1
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Sunshine S, Puschnik AS, Replogle JM, Laurie MT, Liu J, Zha BS, Nuñez JK, Byrum JR, McMorrow AH, Frieman MB, Winkler J, Qiu X, Rosenberg OS, Leonetti MD, Ye CJ, Weissman JS, DeRisi JL, Hein MY. Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq. Nat Commun 2023; 14:6245. [PMID: 37803001 PMCID: PMC10558542 DOI: 10.1038/s41467-023-41788-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/15/2023] [Indexed: 10/08/2023] Open
Abstract
Genomic and proteomic screens have identified numerous host factors of SARS-CoV-2, but efficient delineation of their molecular roles during infection remains a challenge. Here we use Perturb-seq, combining genetic perturbations with a single-cell readout, to investigate how inactivation of host factors changes the course of SARS-CoV-2 infection and the host response in human lung epithelial cells. Our high-dimensional data resolve complex phenotypes such as shifts in the stages of infection and modulations of the interferon response. However, only a small percentage of host factors showed such phenotypes upon perturbation. We further identified the NF-κB inhibitor IκBα (NFKBIA), as well as the translation factors EIF4E2 and EIF4H as strong host dependency factors acting early in infection. Overall, our study provides massively parallel functional characterization of host factors of SARS-CoV-2 and quantitatively defines their roles both in virus-infected and bystander cells.
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Affiliation(s)
- Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- University of California, Berkeley-UCSF Joint Graduate Program in Bioengineering, San Francisco, CA, USA
| | - Beth Shoshana Zha
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Janie R Byrum
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | | | - Matthew B Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Juliane Winkler
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Oren S Rosenberg
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
| | - Marco Y Hein
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Medical University of Vienna, Center for Medical Biochemistry, Vienna, Austria.
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2
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Byrum JR, Waltari E, Janson O, Guo SM, Folkesson J, Chhun BB, Vinden J, Ivanov IE, Forst ML, Li H, Larson AG, Blackmon L, Liu Z, Wu W, Ahyong V, Tato CM, McCutcheon KM, Hoh R, Kelly JD, Martin JN, Peluso MJ, Henrich TJ, Deeks SG, Prakash M, Greenhouse B, Mehta SB, Pak JE. MultiSero: An Open-Source Multiplex-ELISA Platform for Measuring Antibody Responses to Infection. Pathogens 2023; 12:671. [PMID: 37242341 PMCID: PMC10221076 DOI: 10.3390/pathogens12050671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
A multiplexed enzyme-linked immunosorbent assay (ELISA) that simultaneously measures antibody binding to multiple antigens can extend the impact of serosurveillance studies, particularly if the assay approaches the simplicity, robustness, and accuracy of a conventional single-antigen ELISA. Here, we report on the development of multiSero, an open-source multiplex ELISA platform for measuring antibody responses to viral infection. Our assay consists of three parts: (1) an ELISA against an array of proteins in a 96-well format; (2) automated imaging of each well of the ELISA array using an open-source plate reader; and (3) automated measurement of optical densities for each protein within the array using an open-source analysis pipeline. We validated the platform by comparing antibody binding to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) antigens in 217 human sera samples, showing high sensitivity (0.978), specificity (0.977), positive predictive value (0.978), and negative predictive value (0.977) for classifying seropositivity, a high correlation of multiSero determined antibody titers with commercially available SARS-CoV-2 antibody tests, and antigen-specific changes in antibody titer dynamics upon vaccination. The open-source format and accessibility of our multiSero platform can contribute to the adoption of multiplexed ELISA arrays for serosurveillance studies, for SARS-CoV-2 and other pathogens of significance.
