1
|
Sprung RW, Zhang Q, Kramer MH, Christopher MC, Erdmann-Gilmore P, Mi Y, Malone JP, Ley TJ, Townsend RR. Stabilizing the Proteomes of Acute Myeloid Leukemia Cells: Implications for Cancer Proteomics. Mol Cell Proteomics 2024; 23:100716. [PMID: 38219859 PMCID: PMC10864662 DOI: 10.1016/j.mcpro.2024.100716] [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: 08/03/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 01/16/2024] Open
Abstract
Previous work has shown that inhibition of abundant myeloid azurophil granule-associated serine proteases (ELANE [neutrophil elastase], PRTN3 [protease 3], and CTSG [Cathepsin G]) is required to stabilize some proteins in myeloid cells. We therefore hypothesized that effective inhibition of these proteases may be necessary for quantitative proteomic analysis of samples containing myeloid cells. To test this hypothesis, we thawed viably preserved acute myeloid leukemia cells from cryovials in the presence or the absence of diisopropyl fluorophosphate (DFP), a cell-permeable and irreversible serine protease inhibitor. Global proteomic analysis was performed, using label-free and isobaric peptide-labeling quantitation. The presence of DFP resulted in an increase of tryptic peptides (14-57%) and proteins (9-31%). In the absence of DFP, 11 to 31% of peptide intensity came from nontryptic peptides; 52 to 75% had cleavage specificity consistent with activities of ELANE-PRTN3. Treatment with DFP reduced the intensity of nontryptic peptides to 4-8% of the total. ELANE inhibition was 95%, based on diisopropyl phosphate modification of active site serine residue. Overall, the relative abundance of 20% of proteins was significantly altered by DFP treatment. These results suggest that active myeloid serine proteases, released during sample processing, can skew quantitative proteomic measurements. Finally, significant ELANE activity was also detected in Clinical Proteomics Tumor Analysis Consortium datasets of solid tumors (many of which have known myeloid infiltration). In the pancreatic cancer dataset, the median percentage of nontryptic intensity detected across patient samples was 34%, with many patient samples having more than half of their detected peptide intensity from nontryptic cleavage events consistent with ELANE-PRTN3 cleavage specificity. Our study suggests that in vitro cleavage of proteins by myeloid serine proteases may be relevant for proteomic studies of any tumor that contains infiltrating myeloid cells.
Collapse
Affiliation(s)
- Robert W Sprung
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Qiang Zhang
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael H Kramer
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Matthew C Christopher
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Petra Erdmann-Gilmore
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Yiling Mi
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - James P Malone
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.
| | - Timothy J Ley
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - R Reid Townsend
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
2
|
Naish E, Wood AJT, Stewart AP, Routledge M, Morris AC, Chilvers ER, Lodge KM. The formation and function of the neutrophil phagosome. Immunol Rev 2023; 314:158-180. [PMID: 36440666 PMCID: PMC10952784 DOI: 10.1111/imr.13173] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neutrophils are the most abundant circulating leukocyte and are crucial to the initial innate immune response to infection. One of their key pathogen-eliminating mechanisms is phagocytosis, the process of particle engulfment into a vacuole-like structure called the phagosome. The antimicrobial activity of the phagocytic process results from a collaboration of multiple systems and mechanisms within this organelle, where a complex interplay of ion fluxes, pH, reactive oxygen species, and antimicrobial proteins creates a dynamic antimicrobial environment. This complexity, combined with the difficulties of studying neutrophils ex vivo, has led to gaps in our knowledge of how the neutrophil phagosome optimizes pathogen killing. In particular, controversy has arisen regarding the relative contribution and integration of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase-derived antimicrobial agents and granule-delivered antimicrobial proteins. Clinical syndromes arising from dysfunction in these systems in humans allow useful insight into these mechanisms, but their redundancy and synergy add to the complexity. In this article, we review the current knowledge regarding the formation and function of the neutrophil phagosome, examine new insights into the phagosomal environment that have been permitted by technological advances in recent years, and discuss aspects of the phagocytic process that are still under debate.
