genome Center, NY, USA
- Irving Institute for Cancer Dynamics, Columbia University, NY, USA
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3
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Zilbauer M, James KR, Kaur M, Pott S, Li Z, Burger A, Thiagarajah JR, Burclaff J, Jahnsen FL, Perrone F, Ross AD, Matteoli G, Stakenborg N, Sujino T, Moor A, Bartolome-Casado R, Bækkevold ES, Zhou R, Xie B, Lau KS, Din S, Magness ST, Yao Q, Beyaz S, Arends M, Denadai-Souza A, Coburn LA, Gaublomme JT, Baldock R, Papatheodorou I, Ordovas-Montanes J, Boeckxstaens G, Hupalowska A, Teichmann SA, Regev A, Xavier RJ, Simmons A, Snyder MP, Wilson KT. A Roadmap for the Human Gut Cell Atlas. Nat Rev Gastroenterol Hepatol 2023; 20:597-614. [PMID: 37258747 PMCID: PMC10527367 DOI: 10.1038/s41575-023-00784-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/14/2023] [Indexed: 06/02/2023]
Abstract
The number of studies investigating the human gastrointestinal tract using various single-cell profiling methods has increased substantially in the past few years. Although this increase provides a unique opportunity for the generation of the first comprehensive Human Gut Cell Atlas (HGCA), there remains a range of major challenges ahead. Above all, the ultimate success will largely depend on a structured and coordinated approach that aligns global efforts undertaken by a large number of research groups. In this Roadmap, we discuss a comprehensive forward-thinking direction for the generation of the HGCA on behalf of the Gut Biological Network of the Human Cell Atlas. Based on the consensus opinion of experts from across the globe, we outline the main requirements for the first complete HGCA by summarizing existing data sets and highlighting anatomical regions and/or tissues with limited coverage. We provide recommendations for future studies and discuss key methodologies and the importance of integrating the healthy gut atlas with related diseases and gut organoids. Importantly, we critically overview the computational tools available and provide recommendations to overcome key challenges.
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Affiliation(s)
- Matthias Zilbauer
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- University Department of Paediatrics, University of Cambridge, Cambridge, UK.
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Cambridge, UK.
| | - Kylie R James
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mandeep Kaur
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Sebastian Pott
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zhixin Li
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Albert Burger
- Department of Computer Science, Heriot-watt University, Edinburgh, UK
| | - Jay R Thiagarajah
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University', Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Frode L Jahnsen
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Francesca Perrone
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- University Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Alexander D Ross
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- University Department of Paediatrics, University of Cambridge, Cambridge, UK
- University Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Gianluca Matteoli
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Nathalie Stakenborg
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Tomohisa Sujino
- Center for the Diagnostic and Therapeutic Endoscopy, School of Medicine, Keio University, Tokyo, Japan
| | - Andreas Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Raquel Bartolome-Casado
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, UK
| | - Espen S Bækkevold
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ran Zhou
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Bingqing Xie
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shahida Din
- Edinburgh IBD Unit, Western General Hospital, NHS Lothian, Edinburgh, UK
| | - Scott T Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University', Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qiuming Yao
- Department of Computer Science and Engineering, University of Nebraska Lincoln, Lincoln, NE, USA
| | - Semir Beyaz
- Cold Spring Harbour Laboratory, Cold Spring Harbour, New York, NY, USA
| | - Mark Arends
- Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, Institute of Cancer and Genetics, University of Edinburgh, Edinburgh, UK
| | - Alexandre Denadai-Souza
- Laboratory of Mucosal Biology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Lori A Coburn
- Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | | | | | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Guy Boeckxstaens
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | | | - Sarah A Teichmann
- Wellcome Sanger Institute, Hinxton, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK
| | - Aviv Regev
- Genentech, San Francisco, CA, USA
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ramnik J Xavier
- Broad Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Alison Simmons
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Keith T Wilson
- Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
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4
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Gaublomme JT, Li B, McCabe C, Knecht A, Yang Y, Drokhlyansky E, Van Wittenberghe N, Waldman J, Dionne D, Nguyen L, De Jager PL, Yeung B, Zhao X, Habib N, Rozenblatt-Rosen O, Regev A. Nuclei multiplexing with barcoded antibodies for single-nucleus genomics. Nat Commun 2019; 10:2907. [PMID: 31266958 DOI: 10.1101/476036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/22/2019] [Indexed: 05/24/2023] Open
Abstract
Single-nucleus RNA-seq (snRNA-seq) enables the interrogation of cellular states in complex tissues that are challenging to dissociate or are frozen, and opens the way to human genetics studies, clinical trials, and precise cell atlases of large organs. However, such applications are currently limited by batch effects, processing, and costs. Here, we present an approach for multiplexing snRNA-seq, using sample-barcoded antibodies to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter recovered profiles. We develop DemuxEM, a computational tool that detects inter-sample multiplets and assigns singlets to their sample of origin, and validate its accuracy using sex-specific gene expression, species-mixing and natural genetic variation. Our approach will facilitate tissue atlases of isogenic model organisms or from multiple biopsies or longitudinal samples of one donor, and large-scale perturbation screens.