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Affiliation(s)
- Janie R. Byrum
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Eric Waltari
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Owen Janson
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, CA 94143, USA
- EPPIcenter Program, University of California, San Francisco, CA 94143, USA
| | - Syuan-Ming Guo
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Jenny Folkesson
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Bryant B. Chhun
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Joanna Vinden
- Infectious Diseases and Immunity Graduate Program, University of California, Berkeley, CA 94720-3370, USA
| | - Ivan E. Ivanov
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Marcus L. Forst
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Hongquan Li
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Adam G. Larson
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Lena Blackmon
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Ziwen Liu
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Wesley Wu
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Vida Ahyong
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - Cristina M. Tato
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | | | - Rebecca Hoh
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, CA 94143, USA
| | - J. Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
| | - Michael J. Peluso
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, CA 94143, USA
| | - Timothy J. Henrich
- Division of Experimental Medicine, University of California, San Francisco, CA 94110, USA
| | - Steven G. Deeks
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, CA 94143, USA
| | - Manu Prakash
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Bryan Greenhouse
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, CA 94143, USA
- EPPIcenter Program, University of California, San Francisco, CA 94143, USA
| | - Shalin B. Mehta
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
| | - John E. Pak
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
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3
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Ivanov IE, Yeh LH, Perez-Bermejo JA, Byrum JR, Kim JYS, Leonetti MD, Mehta SB. Correlative imaging of the spatio-angular dynamics of biological systems with multimodal instant polarization microscope. Biomed Opt Express 2022; 13:3102-3119. [PMID: 35774313 PMCID: PMC9203109 DOI: 10.1364/boe.455770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 05/29/2023]
Abstract
The spatial and angular organization of biological macromolecules is a key determinant, as well as informative readout, of their function. Correlative imaging of the dynamic spatio-angular architecture of cells and organelles is valuable, but remains challenging with current methods. Correlative imaging of spatio-angular dynamics requires fast polarization-, depth-, and wavelength-diverse measurement of intrinsic optical properties and fluorescent labels. We report a multimodal instant polarization microscope (miPolScope) that combines a broadband polarization-resolved detector, automation, and reconstruction algorithms to enable label-free imaging of phase, retardance, and orientation, multiplexed with fluorescence imaging of concentration, anisotropy, and orientation of molecules at diffraction-limited resolution and high speed. miPolScope enabled multimodal imaging of myofibril architecture and contractile activity of beating cardiomyocytes, cell and organelle architecture of live HEK293T and U2OS cells, and density and anisotropy of white and grey matter of mouse brain tissue across the visible spectrum. We anticipate these developments in joint quantitative imaging of density and anisotropy to enable new studies in tissue pathology, mechanobiology, and imaging-based screens.
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Affiliation(s)
- Ivan E. Ivanov
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - Li-Hao Yeh
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | | | - Janie R. Byrum
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - James Y. S. Kim
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | | | - Shalin B. Mehta
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
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4
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Merkley SD, Goodfellow SM, Guo Y, Wilton ZER, Byrum JR, Schwalm KC, Dinwiddie DL, Gullapalli RR, Deretic V, Jimenez Hernandez A, Bradfute SB, In JG, Castillo EF. Non-autophagy Role of Atg5 and NBR1 in Unconventional Secretion of IL-12 Prevents Gut Dysbiosis and Inflammation. J Crohns Colitis 2021; 16:259-274. [PMID: 34374750 PMCID: PMC8864635 DOI: 10.1093/ecco-jcc/jjab144] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intestinal myeloid cells play a critical role in balancing intestinal homeostasis and inflammation. Here, we report that expression of the autophagy-related 5 [Atg5] protein in myeloid cells prevents dysbiosis and excessive intestinal inflammation by limiting IL-12 production. Mice with a selective genetic deletion of Atg5 in myeloid cells [Atg5ΔMye] showed signs of dysbiosis preceding colitis, and exhibited severe intestinal inflammation upon colitis induction that was characterised by increased IFNγ production. The exacerbated colitis was linked to excess IL-12 secretion from Atg5-deficient myeloid cells and gut dysbiosis. Restoration of the intestinal microbiota or genetic deletion of IL-12 in Atg5ΔMye mice attenuated the intestinal inflammation in Atg5ΔMye mice. Additionally, Atg5 functions to limit IL-12 secretion through modulation of late endosome [LE] acidity. Last, the autophagy cargo receptor NBR1, which accumulates in Atg5-deficient cells, played a role by delivering IL-12 to LE. In summary, Atg5 expression in intestinal myeloid cells acts as an anti-inflammatory brake to regulate IL-12, thus preventing dysbiosis and uncontrolled IFNγ-driven intestinal inflammation.
