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Washburn N, Meccariello R, Duffner J, Getchell K, Holte K, Prod'homme T, Srinivasan K, Prenovitz R, Lansing J, Capila I, Kaundinya G, Manning AM, Bosques CJ. Characterization of Endogenous Human FcγRIII by Mass Spectrometry Reveals Site, Allele and Sequence Specific Glycosylation. Mol Cell Proteomics 2020; 18:534-545. [PMID: 30559323 PMCID: PMC6398215 DOI: 10.1074/mcp.ra118.001142] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 11/21/2018] [Indexed: 12/21/2022] Open
Abstract
Characterization of endogenous FcγRIII glycosylation from healthy donors with different FcγRIIIb genotypes reveals site specific, and allele specific differences in glycosylation as well as noncananonical sequence specific differences in glycosylation. We propose these differences in glycosylation may influence the differential activity seen for neutrophils across genotypes. The importance of IgG glycosylation, Fc-gamma receptor (FcγR) single nucleotide polymorphisms and FcγR copy number variations in fine tuning the immune response has been well established. There is a growing appreciation of the importance of glycosylation of FcγRs in modulating the FcγR-IgG interaction based on the association between the glycosylation of recombinant FcγRs and the kinetics and affinity of the FcγR-IgG interaction. Although glycosylation of recombinant FcγRs has been recently characterized, limited knowledge exists on the glycosylation of endogenous human FcγRs. In order to improve the structural understanding of FcγRs expressed on human cells we characterized the site specific glycosylation of native human FcγRIII from neutrophils of 50 healthy donors and from matched plasma for 43 of these individuals. Through this analysis we have confirmed site specific glycosylation patterns previously reported for soluble FcγRIII from a single donor, identified FcγRIIIb specific Asn45 glycosylation and an allelic effect on glycosylation at Asn162 of FcγRIIIb. Identification of FcγRIIIb specific glycosylation allows for assignment of FcγRIIIb alleles and relative copy number of the two alleles where DNA/RNA is not available. Intriguingly the types of structures found to be elevated at Asn162 in the NA2 allele have been shown to destabilize the Fc:FcγRIII interaction resulting in a faster dissociation rate. These differences in glycosylation may in part explain the differential activity reported for the two alleles which have similar in vitro affinity for IgG.
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Affiliation(s)
- Nathaniel Washburn
- From the ‡Research Department, Momenta Pharmaceuticals, 301 Binney St., Cambridge, Massachusetts 02142.
| | - Robin Meccariello
- From the ‡Research Department, Momenta Pharmaceuticals, 301 Binney St., Cambridge, Massachusetts 02142
| | - Jay Duffner
- From the ‡Research Department, Momenta Pharmaceuticals, 301 Binney St., Cambridge, Massachusetts 02142
| | - Kristen Getchell
- From the ‡Research Department, Momenta Pharmaceuticals, 301 Binney St., Cambridge, Massachusetts 02142
| | - Kimberly Holte
- From the ‡Research Department, Momenta Pharmaceuticals, 301 Binney St., Cambridge, Massachusetts 02142
| | - Thomas Prod'homme
- From the ‡Research Department, Momenta Pharmaceuticals, 301 Binney St., Cambridge, Massachusetts 02142
| | - Karunya Srinivasan
- From the ‡Research Department, Momenta Pharmaceuticals, 301 Binney St., Cambridge, Massachusetts 02142
| | - Robert Prenovitz
- From the ‡Research Department, Momenta Pharmaceuticals, 301 Binney St., Cambridge, Massachusetts 02142
| | - Jonathan Lansing
- From the ‡Research Department, Momenta Pharmaceuticals, 301 Binney St., Cambridge, Massachusetts 02142
| | - Ishan Capila
- From the ‡Research Department, Momenta Pharmaceuticals, 301 Binney St., Cambridge, Massachusetts 02142
| | - Ganesh Kaundinya
