1
|
Zhang Y, Hu J, Zhang X, Liang M, Wang X, Gan D, Li J, Lu X, Wan J, Feng S, Lu X. Protein Signature Differentiating Neutrophils and Myeloid-Derived Suppressor Cells Determined Using a Human Isogenic Cell Line Model and Protein Profiling. Cells 2024; 13:795. [PMID: 38786019 PMCID: PMC11119164 DOI: 10.3390/cells13100795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/01/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) play an essential role in suppressing the antitumor activity of T lymphocytes in solid tumors, thus representing an attractive therapeutic target to enhance the efficacy of immunotherapy. However, the differences in protein expression between MDSCs and their physiological counterparts, particularly polymorphonuclear neutrophils (PMNs), remain inadequately characterized, making the specific identification and targeting of MDSCs difficult. PMNs and PMN-MDSCs share markers such as CD11b+CD14-CD15+/CD66b+, and some MDSC-enriched markers are emerging, such as LOX-1 and CD84. More proteomics studies are needed to identify the signature and markers for MDSCs. Recently, we reported the induced differentiation of isogenic PMNs or MDSCs (referred to as iPMNs and iMDSCs, respectively) from the human promyelocytic cell line HL60. Here, we profiled the global proteomics and membrane proteomics of these cells with quantitative mass spectrometry, which identified a 41-protein signature ("cluster 6") that was upregulated in iMDSCs compared with HL60 and iPMN. We further integrated our cell line-based proteomics data with a published proteomics dataset of normal human primary monocytes and monocyte-derived MDSCs induced by cancer-associated fibroblasts. The analysis identified a 38-protein signature that exhibits an upregulated expression pattern in MDSCs compared with normal monocytes or PMNs. These signatures may provide a hypothesis-generating platform to identify protein biomarkers that phenotypically distinguish MDSCs from their healthy counterparts, as well as potential therapeutic targets that impair MDSCs without harming normal myeloid cells.
Collapse
Affiliation(s)
- Yuting Zhang
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jin Hu
- Mass Spectrometry & Metabolomics Core Facility, Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou 310024, China
| | - Xiashiyao Zhang
- Department of BioHealth Informatics, Luddy School of Informatics, Computing, and Engineering, Indiana University Indianapolis, Indianapolis, IN 46202, USA
| | - Minzhi Liang
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Xuechun Wang
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Dailin Gan
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jun Li
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Xuemin Lu
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jun Wan
- Department of BioHealth Informatics, Luddy School of Informatics, Computing, and Engineering, Indiana University Indianapolis, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Shan Feng
- Mass Spectrometry & Metabolomics Core Facility, Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou 310024, China
| | - Xin Lu
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN 46556, USA
- Tumor Microenvironment and Metastasis Program, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46556, USA
| |
Collapse
|
2
|
von Hardenberg S, Klefenz I, Steinemann D, Di Donato N, Baumann U, Auber B, Klemann C. Current genetic diagnostics in inborn errors of immunity. Front Pediatr 2024; 12:1279112. [PMID: 38659694 PMCID: PMC11039790 DOI: 10.3389/fped.2024.1279112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
New technologies in genetic diagnostics have revolutionized the understanding and management of rare diseases. This review highlights the significant advances and latest developments in genetic diagnostics in inborn errors of immunity (IEI), which encompass a diverse group of disorders characterized by defects in the immune system, leading to increased susceptibility to infections, autoimmunity, autoinflammatory diseases, allergies, and malignancies. Various diagnostic approaches, including targeted gene sequencing panels, whole exome sequencing, whole genome sequencing, RNA sequencing, or proteomics, have enabled the identification of causative genetic variants of rare diseases. These technologies not only facilitated the accurate diagnosis of IEI but also provided valuable insights into the underlying molecular mechanisms. Emerging technologies, currently mainly used in research, such as optical genome mapping, single cell sequencing or the application of artificial intelligence will allow even more insights in the aetiology of hereditary immune defects in the near future. The integration of genetic diagnostics into clinical practice significantly impacts patient care. Genetic testing enables early diagnosis, facilitating timely interventions and personalized treatment strategies. Additionally, establishing a genetic diagnosis is necessary for genetic counselling and prognostic assessments. Identifying specific genetic variants associated with inborn errors of immunity also paved the way for the development of targeted therapies and novel therapeutic approaches. This review emphasizes the challenges related with genetic diagnosis of rare diseases and provides future directions, specifically focusing on IEI. Despite the tremendous progress achieved over the last years, several obstacles remain or have become even more important due to the increasing amount of genetic data produced for each patient. This includes, first and foremost, the interpretation of variants of unknown significance (VUS) in known IEI genes and of variants in genes of unknown significance (GUS). Although genetic diagnostics have significantly contributed to the understanding and management of IEI and other rare diseases, further research, exchange between experts from different clinical disciplines, data integration and the establishment of comprehensive guidelines are crucial to tackle the remaining challenges and maximize the potential of genetic diagnostics in the field of rare diseases, such as IEI.