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Affiliation(s)
- Seth D Merkley
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Samuel M Goodfellow
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Yan Guo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Zoe E R Wilton
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Janie R Byrum
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Kurt C Schwalm
- Department of Pediatrics, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Darrell L Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences, Albuquerque, NM, USA,Clinical and Translational Science Center, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Rama R Gullapalli
- Department of Pathology, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Vojo Deretic
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences, Albuquerque, NM, USA,Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Anthony Jimenez Hernandez
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Steven B Bradfute
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Julie G In
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA,Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eliseo F Castillo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA,Clinical and Translational Science Center, University of New Mexico Health Sciences, Albuquerque, NM, USA,Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences, Albuquerque, NM, USA,Corresponding author: Eliseo F. Castillo, PhD, Department of Internal Medicine, MSC 10 550, 1 University of New Mexico, Albuquerque, New Mexico 87131, USA.
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5
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Byrum JR, Waltari E, Janson O, Guo SM, Folkesson J, Chhun BB, Vinden J, Ivanov IE, Forst ML, Li H, Larson AG, Wu W, Tato CM, McCutcheon KM, Peluso MJ, Henrich TJ, Deeks SG, Prakash M, Greenhouse B, Pak JE, Mehta SB. multiSero: open multiplex-ELISA platform for analyzing antibody responses to SARS-CoV-2 infection. medRxiv 2021. [PMID: 34013298 PMCID: PMC8132273 DOI: 10.1101/2021.05.07.21249238] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Serology has provided valuable diagnostic and epidemiological data on antibody responses to SARS-CoV-2 in diverse patient cohorts. Deployment of high content, multiplex serology platforms across the world, including in low and medium income countries, can accelerate longitudinal epidemiological surveys. Here we report multiSero, an open platform to enable multiplex serology with up to 48 antigens in a 96-well format. The platform consists of three components: ELISA-array of printed proteins, a commercial or home-built plate reader, and modular python software for automated analysis (pysero). We validate the platform by comparing antibody titers against the SARS-CoV-2 Spike, receptor binding domain (RBD), and nucleocapsid (N) in 114 sera from COVID-19 positive individuals and 87 pre-pandemic COVID-19 negative sera. We report data with both a commercial plate reader and an inexpensive, open plate reader (nautilus). Receiver operating characteristic (ROC) analysis of classification with single antigens shows that Spike and RBD classify positive and negative sera with the highest sensitivity at a given specificity. The platform distinguished positive sera from negative sera when the reactivity of the sera was equivalent to the binding of 1 ng mL−1 RBD-specific monoclonal antibody. We developed normalization and classification methods to pool antibody responses from multiple antigens and multiple experiments. Our results demonstrate a performant and accessible pipeline for multiplexed ELISA ready for multiple applications, including serosurveillance, identification of viral proteins that elicit antibody responses, differential diagnosis of circulating pathogens, and immune responses to vaccines.