Collapse
Affiliation(s)
- Emily Naish
- National Heart and Lung InstituteImperial College LondonLondonUK
| | - Alexander JT Wood
- Medical SchoolUniversity of Western AustraliaPerthAustralia
- Department of Critical CareUniversity of MelbourneMelbourneAustralia
| | | | - Matthew Routledge
- Department of MedicineUniversity of CambridgeCambridgeUK
- Division of Immunology, Department of PathologyUniversity of CambridgeCambridgeUK
| | - Andrew Conway Morris
- Department of MedicineUniversity of CambridgeCambridgeUK
- Division of Immunology, Department of PathologyUniversity of CambridgeCambridgeUK
| | - Edwin R Chilvers
- National Heart and Lung InstituteImperial College LondonLondonUK
| | | |
Collapse
|
3
|
Filina YV, Tikhonova IV, Gabdoulkhakova AG, Rizvanov AA, Safronova VG. Mechanisms of ERK phosphorylation triggered via mouse formyl peptide receptor 2. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119356. [PMID: 36087811 DOI: 10.1016/j.bbamcr.2022.119356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/09/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Formyl peptide receptors (FPRs) are expressed in the cells of the innate immune system and provide binding with pathogen and damage-associated molecular patterns with subsequent activation of the phagocytes for defense reactions such as chemotaxis, secretory degranulation and ROS generation. Probably, FPR2 is one of the unique receptors in the organism; it is able to recognize numerous ligands of different chemical structure, and moreover, these ligands can trigger opposite phagocyte responses promoting either pro- or anti-inflammatory reactions. Therefore, FPR2 and its signaling pathways are of intense research interest. We found only slight activation of ERK1/2 in the response to peptide ligand WKYMVM in the accelerating phase of ROS generation and more intense ERK1/2 phosphorylation in the declining phase of it in mouse bone marrow granulocytes. Lipid agonist BML-111 did not induce significant ERK phosphorylation when applied for 10-1800 s. To some extent co-localization of ERK1/2 and NADPH oxidase subunits was observed even in the intact cells and didn't change under FPR2 stimulation by WKYMVM, while direct PKC activation by PMA resulted to more efficient interaction between ERK1/2 and p47phox/p67phox and their translocation to plasma membrane. We have shown that phosphorylation and activation of ERK1/2 in bone marrow granulocytes depended on FPR2-triggered activity of PI3K and PKC, phosphatase DUSP6, and, the most but not the least, on ROS generation. Since blocking of ROS generation led to a slowdown of ERK activation indicating a significant contribution of ROS to the secondary regulation of ERK activity.
Collapse
Affiliation(s)
- Yu V Filina
- Openlab "Gene and Cell Technologies", Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation.
| | - I V Tikhonova
- Laboratory of Cellular Neurobiology, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Russian Federation
| | - A G Gabdoulkhakova
- Openlab "Gene and Cell Technologies", Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation; Central Research Laboratory, Kazan State Medical Academy, Federal State Budgetary Educational Institution of Further Professional Education "Russian Medical Academy of Continuous Professional Education" of the Ministry of Healthcare of the Russian Federation, Kazan, Russian Federation
| | - A A Rizvanov
- Openlab "Gene and Cell Technologies", Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - V G Safronova
- Laboratory of Cellular Neurobiology, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Russian Federation
| |
Collapse
|
4
|
Wood AJ, Vassallo AM, Ruchaud-Sparagano MH, Scott J, Zinnato C, Gonzalez-Tejedo C, Kishore K, D'Santos CS, Simpson AJ, Menon DK, Summers C, Chilvers ER, Okkenhaug K, Morris AC. C5a impairs phagosomal maturation in the neutrophil through phosphoproteomic remodeling. JCI Insight 2020; 5:137029. [PMID: 32634128 PMCID: PMC7455072 DOI: 10.1172/jci.insight.137029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/24/2020] [Indexed: 12/26/2022] Open
Abstract
Critical illness is accompanied by the release of large amounts of the anaphylotoxin, C5a. C5a suppresses antimicrobial functions of neutrophils which is associated with adverse outcomes. The signaling pathways that mediate C5a-induced neutrophil dysfunction are incompletely understood. Healthy donor neutrophils exposed to purified C5a demonstrated a prolonged defect (7 hours) in phagocytosis of Staphylococcus aureus. Phosphoproteomic profiling of 2712 phosphoproteins identified persistent C5a signaling and selective impairment of phagosomal protein phosphorylation on exposure to S. aureus. Notable proteins included early endosomal marker ZFYVE16 and V-ATPase proton channel component ATPV1G1. An assay of phagosomal acidification demonstrated C5a-induced impairment of phagosomal acidification, which was recapitulated in neutrophils from critically ill patients. Examination of the C5a-impaired protein phosphorylation indicated a role for the PI3K VPS34 in phagosomal maturation. Inhibition of VPS34 impaired neutrophil phagosomal acidification and killing of S. aureus. This study provides a phosphoproteomic assessment of human neutrophil signaling in response to S. aureus and its disruption by C5a, identifying a defect in phagosomal maturation and mechanisms of immune failure in critical illness. C5a disrupts the neutrophil phosphoproteomic response to bacteria, impairing phagosomal maturation and bacterial killing.