Collapse
Affiliation(s)
| | - Isabel Klefenz
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Nataliya Di Donato
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Ulrich Baumann
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Bernd Auber
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Christian Klemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
- Department of Pediatric Immunology, Rheumatology and Infectiology, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
| |
Collapse
|
3
|
Petenkova A, Auger SA, Lamb J, Quellier D, Carter C, To OT, Milosevic J, Barghout R, Kugadas A, Lu X, Geddes-McAlister J, Fichorova R, Sykes DB, Distefano MD, Gadjeva M. Prenylcysteine oxidase 1 like protein is required for neutrophil bactericidal activities. Nat Commun 2023; 14:2761. [PMID: 37179332 PMCID: PMC10182992 DOI: 10.1038/s41467-023-38447-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
The bactericidal function of neutrophils is dependent on a myriad of intrinsic and extrinsic stimuli. Using systems immunology approaches we identify microbiome- and infection-induced changes in neutrophils. We focus on investigating the Prenylcysteine oxidase 1 like (Pcyox1l) protein function. Murine and human Pcyox1l proteins share ninety four percent aminoacid homology revealing significant evolutionary conservation and implicating Pcyox1l in mediating important biological functions. Here we show that the loss of Pcyox1l protein results in significant reductions in the mevalonate pathway impacting autophagy and cellular viability under homeostatic conditions. Concurrently, Pcyox1l CRISPRed-out neutrophils exhibit deficient bactericidal properties. Pcyox1l knock-out mice demonstrate significant susceptibility to infection with the gram-negative pathogen Psuedomonas aeruginosa exemplified through increased neutrophil infiltrates, hemorrhaging, and reduced bactericidal functionality. Cumulatively, we ascribe a function to Pcyox1l protein in modulation of the prenylation pathway and suggest connections beween metabolic responses and neutrophil functionality.
Collapse
Affiliation(s)
- Anastasiia Petenkova
- Department of Medicine, Division of Infectious Diseases, Mass General Brigham, Harvard Medical School, Boston, MA, 02115, USA
| | - Shelby A Auger
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jeffrey Lamb
- Department of Medicine, Division of Infectious Diseases, Mass General Brigham, Harvard Medical School, Boston, MA, 02115, USA
| | - Daisy Quellier
- Department of Medicine, Division of Infectious Diseases, Mass General Brigham, Harvard Medical School, Boston, MA, 02115, USA
| | - Cody Carter
- Department of Medicine, Division of Infectious Diseases, Mass General Brigham, Harvard Medical School, Boston, MA, 02115, USA
| | - On Tak To
- Department of Medicine, Division of Infectious Diseases, Mass General Brigham, Harvard Medical School, Boston, MA, 02115, USA
| | - Jelena Milosevic
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Rana Barghout
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Abirami Kugadas
- Department of Medicine, Division of Infectious Diseases, Mass General Brigham, Harvard Medical School, Boston, MA, 02115, USA
| | - Xiaoxiao Lu
- Department of Medicine, Division of Infectious Diseases, Mass General Brigham, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Raina Fichorova
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Mihaela Gadjeva
- Department of Medicine, Division of Infectious Diseases, Mass General Brigham, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard University, Faculty of Arts and Sciences, Cambridge, MA, 02138, USA.