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6
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Cannon JL, Moses ME, Byrum JR, Mrass P, Fricke GM, Tasnim H. Modeling T Cell Motion in Tissues During Immune Responses. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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7
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Tasnim H, Fricke GM, Byrum JR, Sotiris JO, Cannon JL, Moses ME. Quantitative Measurement of Naïve T Cell Association With Dendritic Cells, FRCs, and Blood Vessels in Lymph Nodes. Front Immunol 2018; 9:1571. [PMID: 30093900 PMCID: PMC6070610 DOI: 10.3389/fimmu.2018.01571] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/25/2018] [Indexed: 12/25/2022] Open
Abstract
T cells play a vital role in eliminating pathogenic infections. To activate, naïve T cells search lymph nodes (LNs) for dendritic cells (DCs). Positioning and movement of T cells in LNs is influenced by chemokines including CCL21 as well as multiple cell types and structures in the LNs. Previous studies have suggested that T cell positioning facilitates DC colocalization leading to T:DC interaction. Despite the influence chemical signals, cells, and structures can have on naïve T cell positioning, relatively few studies have used quantitative measures to directly compare T cell interactions with key cell types. Here, we use Pearson correlation coefficient (PCC) and normalized mutual information (NMI) to quantify the extent to which naïve T cells spatially associate with DCs, fibroblastic reticular cells (FRCs), and blood vessels in LNs. We measure spatial associations in physiologically relevant regions. We find that T cells are more spatially associated with FRCs than with their ultimate targets, DCs. We also investigated the role of a key motility chemokine receptor, CCR7, on T cell colocalization with DCs. We find that CCR7 deficiency does not decrease naïve T cell association with DCs, in fact, CCR7-/- T cells show slightly higher DC association compared with wild type T cells. By revealing these associations, we gain insights into factors that drive T cell localization, potentially affecting the timing of productive T:DC interactions and T cell activation.
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Affiliation(s)
- Humayra Tasnim
- Moses Biological Computation Laboratory, Department of Computer Science, The University of New Mexico, Albuquerque, NM, United States
| | - G. Matthew Fricke
- Moses Biological Computation Laboratory, Department of Computer Science, The University of New Mexico, Albuquerque, NM, United States
- UNM Center for Advanced Research Computing (CARC), The University of New Mexico, Albuquerque, NM, United States
| | - Janie R. Byrum
- The Cannon Laboratory, Molecular Genetics & Microbiology, The University of New Mexico, Albuquerque, NM, United States
| | - Justyna O. Sotiris
- Moses Biological Computation Laboratory, Department of Computer Science, The University of New Mexico, Albuquerque, NM, United States
| | - Judy L. Cannon
- The Cannon Laboratory, Molecular Genetics & Microbiology, The University of New Mexico, Albuquerque, NM, United States
- Department of Pathology, The University of New Mexico, Albuquerque, NM, United States
- Autophagy, Inflammation, and Metabolism Center of Biomedical Research Excellence, The University of New Mexico, Albuquerque, NM, United States
| | - Melanie E. Moses
- Moses Biological Computation Laboratory, Department of Computer Science, The University of New Mexico, Albuquerque, NM, United States
- Biology Department, The University of New Mexico, Albuquerque, NM, United States
- Santa Fe Institute, Santa Fe, NM, United States
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8
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Mrass P, Oruganti SR, Fricke GM, Tafoya J, Byrum JR, Yang L, Hamilton SL, Miller MJ, Moses ME, Cannon JL. ROCK regulates the intermittent mode of interstitial T cell migration in inflamed lungs. Nat Commun 2017; 8:1010. [PMID: 29044117 PMCID: PMC5647329 DOI: 10.1038/s41467-017-01032-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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: 08/11/2016] [Accepted: 08/14/2017] [Indexed: 12/27/2022] Open
Abstract
Effector T cell migration through tissues can enable control of infection or mediate inflammatory damage. Nevertheless, the molecular mechanisms that regulate migration of effector T cells within the interstitial space of inflamed lungs are incompletely understood. Here, we show T cell migration in a mouse model of acute lung injury with two-photon imaging of intact lung tissue. Computational analysis indicates that T cells migrate with an intermittent mode, switching between confined and almost straight migration, guided by lung-associated vasculature. Rho-associated protein kinase (ROCK) is required for both high-speed migration and straight motion. By contrast, inhibition of Gαi signaling with pertussis toxin affects speed but not the intermittent migration of lung-infiltrating T cells. Computational modeling shows that an intermittent migration pattern balances both search area and the duration of contacts between T cells and target cells. These data identify that ROCK-dependent intermittent T cell migration regulates tissue-sampling during acute lung injury. ROCK is associated with T cell movement in lymph nodes. Here the authors use an LPS lung damage model and two-photon imaging to show that CD8+ T cells in lung tissue engage in ROCK-dependent fast linear migration alternating with bursts of slower confined migration that together optimize contact with target cells.