- From the ‡Research Department, Momenta Pharmaceuticals, 301 Binney St., Cambridge, Massachusetts 02142
| | - Anthony M Manning
- From the ‡Research Department, Momenta Pharmaceuticals, 301 Binney St., Cambridge, Massachusetts 02142
| | - Carlos J Bosques
- From the ‡Research Department, Momenta Pharmaceuticals, 301 Binney St., Cambridge, Massachusetts 02142
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2
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Tran HQ, Mills RH, Peters NV, Holder MK, de Vries GJ, Knight R, Chassaing B, Gonzalez DJ, Gewirtz AT. Associations of the Fecal Microbial Proteome Composition and Proneness to Diet-induced Obesity. Mol Cell Proteomics 2019; 18:1864-1879. [PMID: 31262998 PMCID: PMC6731084 DOI: 10.1074/mcp.ra119.001623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 06/10/2019] [Indexed: 12/16/2022] Open
Abstract
Consumption of refined high-fat, low-fiber diets promotes development of obesity and its associated consequences. Although genetics play an important role in dictating susceptibility to such obesogenic diets, mice with nearly uniform genetics exhibit marked heterogeneity in their extent of obesity in response to such diets. This suggests non-genetic determinants play a role in diet-induced obesity. Hence, we sought to identify parameters that predict, and/or correlate with, development of obesity in response to an obesogenic diet. We assayed behavior, metabolic parameters, inflammatory markers/cytokines, microbiota composition, and the fecal metaproteome, in a cohort of mice (n = 50) prior to, and the 8 weeks following, administration of an obesogenic high-fat low-fiber diet. Neither behavioral testing nor quantitation of inflammatory markers broadly predicted severity of diet-induced obesity. Although, the small subset of mice that exhibited basal elevations in serum IL-6 (n = 5) were among the more obese mice in the cohort. While fecal microbiota composition changed markedly in response to the obesogenic diet, it lacked the ability to predict which mice were relative prone or resistant to obesity. In contrast, fecal metaproteome analysis revealed functional and taxonomic differences among the proteins associated with proneness to obesity. Targeted interrogation of microbiota composition data successfully validated the taxonomic differences seen in the metaproteome. Although future work will be needed to determine the breadth of applicability of these associations to other cohorts of animals and humans, this study nonetheless highlights the potential power of gut microbial proteins to predict and perhaps impact development of obesity.
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Affiliation(s)
- Hao Q Tran
- ‡Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA
| | - Robert H Mills
- §Department of Pharmacology, University of California, San Diego, CA; ¶Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA; ‖Department of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, CA; **Center for Microbiome Innovation, University of California, San Diego, CA
| | - Nicole V Peters
- ‡‡Neuroscience Institute, Georgia State University, Atlanta, GA
| | - Mary K Holder
- ‡‡Neuroscience Institute, Georgia State University, Atlanta, GA; §§School of Psychology, Georgia Institute of Technology, Atlanta, GA 30332
| | | | - Rob Knight
- ‖Department of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, CA; **Center for Microbiome Innovation, University of California, San Diego, CA
| | - Benoit Chassaing
- ‡Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA; ‡‡Neuroscience Institute, Georgia State University, Atlanta, GA
| | - David J Gonzalez
- §Department of Pharmacology, University of California, San Diego, CA; ¶Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA; **Center for Microbiome Innovation, University of California, San Diego, CA.
| | - Andrew T Gewirtz
- ‡Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA.