| |
Collapse
|
4
|
Ince LM, Barnoud C, Lutes LK, Pick R, Wang C, Sinturel F, Chen CS, de Juan A, Weber J, Holtkamp SJ, Hergenhan SM, Geddes-McAlister J, Ebner S, Fontannaz P, Meyer B, Vono M, Jemelin S, Dibner C, Siegrist CA, Meissner F, Graw F, Scheiermann C. Influence of circadian clocks on adaptive immunity and vaccination responses. Nat Commun 2023; 14:476. [PMID: 36717561 PMCID: PMC9885059 DOI: 10.1038/s41467-023-35979-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/11/2023] [Indexed: 02/01/2023] Open
Abstract
The adaptive immune response is under circadian control, yet, why adaptive immune reactions continue to exhibit circadian changes over long periods of time is unknown. Using a combination of experimental and mathematical modeling approaches, we show here that dendritic cells migrate from the skin to the draining lymph node in a time-of-day-dependent manner, which provides an enhanced likelihood for functional interactions with T cells. Rhythmic expression of TNF in the draining lymph node enhances BMAL1-controlled ICAM-1 expression in high endothelial venules, resulting in lymphocyte infiltration and lymph node expansion. Lymph node cellularity continues to be different for weeks after the initial time-of-day-dependent challenge, which governs the immune response to vaccinations directed against Hepatitis A virus as well as SARS-CoV-2. In this work, we present a mechanistic understanding of the time-of-day dependent development and maintenance of an adaptive immune response, providing a strategy for using time-of-day to optimize vaccination regimes.
Collapse
Affiliation(s)
- Louise Madeleine Ince
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Division of Pharmacology & Toxicology, College of Pharmacy, University of Texas at Austin, Austin, TX, USA
| | - Coline Barnoud
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Lydia Kay Lutes
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Robert Pick
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Chen Wang
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Flore Sinturel
- Department of Medicine, Division of Endocrinology, Diabetes, Nutrition and Patient Education, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Chien-Sin Chen
- Walter-Brendel-Centre of Experimental Medicine, Ludwig-Maximilians-University Munich, BioMedical Centre, Planegg-Martinsried, Germany
| | - Alba de Juan
- Walter-Brendel-Centre of Experimental Medicine, Ludwig-Maximilians-University Munich, BioMedical Centre, Planegg-Martinsried, Germany
| | - Jasmin Weber
- Walter-Brendel-Centre of Experimental Medicine, Ludwig-Maximilians-University Munich, BioMedical Centre, Planegg-Martinsried, Germany
| | - Stephan J Holtkamp
- Walter-Brendel-Centre of Experimental Medicine, Ludwig-Maximilians-University Munich, BioMedical Centre, Planegg-Martinsried, Germany
| | - Sophia Martina Hergenhan
- Walter-Brendel-Centre of Experimental Medicine, Ludwig-Maximilians-University Munich, BioMedical Centre, Planegg-Martinsried, Germany
| | - Jennifer Geddes-McAlister
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Stefan Ebner
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany.,Systems Immunology and Proteomics, Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Paola Fontannaz
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,World Health Organization Collaborating Center for Vaccine Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Benjamin Meyer
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,World Health Organization Collaborating Center for Vaccine Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Maria Vono
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,World Health Organization Collaborating Center for Vaccine Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Stéphane Jemelin
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Charna Dibner
- Department of Medicine, Division of Endocrinology, Diabetes, Nutrition and Patient Education, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Claire-Anne Siegrist
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,World Health Organization Collaborating Center for Vaccine Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Felix Meissner
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany.,Systems Immunology and Proteomics, Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Frederik Graw
- BioQuant - Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
| | - Christoph Scheiermann