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Affiliation(s)
- Paulus Mrass
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, MSC 08 4660, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Sreenivasa Rao Oruganti
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, MSC 08 4660, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - G Matthew Fricke
- Department of Computer Science, University of New Mexico, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Justyna Tafoya
- Department of Computer Science, University of New Mexico, 1 University of New Mexico, Albuquerque, NM, 87131, USA.,Department of Mathematics, University of New Mexico, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Janie R Byrum
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, MSC 08 4660, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Lihua Yang
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Samantha L Hamilton
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Mark J Miller
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Melanie E Moses
- Department of Computer Science, University of New Mexico, 1 University of New Mexico, Albuquerque, NM, 87131, USA.,Department of Biology, University of New Mexico, 1 University of New Mexico, Albuquerque, NM, 87131, USA.,External Faculty, Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA
| | - Judy L Cannon
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, MSC 08 4660, 1 University of New Mexico, Albuquerque, NM, 87131, USA.
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9
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Mrass P, Oruganti SR, Byrum JR, Moses ME, Cannon JL. ROCK is essential for directionally persistent migration of CD8+ effector T cells within inflamed lung. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.119.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Recruitment of effector T lymphocytes into peripheral tissues, such as inflamed lung, contributes to an effective protection against infection and cancer. The rate of pathogen detection might be further influenced by the motility of recruited immune cells within three-dimensional tissues. Indeed, recent two-photon studies have shown that effector T cells navigate actively through inflamed lung tissue, but the molecular mechanisms that regulate this process are poorly characterized. Here, we used two-photon imaging of a murine lung treated with endotoxin to quantitatively analyze tissue navigation of lung-infiltrating CD8+ effector T cells. Tracking of individual T cells within inflamed lung tissue for several hours revealed that T cell movement transitions between periods of high directional persistence and confinement. Some T cells also moved in alignment with the vasculature. Treatment with pertussis toxin to inhibit chemokine receptor-dependent Gi-type G protein signaling led to a moderate reduction of the speed of lung-infiltrating T cells. Strikingly, pharmacological inhibition of the molecule ROCK, which promotes cytoskeleton-dependent squeezing through dense environments, led to a pronounced reduction of speed and almost completely abolished directional persistence of lung-infiltrating effector T cells. Together, these results show that migration of lung-infiltrating T cells is fine-tuned by environmental signals and dependent on the cell-intrinsic ROCK-signaling pathway.
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10
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Vinjamoori DV, Byrum JR, Hayes T, Das PK. Challenges and opportunities in the analysis of raffinose oligosaccharides, pentosans, phytate, and glucosinolates. J Anim Sci 2004; 82:319-28. [PMID: 14753376 DOI: 10.2527/2004.821319x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this paper, the status of the analytical technologies for assaying animal antinutritional compounds, such as raffinose oligosaccharides, pentosans, phytic acid, and glucosinolates, is reviewed in terms of selectivity, sensitivity, and sample throughput. The implementation of simplified sample preparation schemes, use of novel separation approaches, and alternate detector technologies are discussed. The challenges and opportunities posed by these assays are highlighted along with the recommendations for best analytical practices.
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Affiliation(s)
- D V Vinjamoori
- Crop Analytics, Monsanto Company, St. Louis, MO 63167, USA.
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