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3
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Guasp P, Lorente E, Martín-Esteban A, Barnea E, Romania P, Fruci D, Kuiper JW, Admon A, López de Castro JA. Redundancy and Complementarity between ERAP1 and ERAP2 Revealed by their Effects on the Behcet's Disease-associated HLA-B*51 Peptidome. Mol Cell Proteomics 2019; 18:1491-1510. [PMID: 31092671 PMCID: PMC6682995 DOI: 10.1074/mcp.ra119.001515] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 04/22/2019] [Indexed: 11/06/2022] Open
Abstract
The endoplasmic reticulum aminopeptidases ERAP1 and ERAP2 trim peptides to be loaded onto HLA molecules, including the main risk factor for Behçet's disease HLA-B*51. ERAP1 is also a risk factor among HLA-B*51-positive individuals, whereas no association is known with ERAP2. This study addressed the mutual relationships between both enzymes in the processing of an HLA-bound peptidome, interrogating their differential association with Behçet's disease. CRISPR/Cas9 was used to generate knock outs of ERAP1, ERAP2 or both from transfectant 721.221-HLA-B*51:01 cells. The surface expression of HLA-B*51 was reduced in all cases. The effects of depleting each or both enzymes on the B*51:01 peptidome were analyzed by quantitative label-free mass spectrometry. Substantial quantitative alterations of peptide length, subpeptidome balance, N-terminal residue usage, affinity and presentation of noncanonical ligands were observed. These effects were often different in the presence or absence of the other enzyme, revealing their mutual dependence. In the absence of ERAP1, ERAP2 showed similar and significant processing of B*51:01 ligands, indicating functional redundancy. The high overlap between the peptidomes of wildtype and double KO cells indicates that a large majority of B*51:01 ligands are present in the ER even in the absence of ERAP1/ERAP2. These results indicate that both enzymes have distinct, but complementary and partially redundant effects on the B*51:01 peptidome, leading to its optimization and maximal surface expression. The distinct effects of both enzymes on the HLA-B*51 peptidome provide a basis for their differential association with Behçet's disease and suggest a pathogenetic role of the B*51:01 peptidome.
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Affiliation(s)
- Pablo Guasp
- ‡Centro de Biología Molecular Severo Ochoa (CSIC-UAM), 28049 Madrid, Spain
| | - Elena Lorente
- ‡Centro de Biología Molecular Severo Ochoa (CSIC-UAM), 28049 Madrid, Spain
| | | | - Eilon Barnea
- §Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Paolo Romania
- ¶Immuno-Oncology Laboratory, Paediatric Haematology/Oncology Department, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Doriana Fruci
- ¶Immuno-Oncology Laboratory, Paediatric Haematology/Oncology Department, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - JonasJ W Kuiper
- ‖Department of Ophthalmology, Laboratory of Translational Immunology, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Arie Admon
- §Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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4
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Danquah BD, Röwer C, Opuni KM, El-Kased R, Frommholz D, Illges H, Koy C, Glocker MO. Intact Transition Epitope Mapping - Targeted High-Energy Rupture of Extracted Epitopes (ITEM-THREE). Mol Cell Proteomics 2019; 18:1543-1555. [PMID: 31147491 PMCID: PMC6683010 DOI: 10.1074/mcp.ra119.001429] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 03/04/2019] [Revised: 05/14/2019] [Indexed: 12/31/2022] Open
Abstract
Epitope mapping, which is the identification of antigenic determinants, is essential for the design of novel antibody-based therapeutics and diagnostic tools. ITEM-THREE is a mass spectrometry-based epitope mapping method that can identify epitopes on antigens upon generating an immune complex in electrospray-compatible solutions by adding an antibody of interest to a mixture of peptides from which at least one holds the antibody's epitope. This mixture is nano-electrosprayed without purification. Identification of the epitope peptide is performed within a mass spectrometer that provides an ion mobility cell sandwiched in-between two collision cells and where this ion manipulation setup is flanked by a quadrupole mass analyzer on one side and a time-of-flight mass analyzer on the other side. In a stepwise fashion, immune-complex ions are separated from unbound peptide ions and dissociated to release epitope peptide ions. Immune complex-released peptide ions are separated from antibody ions and fragmented by collision induced dissociation. Epitope-containing peptide fragment ions are recorded, and mass lists are submitted to unsupervised data base search thereby retrieving both, the amino acid sequence of the epitope peptide and the originating antigen. ITEM-THREE was developed with antiTRIM21 and antiRA33 antibodies for which the epitopes were known, subjecting them to mixtures of synthetic peptides of which one contained the respective epitope. ITEM-THREE was then successfully tested with an enzymatic digest of His-tagged recombinant human β-actin and an antiHis-tag antibody, as well as with an enzymatic digest of recombinant human TNFα and an antiTNFα antibody whose epitope was previously unknown.