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland. .,Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland. .,Walter-Brendel-Centre of Experimental Medicine, Ludwig-Maximilians-University Munich, BioMedical Centre, Planegg-Martinsried, Germany. .,Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
| |
Collapse
|
5
|
Yeung J, Lamb J, Krieger JR, Gadjeva M, Geddes-McAlister J. Quantitative Proteomic Profiling of Murine Ocular Tissue and the Extracellular Environment. ACTA ACUST UNITED AC 2021; 10:e83. [PMID: 32897649 DOI: 10.1002/cpmo.83] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometry-based proteomics provides a robust and reliable method for detecting and quantifying changes in protein abundance among samples, including cells, tissues, organs, and supernatants. Physical damage or inflammation can compromise the ocular surface permitting colonization by bacterial pathogens, commonly Pseudomonas aeruginosa, and the formation of biofilms. The interplay between P. aeruginosa and the immune system at the site of infection defines the host's ability to defend against bacterial invasion and promote clearance of infection. Profiling of the ocular tissue following infection describes the nature of the host innate immune response and specifically the presence and abundance of neutrophil-associated proteins to neutralize the bacterial biofilm. Moreover, detection of unique proteins produced by P. aeruginosa enable identification of the bacterial species and may serve as a diagnostic approach in a clinical setting. Given the emergence and prevalence of antimicrobial resistant bacterial strains, the ability to rapidly diagnose a bacterial infection promoting quick and accurate treatment will reduce selective pressure towards resistance. Furthermore, the ability to define differences in the host immune response towards bacterial invasion enhances our understanding of innate immune system regulation at the ocular surface. Here, we describe murine ocular infection and sample collection, as well as outline protocols for protein extraction and mass spectrometry profiling from corneal tissue and extracellular environment (eye wash) samples. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Murine model of ocular infection Basic Protocol 2: Murine model sample collection Basic Protocol 3: Protein extraction from eye wash Basic Protocol 4: Protein extraction from corneal tissue Basic Protocol 5: Mass spectrometry-based proteomics and bioinformatics from eye wash and corneal tissue samples.
Collapse
Affiliation(s)
- Jason Yeung
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jeffrey Lamb
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Mihaela Gadjeva
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | |
Collapse
|
6
|
Lin T, Quellier D, Lamb J, Voisin T, Baral P, Bock F, Schönberg A, Mirchev R, Pier G, Chiu I, Gadjeva M. Pseudomonas aeruginosa-induced nociceptor activation increases susceptibility to infection. PLoS Pathog 2021; 17:e1009557. [PMID: 33956874 PMCID: PMC8101935 DOI: 10.1371/journal.ppat.1009557] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 04/13/2021] [Indexed: 12/17/2022] Open
Abstract
We report a rapid reduction in blink reflexes during in vivo ocular Pseudomonas aeruginosa infection, which is commonly attributed and indicative of functional neuronal damage. Sensory neurons derived in vitro from trigeminal ganglia (TG) were able to directly respond to P. aeruginosa but reacted significantly less to strains of P. aeruginosa that lacked virulence factors such as pili, flagella, or a type III secretion system. These observations led us to explore the impact of neurons on the host's susceptibility to P. aeruginosa keratitis. Mice were treated with Resiniferatoxin (RTX), a potent activator of Transient Receptor Potential Vanilloid 1 (TRPV1) channels, which significantly ablated corneal sensory neurons, exhibited delayed disease progression that was exemplified with decreased bacterial corneal burdens and altered neutrophil trafficking. Sensitization to disease was due to the increased frequencies of CGRP-induced ICAM-1+ neutrophils in the infected corneas and reduced neutrophil bactericidal activities. These data showed that sensory neurons regulate corneal neutrophil responses in a tissue-specific matter affecting disease progression during P. aeruginosa keratitis. Hence, therapeutic modalities that control nociception could beneficially impact anti-infective therapy.