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Affiliation(s)
- Jellert T Gaublomme
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02129, USA
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Abigail Knecht
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Yiming Yang
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02129, USA
| | - Eugene Drokhlyansky
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | | | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Lan Nguyen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Columbia University Medical Center, New York, NY, 10019, USA
| | | | | | - Naomi Habib
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Edmond and Lily Safra Center for Brain Sciences, Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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5
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Rezende RM, da Cunha AP, Kuhn C, Rubino S, M'Hamdi H, Gabriely G, Vandeventer T, Liu S, Cialic R, Pinheiro-Rosa N, Oliveira RP, Gaublomme JT, Obholzer N, Kozubek J, Pochet N, Faria AMC, Weiner HL. Identification and characterization of latency-associated peptide-expressing γδ T cells. Nat Commun 2015; 6:8726. [PMID: 26644347 PMCID: PMC4686827 DOI: 10.1038/ncomms9726] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/24/2015] [Indexed: 02/06/2023] Open
Abstract
γδ T cells are a subset of lymphocytes specialized in protecting the host against pathogens and tumours. Here we describe a subset of regulatory γδ T cells that express the latency-associated peptide (LAP), a membrane-bound TGF-β1. Thymic CD27+IFN-γ+CCR9+α4β7+TCRγδ+ cells migrate to the periphery, particularly to Peyer's patches and small intestine lamina propria, where they upregulate LAP, downregulate IFN-γ via ATF-3 expression and acquire a regulatory phenotype. TCRγδ+LAP+ cells express antigen presentation molecules and function as antigen presenting cells that induce CD4+Foxp3+ regulatory T cells, although TCRγδ+LAP+ cells do not themselves express Foxp3. Identification of TCRγδ+LAP+ regulatory cells provides an avenue for understanding immune regulation and biologic processes linked to intestinal function and disease. Latency-associated peptide (LAP) is a membrane-bound form of TGF-β1. Here the authors show that LAP marks a subset of regulatory γδ T cells with innate gut-homing properties, which present antigen and induce CD4+ Foxp3+ in Peyer's patches and lamina propria.
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Affiliation(s)
- Rafael M Rezende
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Andre P da Cunha
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Chantal Kuhn
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Stephen Rubino
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hanane M'Hamdi
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Rheumatology Unit, Department of Medicine at Karolinska University Hospital, Karolinska Institute, Solna, Stockholm 17177, Sweden
| | - Galina Gabriely
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Tyler Vandeventer
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Shirong Liu
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ron Cialic
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Natalia Pinheiro-Rosa
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31.270-901, Brazil
| | - Rafael P Oliveira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31.270-901, Brazil
| | - Jellert T Gaublomme
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Nikolaus Obholzer
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - James Kozubek
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Nathalie Pochet
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
| | - Ana M C Faria
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31.270-901, Brazil
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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6
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Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, Ding R, Raychowdhury R, Friedman N, Hacohen N, Park H, May AP, Regev A. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature 2014; 510:363-9. [PMID: 24919153 PMCID: PMC4193940 DOI: 10.1038/nature13437] [Citation(s) in RCA: 671] [Impact Index Per Article: 67.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 05/02/2014] [Indexed: 12/23/2022]
Abstract
High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendritic cells spanning several experimental conditions. We find substantial variation between identically stimulated dendritic cells, in both the fraction of cells detectably expressing a given messenger RNA and the transcript's level within expressing cells. Distinct gene modules are characterized by different temporal heterogeneity profiles. In particular, a 'core' module of antiviral genes is expressed very early by a few 'precocious' cells in response to uniform stimulation with a pathogenic component, but is later activated in all cells. By stimulating cells individually in sealed microfluidic chambers, analysing dendritic cells from knockout mice, and modulating secretion and extracellular signalling, we show that this response is coordinated by interferon-mediated paracrine signalling from these precocious cells. Notably, preventing cell-to-cell communication also substantially reduces variability between cells in the expression of an early-induced 'peaked' inflammatory module, suggesting that paracrine signalling additionally represses part of the inflammatory program. Our study highlights the importance of cell-to-cell communication in controlling cellular heterogeneity and reveals general strategies that multicellular populations can use to establish complex dynamic responses.