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Affiliation(s)
- Bright D Danquah
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Claudia Röwer
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | | | - Reham El-Kased
- ¶Microbiology and Immunology Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - David Frommholz
- ‖University of Applied Sciences Bonn-Rhein-Sieg, Immunology and Cell Biology, Rheinbach, Germany
| | - Harald Illges
- ‖University of Applied Sciences Bonn-Rhein-Sieg, Immunology and Cell Biology, Rheinbach, Germany;; **University of Applied Sciences Bonn-Rhein-Sieg, Institute for Functional Gene Analytics, Rheinbach, Germany
| | - Cornelia Koy
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Michael O Glocker
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany.
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5
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Wu X, Yang D, Zhao F, Yang ZH, Wang D, Qiao M, Fang Y, Li W, Wu R, He P, Cong Y, Chen C, Hu L, Yan Y, Xie C, Wu Y, Han J, Zhong CQ. Quantification of Dynamic Protein Interactions and Phosphorylation in LPS Signaling Pathway by SWATH-MS. Mol Cell Proteomics 2019; 18:1054-1069. [PMID: 30850422 PMCID: PMC6553925 DOI: 10.1074/mcp.ra119.001380] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 02/10/2019] [Revised: 03/04/2019] [Indexed: 11/06/2022] Open
Abstract
Lipopolysaccharide (LPS)-induced macrophage activation is a prototype of innate immune response. Although key effector proteins in LPS signaling pathway have been revealed, the map of dynamic protein interactions and phosphorylation as well as the stoichiometry of protein complexes are lacking. Here we present a dynamic map of protein interactions and phosphorylation in MyD88, TRAF6 and NEMO complexes obtained by SWATH-MS. The comprehensive MS measurement leads to quantification of up to about 3,000 proteins across about 21-40 IP samples. We detected and quantified almost all known interactors of MyD88, TRAF6 and NEMO. By analyzing these quantitative data, we uncovered differential recruitment of IRAK family proteins to LPS-induced signaling complexes and determined the stoichiometry of the Myddosome complex. In addition, quantitative phosphoproteomics analysis identified a number of unreported high-confidence phosphosites on the key proteins in LPS signaling pathway. Collectively, data of dynamic protein interactions and phosphorylation presented by this study could be a resource for further study of the LPS signaling pathway.
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Affiliation(s)
- Xiurong Wu
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Daowei Yang
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Fu Zhao
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Zhang-Hua Yang
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Dazheng Wang
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Muzhen Qiao
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Yuan Fang
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Wanyun Li
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Rui Wu
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Peng He
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Yu Cong
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Chang'an Chen
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Lichen Hu
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Yihua Yan
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Changchuan Xie
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Yaying Wu
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Jiahuai Han
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Chuan-Qi Zhong
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
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6
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Chandler KB, Mehta N, Leon DR, Suscovich TJ, Alter G, Costello CE. Multi-isotype Glycoproteomic Characterization of Serum Antibody Heavy Chains Reveals Isotype- and Subclass-Specific N-Glycosylation Profiles. Mol Cell Proteomics 2019; 18:686-703. [PMID: 30659065 PMCID: PMC6442369 DOI: 10.1074/mcp.ra118.001185] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [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: 11/02/2018] [Revised: 01/16/2019] [Indexed: 01/16/2023] Open
Abstract
Antibodies are critical glycoproteins that bridge the innate and adaptive immune systems to provide protection against infection. The isotype/subclass of the antibody, the co-translational N-glycosylation on the CH2 domain, and the remodeling of the N-linked glycans during passage through the ER and Golgi are the known variables within the Fc domain that program antibody effector function. Through investigations of monoclonal therapeutics, it has been observed that addition or removal of specific monosaccharide residues from antibody N-glycans can influence the potency of antibodies, highlighting the importance of thoroughly characterizing antibody N-glycosylation. Although IgGs usually have a single N-glycosylation site and are well studied, other antibody isotypes, e.g. IgA and IgM, that are the first responders in certain diseases, have two to five sites/monomer of antibody, and little is known about their N-glycosylation. Here we employ a nLC-MS/MS method using stepped-energy higher energy collisional dissociation to characterize the N-glycan repertoire and site occupancy of circulating serum antibodies. We simultaneously determined the site-specific N-linked glycan repertoire for IgG1, IgG4, IgA1, IgA2, and IgM in individual healthy donors. Compared with IgG1, IgG4 displayed a higher relative abundance of G1S1F and a lower relative abundance of G1FB. IgA1 and IgA2 displayed mostly biantennary N-glycans. IgA2 variants with the either serine (S93) or proline (P93) were detected. In digests of the sera from a subset of donors, we detected an unmodified peptide containing a proline residue at position 93; this substitution would strongly disfavor N-glycosylation at N92. IgM sites N46, N209, and N272 displayed mostly complex glycans, whereas sites N279 and N439 displayed higher relative abundances of high-mannose glycoforms. This multi-isotype approach is a crucial step toward developing a platform to define disease-specific N-glycan signatures for different isotypes to help tune antibodies to induce protection. Data are available via ProteomeXchange with identifier PXD010911.
