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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.
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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
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2
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McKenna E, Mhaonaigh AU, Wubben R, Dwivedi A, Hurley T, Kelly LA, Stevenson NJ, Little MA, Molloy EJ. Neutrophils: Need for Standardized Nomenclature. Front Immunol 2021; 12:602963. [PMID: 33936029 PMCID: PMC8081893 DOI: 10.3389/fimmu.2021.602963] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/17/2021] [Indexed: 12/15/2022] Open
Abstract
Neutrophils are the most abundant innate immune cell with critical anti-microbial functions. Since the discovery of granulocytes at the end of the nineteenth century, the cells have been given many names including phagocytes, polymorphonuclear neutrophils (PMN), granulocytic myeloid derived suppressor cells (G-MDSC), low density neutrophils (LDN) and tumor associated neutrophils (TANS). This lack of standardized nomenclature for neutrophils suggest that biologically distinct populations of neutrophils exist, particularly in disease, when in fact these may simply be a manifestation of the plasticity of the neutrophil as opposed to unique populations. In this review, we profile the surface markers and granule expression of each stage of granulopoiesis to offer insight into how each stage of maturity may be identified. We also highlight the remarkable surface marker expression profiles between the supposed neutrophil populations.
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Affiliation(s)
- Ellen McKenna
- Discipline of Paediatrics, Trinity College, The University of Dublin, Dublin, Ireland.,Paediatric Research Laboratory, Trinity Translational Medicine Institute (TTMI), St James' Hospital, Dublin, Ireland
| | | | - Richard Wubben
- Viral Immunology Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Dublin, Ireland
| | - Amrita Dwivedi
- Trinity Health Kidney Centre, TTMI, Trinity College, Dublin, Ireland
| | - Tim Hurley
- Discipline of Paediatrics, Trinity College, The University of Dublin, Dublin, Ireland.,Paediatric Research Laboratory, Trinity Translational Medicine Institute (TTMI), St James' Hospital, Dublin, Ireland.,Neonatology, Coombe Women and Infant's University Hospital, Dublin, Ireland
| | - Lynne A Kelly
- Discipline of Paediatrics, Trinity College, The University of Dublin, Dublin, Ireland.,Paediatric Research Laboratory, Trinity Translational Medicine Institute (TTMI), St James' Hospital, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland
| | - Nigel J Stevenson
- Viral Immunology Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Dublin, Ireland.,Viral Immunology Group, Royal College of Surgeons in Ireland-Medical University of Bahrain, Zallaq, Bahrain
| | - Mark A Little
- Trinity Health Kidney Centre, TTMI, Trinity College, Dublin, Ireland.,Irish Centre for Vascular Biology, Trinity College Dublin, Dublin, Ireland
| | - Eleanor J Molloy
- Discipline of Paediatrics, Trinity College, The University of Dublin, Dublin, Ireland.,Paediatric Research Laboratory, Trinity Translational Medicine Institute (TTMI), St James' Hospital, Dublin, Ireland.,Neonatology, Coombe Women and Infant's University Hospital, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland.,Neonatology, Children's Hospital Ireland (CHI) at Crumlin, Dublin, Ireland.,Paediatrics, CHI at Tallaght, Tallaght University Hospital, Dublin, Ireland
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Mirzaei R, Ranjbar R, Karampoor S, Goodarzi R, Hasanvand H. The Human Immune System toward Staphylococcus aureus. Open Microbiol J 2020. [DOI: 10.2174/1874285802014010164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The immune system is responsible for protecting the host from pathogens, and it has evolved to deal with these pathogens. On the other hand, the co-evolution of pathogenic bacteria with hosts has led to the rise of an array of virulence genes that enable pathogen bacteria to evade or modulate the immune system. Staphylococcus aureus is a significant pathogen of humans that encodes several virulence factors that can modulate or evade from the innate and adaptive arm of the immune system. Overall, the immune reaction toward S. aureus contributes to stimulate innate and adaptive reactions. A profound understanding of the immune response to S. aureus infections will be critical for the development of vaccines and novel therapies. In this review, we summarized and discussed the novel information about the human immune system against S. aureus.