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Affiliation(s)
- Alex K Shalek
- 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA [3] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [4]
| | - Rahul Satija
- 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2]
| | - Joe Shuga
- 1] Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA [2]
| | - John J Trombetta
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Dave Gennert
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Diana Lu
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Peilin Chen
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA
| | - Rona S Gertner
- 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Jellert T Gaublomme
- 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Nir Yosef
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Schraga Schwartz
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Brian Fowler
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA
| | - Suzanne Weaver
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA
| | - Jing Wang
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA
| | - Xiaohui Wang
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA
| | - Ruihua Ding
- 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Raktima Raychowdhury
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Nir Friedman
- School of Computer Science and Engineering, Hebrew University, 91904 Jerusalem, Israel
| | - Nir Hacohen
- 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Center for Immunology and Inflammatory Diseases & Department of Medicine, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | - Hongkun Park
- 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA [3] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Andrew P May
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA
| | - Aviv Regev
- 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, USA
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7
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Yosef N, Shalek AK, Gaublomme JT, Jin H, Lee Y, Awasthi A, Wu C, Karwacz K, Xiao S, Jorgolli M, Gennert D, Satija R, Shakya A, Lu DY, Trombetta JJ, Pillai MR, Ratcliffe PJ, Coleman ML, Bix M, Tantin D, Park H, Kuchroo VK, Regev A. Dynamic regulatory network controlling TH17 cell differentiation. Nature 2013; 496:461-8. [PMID: 23467089 PMCID: PMC3637864 DOI: 10.1038/nature11981] [Citation(s) in RCA: 493] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 02/05/2013] [Indexed: 12/12/2022]
Abstract
Despite their importance, the molecular circuits that control the differentiation of naïve T cells remain largely unknown. Recent studies that reconstructed regulatory networks in mammalian cells have focused on short-term responses and relied on perturbation-based approaches that cannot be readily applied to primary T cells. Here, we combine transcriptional profiling at high temporal resolution, novel computational algorithms, and innovative nanowire-based tools for performing perturbations in primary T cells to systematically derive and experimentally validate a model of the dynamic regulatory network that controls Th17 differentiation. The network consists of two self-reinforcing, but mutually antagonistic, modules, with 12 novel regulators, whose coupled action may be essential for maintaining the balance between Th17 and other CD4+ T cell subsets. Overall, our study identifies and validates 39 regulatory factors, embeds them within a comprehensive temporal network and reveals its organizational principles, and highlights novel drug targets for controlling Th17 differentiation.
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Affiliation(s)
- Nir Yosef
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
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8
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Na YR, Kim SY, Gaublomme JT, Shalek AK, Jorgolli M, Park H, Yang EG. Probing enzymatic activity inside living cells using a nanowire-cell "sandwich" assay. Nano Lett 2013; 13:153-8. [PMID: 23244056 PMCID: PMC3541459 DOI: 10.1021/nl3037068] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Developing a detailed understanding of enzyme function in the context of an intracellular signal transduction pathway requires minimally invasive methods for probing enzyme activity in situ. Here, we describe a new method for monitoring enzyme activity in living cells by sandwiching live cells between two vertical silicon nanowire (NW) arrays. Specifically, we use the first NW array to immobilize the cells and then present enzymatic substrates intracellularly via the second NW array by utilizing the NWs' ability to penetrate cellular membranes without affecting cells' viability or function. This strategy, when coupled with fluorescence microscopy and mass spectrometry, enables intracellular examination of protease, phosphatase, and protein kinase activities, demonstrating the assay's potential in uncovering the physiological roles of various enzymes.