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Affiliation(s)
- Kevin Brown Chandler
- From the ‡Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts
| | - Nickita Mehta
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | - Deborah R Leon
- From the ‡Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts
| | - Todd J Suscovich
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | - Catherine E Costello
- From the ‡Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts;.
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7
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Grabowski P, Hesse S, Hollizeck S, Rohlfs M, Behrends U, Sherkat R, Tamary H, Ünal E, Somech R, Patıroğlu T, Canzar S, van der Werff Ten Bosch J, Klein C, Rappsilber J. Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition. Mol Cell Proteomics 2019; 18:760-772. [PMID: 30630937 PMCID: PMC6442368 DOI: 10.1074/mcp.ra118.001141] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 10/17/2018] [Revised: 12/14/2018] [Indexed: 11/06/2022] Open
Abstract
Neutrophil granulocytes are critical mediators of innate immunity and tissue regeneration. Rare diseases of neutrophil granulocytes may affect their differentiation and/or functions. However, there are very few validated diagnostic tests assessing the functions of neutrophil granulocytes in these diseases. Here, we set out to probe omics analysis as a novel diagnostic platform for patients with defective differentiation and function of neutrophil granulocytes. We analyzed highly purified neutrophil granulocytes from 68 healthy individuals and 16 patients with rare monogenic diseases. Cells were isolated from fresh venous blood (purity >99%) and used to create a spectral library covering almost 8000 proteins using strong cation exchange fractionation. Patient neutrophil samples were then analyzed by data-independent acquisition proteomics, quantifying 4154 proteins in each sample. Neutrophils with mutations in the neutrophil elastase gene ELANE showed large proteome changes that suggest these mutations may affect maturation of neutrophil granulocytes and initiate misfolded protein response and cellular stress mechanisms. In contrast, only few proteins changed in patients with leukocyte adhesion deficiency (LAD) and chronic granulomatous disease (CGD). Strikingly, neutrophil transcriptome analysis showed no correlation with its proteome. In case of two patients with undetermined genetic causes, proteome analysis guided the targeted genetic diagnostics and uncovered the underlying genomic mutations. Data-independent acquisition proteomics may help to define novel pathomechanisms in neutrophil diseases and provide a clinically useful diagnostic dimension.
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Affiliation(s)
- Piotr Grabowski
- From the ‡Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Sebastian Hesse
- §Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, 80337 Munich, Germany
| | - Sebastian Hollizeck
- §Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, 80337 Munich, Germany
| | - Meino Rohlfs
- §Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, 80337 Munich, Germany
| | - Uta Behrends
- ‖Children's Hospital, Hematology-Oncology, Technical University Munich, 80804 Munich, Germany
| | - Roya Sherkat
- Acquired Immunodeficiency Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hannah Tamary
- Schneider Children's Medical Center of Israel, Petah Tikva, Sackler School of Medicine, Tel Aviv University, Israel
| | - Ekrem Ünal
- Department of Pediatrics, Division of Pediatric Hematology & Oncology, Erciyes University, Kayseri, Turkey
| | - Raz Somech
- Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University Tel Aviv, Israel
| | - Türkan Patıroğlu
- Department of Pediatrics, Division of Pediatric Hematology & Oncology, Erciyes University, Kayseri, Turkey
| | - Stefan Canzar
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Christoph Klein
- §Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, 80337 Munich, Germany;.
| | - Juri Rappsilber
- From the ‡Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany;; ¶Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK;.