Collapse
Affiliation(s)
- Tiffany Lin
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daisy Quellier
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jeffrey Lamb
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Tiphaine Voisin
- Department of Immunology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pankaj Baral
- Department of Immunology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Felix Bock
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Alfrun Schönberg
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Rossen Mirchev
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gerald Pier
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Isaac Chiu
- Department of Immunology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mihaela Gadjeva
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
7
|
Sukumaran A, Woroszchuk E, Ross T, Geddes-McAlister J. Proteomics of host-bacterial interactions: new insights from dual perspectives. Can J Microbiol 2020; 67:213-225. [PMID: 33027598 DOI: 10.1139/cjm-2020-0324] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass-spectrometry (MS)-based proteomics is a powerful and robust platform for studying the interactions between biological systems during health and disease. Bacterial infections represent a significant threat to global health and drive the pursuit of novel therapeutic strategies to combat emerging and resistant pathogens. During infection, the interplay between a host and pathogen determines the ability of the microbe to survive in a hostile environment and promotes an immune response by the host as a protective measure. It is the protein-level changes from either biological system that define the outcome of infection, and MS-based proteomics provides a rapid and effective platform to identify such changes. In particular, proteomics detects alterations in protein abundance, quantifies protein secretion and (or) release, measures an array of post-translational modifications that influence signaling cascades, and profiles protein-protein interactions through protein complex and (or) network formation. Such information provides new insight into the role of known and novel bacterial effectors, as well as the outcome of host cell activation. In this Review, we highlight the diverse applications of MS-based proteomics in profiling the relationship between bacterial pathogens and the host. Our work identifies a plethora of strategies for exploring mechanisms of infection from dual perspectives (i.e., host and pathogen), and we suggest opportunities to extrapolate the current knowledgebase to other biological systems for applications in therapeutic discovery.
Collapse
Affiliation(s)
- Arjun Sukumaran
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada.,Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Elizabeth Woroszchuk
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada.,Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Taylor Ross
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada.,Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Jennifer Geddes-McAlister
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada.,Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
8
|
Muselius B, Sukumaran A, Yeung J, Geddes-McAlister J. Iron Limitation in Klebsiella pneumoniae Defines New Roles for Lon Protease in Homeostasis and Degradation by Quantitative Proteomics. Front Microbiol 2020; 11:546. [PMID: 32390954 PMCID: PMC7194016 DOI: 10.3389/fmicb.2020.00546] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 03/12/2020] [Indexed: 01/24/2023] Open
Abstract
Nutrient adaptation is key in limiting environments for the promotion of microbial growth and survival. In microbial systems, iron is an essential component for many cellular processes, and bioavailability varies greatly among different conditions. In the bacterium, Klebsiella pneumoniae, the impact of iron limitation is known to alter transcriptional expression of iron-acquisition pathways and influence secretion of iron-binding siderophores, however, a comprehensive view of iron limitation at the protein level remains to be defined. Here, we apply a mass-spectrometry-based quantitative proteomics strategy to profile the global impact of iron limitation on the cellular proteome and extracellular environment (secretome) of K. pneumoniae. Our data define the impact of iron on proteins involved in transcriptional regulation and emphasize the modulation of a vast array of proteins associated with iron acquisition, transport, and binding. We also identify proteins in the extracellular environment associated with conventional and non-conventional modes of secretion, as well as vesicle release. In particular, we demonstrate a new role for Lon protease in promoting iron homeostasis outside of the cell. Characterization of a Lon protease mutant in K. pneumoniae validates roles in bacterial growth, cell division, and virulence, and uncovers novel degradation candidates of Lon protease associated with improved iron utilization strategies in the absence of the enzyme. Overall, we provide evidence of unique connections between Lon and iron in a bacterial system and suggest a new role for Lon protease in the extracellular environment during nutrient limitation.
Collapse
|
9
|
Yeung J, Gadjeva M, Geddes-McAlister J. Label-Free Quantitative Proteomics Distinguishes General and Site-Specific Host Responses to Pseudomonas aeruginosa Infection at the Ocular Surface. Proteomics 2020; 20:e1900290. [PMID: 31874121 PMCID: PMC7079286 DOI: 10.1002/pmic.201900290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 12/07/2019] [Indexed: 01/01/2023]
Abstract
Mass spectrometry-based proteomics enables the unbiased and sensitive profiling of cellular proteomes and extracellular environments. Recent technological and bioinformatic advances permit identifying dual biological systems in a single experiment, supporting investigation of infection from both the host and pathogen perspectives. At the ocular surface, Pseudomonas aeruginosa is commonly associated with biofilm formation and inflammation of the ocular tissues, causing damage to the eye. The interaction between P. aeruginosa and the immune system at the site of infection describes limitations in clearance of infection and enhanced pathogenesis. Here, the extracellular environment (eye wash) of murine ocular surfaces infected with a clinical isolate of P. aeruginosa is profiled and neutrophil marker proteins are detected, indicating neutrophil recruitment to the site of infection. The first potential diagnostic markers of P. aeruginosa-associated keratitis are also identified. In addition, the deepest murine corneal proteome to date is defined and proteins, categories, and networks critical to the host response are detected. Moreover, the first identification of bacterial proteins attached to the ocular surface is reported. The findings are validated through in silico comparisons and enzymatic profiling. Overall, the work provides comprehensive profiling of the host-pathogen interface and uncovers differences between general and site-specific host responses to infection.