Collapse
Affiliation(s)
- Alexander Jt Wood
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, United Kingdom
| | - Arlette M Vassallo
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, United Kingdom
| | | | - Jonathan Scott
- Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Carmelo Zinnato
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, United Kingdom
| | - Carmen Gonzalez-Tejedo
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, United Kingdom
| | - Kamal Kishore
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, United Kingdom
| | - Clive S D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, United Kingdom
| | - A John Simpson
- Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom.,Newcastle upon Tyne Hospitals NHS Foundation Trust, Queen Victoria Road, Newcastle upon Tyne, United Kingdom
| | - David K Menon
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, United Kingdom
| | - Charlotte Summers
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, United Kingdom
| | - Edwin R Chilvers
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, United Kingdom.,National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Klaus Okkenhaug
- Division of Immunology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom
| | - Andrew Conway Morris
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, United Kingdom.,Division of Immunology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom
| |
Collapse
|
5
|
Cassatella MA, Östberg NK, Tamassia N, Soehnlein O. Biological Roles of Neutrophil-Derived Granule Proteins and Cytokines. Trends Immunol 2019; 40:648-664. [PMID: 31155315 DOI: 10.1016/j.it.2019.05.003] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 12/30/2022]
Abstract
Neutrophils, the most abundant white blood cells in human circulation, entertain intense interactions with other leukocyte subsets, platelets, and stromal cells. Molecularly, such interactions are typically communicated through proteins generated during granulopoiesis, stored in granules, or produced on demand. Here, we provide an overview of the mammalian regulation of granule protein production in the bone marrow and the de novo synthesis of cytokines by neutrophils recruited to tissues. In addition, we discuss some of the known biological roles of these protein messengers, and how neutrophil-borne granule proteins and cytokines can synergize to modulate inflammation and tumor development. Decoding the neutrophil interactome is important for therapeutically neutralizing individual proteins to putatively dampen inflammation, or for delivering modified neutrophil-borne proteins to boost host defense.
Collapse
Affiliation(s)
| | - Nataliya K Östberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden; Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nicola Tamassia
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | - Oliver Soehnlein
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden; Department of Medicine, Karolinska Institutet, Stockholm, Sweden; Institute for Cardiovascular Prevention (IPEK), Klinikum der LMU, München, Germany; German Centre for Cardiovascular Research (DZHK), Partner site, Munich, Germany.
| |
Collapse
|
6
|
Thiele T, Braune J, Dhople V, Hammer E, Scharf C, Greinacher A, Völker U, Steil L. Proteomic profile of platelets during reconstitution of platelet counts after apheresis. Proteomics Clin Appl 2016; 10:831-8. [DOI: 10.1002/prca.201500134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/29/2016] [Accepted: 03/29/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Thomas Thiele
- Institut für Immunologie und Transfusionsmedizin; University Medicine Greifswald; Greifswald Germany
| | - Johannes Braune
- Institut für Immunologie und Transfusionsmedizin; University Medicine Greifswald; Greifswald Germany
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung; University Medicine Greifswald; Greifswald Germany
| | - Vishnu Dhople
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung; University Medicine Greifswald; Greifswald Germany
| | - Elke Hammer
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung; University Medicine Greifswald; Greifswald Germany
| | - Christian Scharf
- Klinik und Poliklinik für Hals-Nasen-Ohrenkrankheiten, Kopf- und Halschirurgie; University Medicine Greifswald; Greifswald Germany
| | - Andreas Greinacher
- Institut für Immunologie und Transfusionsmedizin; University Medicine Greifswald; Greifswald Germany
| | - Uwe Völker
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung; University Medicine Greifswald; Greifswald Germany
| | - Leif Steil
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung; University Medicine Greifswald; Greifswald Germany
| |
Collapse
|