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8
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Nanaware PP, Jurewicz MM, Leszyk JD, Shaffer SA, Stern LJ. HLA-DO Modulates the Diversity of the MHC-II Self-peptidome. Mol Cell Proteomics 2019; 18:490-503. [PMID: 30573663 PMCID: PMC6398211 DOI: 10.1074/mcp.ra118.000956] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 07/05/2018] [Revised: 11/26/2018] [Indexed: 12/30/2022] Open
Abstract
Presentation of antigenic peptides on MHC-II molecules is essential for tolerance to self and for initiation of immune responses against foreign antigens. DO (HLA-DO in humans, H2-O in mice) is a nonclassical MHC-II protein that has been implicated in control of autoimmunity and regulation of neutralizing antibody responses to viruses. These effects likely are related to a role of DO in selecting MHC-II epitopes, but previous studies examining the effect of DO on presentation of selected CD4 T cell epitopes have been contradictory. To understand how DO modulates MHC-II antigen presentation, we characterized the full spectrum of peptides presented by MHC-II molecules expressed by DO-sufficient and DO-deficient antigen-presenting cells in vivo and in vitro using quantitative mass spectrometry approaches. We found that DO controlled the diversity of the presented peptide repertoire, with a subset of peptides presented only when DO was expressed. Antigen-presenting cells express another nonclassical MHC-II protein, DM, which acts as a peptide editor by preferentially catalyzing the exchange of less stable MHC-II peptide complexes, and which is inhibited when bound to DO. Peptides presented uniquely in the presence of DO were sensitive to DM-mediated exchange, suggesting that decreased DM editing was responsible for the increased diversity. DO-deficient mice mounted CD4 T cell responses against wild-type antigen-presenting cells, but not vice versa, indicating that DO-dependent alterations in the MHC-II peptidome could be recognized by circulating T cells. These data suggest that cell-specific and regulated expression of HLA-DO serves to fine-tune MHC-II peptidomes, in order to enhance self-tolerance to a wide spectrum of epitopes while allowing focused presentation of immunodominant epitopes during an immune response.
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Affiliation(s)
- Padma P Nanaware
- From the ‡Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Mollie M Jurewicz
- From the ‡Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - John D Leszyk
- §Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts 01545
| | - Scott A Shaffer
- §Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts 01545
- ¶Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Lawrence J Stern
- From the ‡Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01605;
- ¶Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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9
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Månberg A, Bradley F, Qundos U, Guthrie BL, Birse K, Noël-Romas L, Lindskog C, Bosire R, Kiarie J, Farquhar C, Burgener AD, Nilsson P, Broliden K. A High-throughput Bead-based Affinity Assay Enables Analysis of Genital Protein Signatures in Women At Risk of HIV Infection. Mol Cell Proteomics 2019; 18:461-476. [PMID: 30504243 PMCID: PMC6398207 DOI: 10.1074/mcp.ra118.000757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 03/21/2018] [Revised: 11/29/2018] [Indexed: 01/28/2023] Open
Abstract
Women at high risk of HIV infection, including sex workers and those with active genital inflammation, have molecular signatures of immune activation and epithelial barrier remodeling in samples of their genital mucosa. These alterations in the local immunological milieu are likely to impact HIV susceptibility. We here analyze host genital protein signatures in HIV uninfected women, with high frequency of condom use, living in HIV-serodiscordant relationships. Cervicovaginal secretions from women living in HIV-serodiscordant relationships (n = 62) were collected at three time points over 12 months. Women living in HIV-negative seroconcordant relationships (controls, n = 25) were sampled at one time point. All study subjects were examined for demographic parameters associated with susceptibility to HIV infection. The cervicovaginal samples were analyzed using a high-throughput bead-based affinity assay. Proteins involved in epithelial barrier function and inflammation were increased in HIV-serodiscordant women. By combining several methods of analysis, a total of five proteins (CAPG, KLK10, SPRR3, elafin/PI3, CSTB) were consistently associated with this study group. Proteins analyzed using the affinity set-up were further validated by label-free tandem mass spectrometry in a partially overlapping cohort with concordant results. Women living in HIV-serodiscordant relationships thus had elevated levels of proteins involved in epithelial barrier function and inflammation despite low prevalence of sexually transmitted infections and a high frequency of safe sex practices. The identified proteins are important markers to follow during assessment of mucosal HIV susceptibility factors and a high-throughput bead-based affinity set-up could be a suitable method for such evaluation.