Collapse
Affiliation(s)
- J. Yeung
- Molecular and Cellular Biology Department, University of Guelph, Guelph, Ontario, Canada
| | - M. Gadjeva
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - J. Geddes-McAlister
- Molecular and Cellular Biology Department, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
10
|
Geddes-McAlister J, Kugadas A, Gadjeva M. Tasked with a Challenging Objective: Why Do Neutrophils Fail to Battle Pseudomonas aeruginosa Biofilms. Pathogens 2019; 8:pathogens8040283. [PMID: 31817091 PMCID: PMC6963930 DOI: 10.3390/pathogens8040283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/26/2019] [Accepted: 12/02/2019] [Indexed: 01/28/2023] Open
Abstract
Multidrug-resistant (MDR) bacterial infections are a leading cause of mortality, affecting approximately 250,000 people in Canada and over 2 million people in the United States, annually. The lack of efficacy of antibiotic-based treatments is often caused by inability of the drug to penetrate bacterial biofilms in sufficient concentrations, posing a major therapeutic challenge. Here, we review the most recent information about the architecture of Pseudomonas aeruginosa biofilms in vivo and describe how advances in imaging and mass spectroscopy analysis bring about novel therapeutic options and challenge existing dogmas.
Collapse
Affiliation(s)
| | - Abirami Kugadas
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Mihaela Gadjeva
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
- Correspondence: ; Tel.: +1-617-525-2268; Fax: +1-617-525-2510
| |
Collapse
|
11
|
Sukumaran A, Coish J, Yeung J, Muselius B, Gadjeva M, MacNeil A, Geddes-McAlister J. Decoding communication patterns of the innate immune system by quantitative proteomics. J Leukoc Biol 2019; 106:1221-1232. [PMID: 31556465 PMCID: PMC7309189 DOI: 10.1002/jlb.2ri0919-302r] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 12/15/2022] Open
Abstract
The innate immune system is a collective network of cell types involved in cell recruitment and activation using a robust and refined communication system. Engagement of receptor-mediated intracellular signaling initiates communication cascades by conveying information about the host cell status to surrounding cells for surveillance and protection. Comprehensive profiling of innate immune cells is challenging due to low cell numbers, high dynamic range of the cellular proteome, low abundance of secreted proteins, and the release of degradative enzymes (e.g., proteases). However, recent advances in mass spectrometry-based proteomics provides the capability to overcome these limitations through profiling the dynamics of cellular processes, signaling cascades, post-translational modifications, and interaction networks. Moreover, integration of technologies and molecular datasets provide a holistic view of a complex and intricate network of communications underscoring host defense and tissue homeostasis mechanisms. In this Review, we explore the diverse applications of mass spectrometry-based proteomics in innate immunity to define communication patterns of the innate immune cells during health and disease. We also provide a technical overview of mass spectrometry-based proteomic workflows, with a focus on bottom-up approaches, and we present the emerging role of proteomics in immune-based drug discovery while providing a perspective on new applications in the future.
Collapse
Affiliation(s)
- A. Sukumaran
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - J.M. Coish
- Department of Health Sciences, Brock University, St. Catharines, ON, L2S 3A1
| | - J. Yeung
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - B. Muselius
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - M. Gadjeva
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA 02115
| | - A.J. MacNeil
- Department of Health Sciences, Brock University, St. Catharines, ON, L2S 3A1
| | - J. Geddes-McAlister
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON, Canada, N1G 2W1
| |
Collapse
|