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Zamolodchikova TS, Tolpygo SM, Svirshchevskaya EV. Cathepsin G-Not Only Inflammation: The Immune Protease Can Regulate Normal Physiological Processes. Front Immunol 2020; 11:411. [PMID: 32194574 PMCID: PMC7062962 DOI: 10.3389/fimmu.2020.00411] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/21/2020] [Indexed: 12/17/2022] Open
Affiliation(s)
- Tatyana S Zamolodchikova
- Physiology of Motivation Laboratory, P. K. Anokhin Institute of Normal Physiology, Moscow, Russia
| | - Svetlana M Tolpygo
- Physiology of Motivation Laboratory, P. K. Anokhin Institute of Normal Physiology, Moscow, Russia
| | - Elena V Svirshchevskaya
- Immunology Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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Chairatana P, Nolan EM. Human α-Defensin 6: A Small Peptide That Self-Assembles and Protects the Host by Entangling Microbes. Acc Chem Res 2017; 50:960-967. [PMID: 28296382 DOI: 10.1021/acs.accounts.6b00653] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Human α-defensin 6 (HD6) is a 32-residue cysteine-rich peptide that contributes to innate immunity by protecting the host at mucosal sites. This peptide is produced in small intestinal Paneth cells, stored as an 81-residue precursor peptide named proHD6 in granules, and released into the lumen. One unusual feature of HD6 is that it lacks the broad-spectrum antimicrobial activity observed for other human α-defensins, including the Paneth cell peptide human α-defensin 5 (HD5). HD6 exhibits unprecedented self-assembly properties, which confer an unusual host-defense function. HD6 monomers self-assemble into higher-order oligomers termed "nanonets", which entrap microbes and prevent invasive gastrointestinal pathogens such as Salmonella enterica serovar Typhimurium and Listeria monocytogenes from entering host cells. One possible advantage of this host-defense mechanism is that HD6 helps to keep microbes in the lumen such that they can be excreted or attacked by other components of the immune system, such as recruited neutrophils. In this Account, we report our current understanding of HD6 and focus on work published since 2012 when Bevins and co-workers described the discovery of HD6 nanonets in the literature. First, we present studies that address the biosynthesis, storage, and maturation of HD6, which demonstrate that nature uses a propeptide strategy to spatially and temporally control the formation of HD6 nanonets in the small intestine. The propeptide is stored in Paneth cell granules, and proteolysis occurs during or following release into the lumen, which affords the 32-residue mature peptide that self-assembles. We subsequently highlight structure-function studies that provide a foundation for understanding the molecular basis for why HD6 exhibits unusual self-assembly properties compared with other characterized defensins. The disposition of hydrophobic residues in the HD6 primary structure differs from that of other human α-defensins and is an important structural determinant for oligomerization. Lastly, we consider functional studies that illuminate how HD6 contributes to mucosal immunity. We recently discovered that in addition to blocking bacterial invasion into host epithelial cells by Gram-negative and Gram-positive gastrointestinal pathogens, HD6 suppresses virulence traits displayed by the opportunistic human fungal pathogen Candida albicans. In particular, we found that C. albicans biofilm formation, which causes complications in the treatment of candidiasis, is inhibited by HD6. This observation suggests that HD6 may contribute to intestinal homeostasis by helping to keep C. albicans in its commensal state. We intend for this Account to inspire further biochemical, biophysical, and biological investigations that will advance our understanding of HD6 in mucosal immunity and the host-microbe interaction.
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Affiliation(s)
- Phoom Chairatana
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Hemshekhar M, Anaparti V, Mookherjee N. Functions of Cationic Host Defense Peptides in Immunity. Pharmaceuticals (Basel) 2016; 9:ph9030040. [PMID: 27384571 PMCID: PMC5039493 DOI: 10.3390/ph9030040] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 12/12/2022] Open
Abstract
Cationic host defense peptides are a widely distributed family of immunomodulatory molecules with antimicrobial properties. The biological functions of these peptides include the ability to influence innate and adaptive immunity for efficient resolution of infections and simultaneous modulation of inflammatory responses. This unique dual bioactivity of controlling infections and inflammation has gained substantial attention in the last three decades and consequent interest in the development of these peptide mimics as immunomodulatory therapeutic candidates. In this review, we summarize the current literature on the wide range of functions of cationic host defense peptides in the context of the mammalian immune system.
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Affiliation(s)
- Mahadevappa Hemshekhar
- Manitoba Centre for Proteomics and Systems Biology, Departments of Internal Medicine and Immunology, University of Manitoba, Winnipeg, MB R3E3P4, Canada.
| | - Vidyanand Anaparti
- Manitoba Centre for Proteomics and Systems Biology, Departments of Internal Medicine and Immunology, University of Manitoba, Winnipeg, MB R3E3P4, Canada.
| | - Neeloffer Mookherjee
- Manitoba Centre for Proteomics and Systems Biology, Departments of Internal Medicine and Immunology, University of Manitoba, Winnipeg, MB R3E3P4, Canada.
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Chairatana P, Chu H, Castillo PA, Shen B, Bevins CL, Nolan EM. Proteolysis Triggers Self-Assembly and Unmasks Innate Immune Function of a Human α-Defensin Peptide. Chem Sci 2015; 7:1738-1752. [PMID: 27076903 PMCID: PMC4827351 DOI: 10.1039/c5sc04194e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human α-defensin 6 (HD6) is a unique peptide of the defensin family that provides innate immunity in the intestine by self-assembling to form high-order oligomers that entrap bacteria and prevent host cell invasion. Here, we report critical steps in the self-assembly pathway of HD6. We demonstrate that HD6 is localized in secretory granules of small intestinal Paneth cells. HD6 is stored in these granules as an 81-residue propeptide (proHD6), and is recovered from ileal lumen as a 32-residue mature peptide. The propeptide neither forms higher-order oligomers, nor agglutinates bacteria, nor prevents Listeria monocytogenes invasion into epithelial cells. The Paneth cell granules also contain the protease trypsin, and trypsin-catalyzed hydrolysis of proHD6 liberates mature HD6, unmasking its latent activities. This work illustrates a remarkable example of how nature utilizes a propeptide strategy to spatially and temporally control peptide self-assembly, and thereby initiates innate immune function in the human intestine.
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Affiliation(s)
- Phoom Chairatana
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hiutung Chu
- Department of Microbiology and Immunology, University of California Davis School of Medicine, Davis, CA 95616, USA
| | - Patricia A Castillo
- Department of Microbiology and Immunology, University of California Davis School of Medicine, Davis, CA 95616, USA
| | - Bo Shen
- Department of General Internal Medicine and Gastroenterology and Hepatology, The Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Charles L Bevins
- Department of Microbiology and Immunology, University of California Davis School of Medicine, Davis, CA 95616, USA
| | - Elizabeth M Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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