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Affiliation(s)
- Yu-Ran Na
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, South Korea
| | - So Yeon Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, South Korea
| | - Jellert T. Gaublomme
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Alex K. Shalek
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Marsela Jorgolli
- Department of Physics, Harvard University, 17 Oxford Street, Cambridge, MA 02138, USA
| | - Hongkun Park
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, 17 Oxford Street, Cambridge, MA 02138, USA
| | - Eun Gyeong Yang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, South Korea
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9
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Shalek AK, Gaublomme JT, Wang L, Yosef N, Chevrier N, Andersen MS, Robinson JT, Pochet N, Neuberg D, Gertner R, Amit I, Brown JR, Hacohen N, Regev A, Wu CJ, Park H. Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia. Nano Lett 2012; 12:6498-504. [PMID: 23190424 PMCID: PMC3573729 DOI: 10.1021/nl3042917] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Indexed: 05/10/2023]
Abstract
A circuit level understanding of immune cells and hematological cancers has been severely impeded by a lack of techniques that enable intracellular perturbation without significantly altering cell viability and function. Here, we demonstrate that vertical silicon nanowires (NWs) enable gene-specific manipulation of diverse murine and human immune cells with negligible toxicity. To illustrate the power of the technique, we then apply NW-mediated gene silencing to investigate the role of the Wnt signaling pathway in chronic lymphocytic leukemia (CLL). Remarkably, CLL-B cells from different patients exhibit tremendous heterogeneity in their response to the knockdown of a single gene, LEF1. This functional heterogeneity defines three distinct patient groups not discernible by conventional CLL cytogenetic markers and provides a prognostic indicator for patients' time to first therapy. Analyses of gene expression signatures associated with these functional patient subgroups reveal unique insights into the underlying molecular basis for disease heterogeneity. Overall, our findings suggest a functional classification that can potentially guide the selection of patient-specific therapies in CLL and highlight the opportunities for nanotechnology to drive biological inquiry.
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Affiliation(s)
- Alex K. Shalek
- Department
of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street,
Cambridge, Massachusetts 02138, United States
| | - Jellert T. Gaublomme
- Department
of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street,
Cambridge, Massachusetts 02138, United States
| | - Lili Wang
- Department
of Medicine, Harvard Medical School and Cancer Vaccine Center and Department of
Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
02115, United States
| | - Nir Yosef
- Broad Institute of MIT
and Harvard, 7 Cambridge Center, Cambridge, Massachusetts
02142, United States
| | - Nicolas Chevrier
- Broad Institute of MIT
and Harvard, 7 Cambridge Center, Cambridge, Massachusetts
02142, United States
| | - Mette S. Andersen
- Department
of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street,
Cambridge, Massachusetts 02138, United States
| | - Jacob T. Robinson
- Department
of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street,
Cambridge, Massachusetts 02138, United States
| | - Nathalie Pochet
- Broad Institute of MIT
and Harvard, 7 Cambridge Center, Cambridge, Massachusetts
02142, United States
| | - Donna Neuberg
- Department
of Medicine, Harvard Medical School and Cancer Vaccine Center and Department of
Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
02115, United States
| | - Rona
S. Gertner
- Department
of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street,
Cambridge, Massachusetts 02138, United States
| | - Ido Amit
- Broad Institute of MIT
and Harvard, 7 Cambridge Center, Cambridge, Massachusetts
02142, United States
| | - Jennifer R. Brown
- Department
of Medicine, Harvard Medical School and Cancer Vaccine Center and Department of
Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
02115, United States
| | - Nir Hacohen
- Broad Institute of MIT
and Harvard, 7 Cambridge Center, Cambridge, Massachusetts
02142, United States
| | - Aviv Regev
- Broad Institute of MIT
and Harvard, 7 Cambridge Center, Cambridge, Massachusetts
02142, United States
- Howard
Hughes Medical Institute,
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, United States
| | - Catherine J. Wu
- Department
of Medicine, Harvard Medical School and Cancer Vaccine Center and Department of
Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
02115, United States
| | - Hongkun Park
- Department
of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street,
Cambridge, Massachusetts 02138, United States
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