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Affiliation(s)
- Anna Månberg
- From the ‡Affinity Proteomics, SciLifeLab, Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Frideborg Bradley
- §Department of Medicine Solna, Unit of Infectious Diseases, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden;
| | - Ulrika Qundos
- From the ‡Affinity Proteomics, SciLifeLab, Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Brandon L Guthrie
- ¶Department of Global Health and Department of Epidemiology Health, University of Washington, Seattle, Washington
| | - Kenzie Birse
- ‖Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- **National HIV and Retrovirology Labs, JC Wilt Infectious Disease Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Laura Noël-Romas
- ‖Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- **National HIV and Retrovirology Labs, JC Wilt Infectious Disease Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Cecilia Lindskog
- ‡‡SciLifeLab, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Rose Bosire
- §§Kenya Medical Research Institute, Nairobi, Kenya
| | - James Kiarie
- ¶¶Department of Obstetrics and Gynecology, University of Nairobi, Nairobi, Kenya
| | - Carey Farquhar
- ‖‖Department of Medicine, Global Health, and Epidemiology, University of Washington, Seattle, Washington
| | - Adam D Burgener
- §Department of Medicine Solna, Unit of Infectious Diseases, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
- ‖Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- **National HIV and Retrovirology Labs, JC Wilt Infectious Disease Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Peter Nilsson
- From the ‡Affinity Proteomics, SciLifeLab, Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Kristina Broliden
- §Department of Medicine Solna, Unit of Infectious Diseases, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
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10
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Pauwels AM, Härtlova A, Peltier J, Driege Y, Baudelet G, Brodin P, Trost M, Beyaert R, Hoffmann E. Spatiotemporal Changes of the Phagosomal Proteome in Dendritic Cells in Response to LPS Stimulation. Mol Cell Proteomics 2019; 18:909-922. [PMID: 30808727 DOI: 10.1074/mcp.ra119.001316] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/23/2019] [Indexed: 12/15/2022] Open
Abstract
Dendritic cells (DCs) are professional phagocytes that use innate sensing and phagocytosis to internalize and degrade self as well as foreign material, such as pathogenic bacteria, within phagosomes. These intracellular compartments are equipped to generate antigenic peptides that serve as source for antigen presentation to T cells initiating adaptive immune responses. The phagosomal proteome of DCs is only partially studied and is highly dynamic as it changes during phagosome maturation, when phagosomes sequentially interact with endosomes and lysosomes. In addition, the activation status of the phagocyte can modulate the phagosomal composition and is able to shape phagosomal functions.In this study, we determined spatiotemporal changes of the proteome of DC phagosomes during their maturation and compared resting and lipopolysaccharide (LPS)-stimulated bone marrow-derived DCs by label-free, quantitative mass spectrometry. Ovalbumin-coupled latex beads were used as phagocytosis model system and revealed that LPS-treated DCs show decreased recruitment of proteins involved in phagosome maturation, such as subunits of the vacuolar proton ATPase, cathepsin B, D, S, and RAB7. In contrast, those phagosomes were characterized by an increased recruitment of proteins involved in antigen cross-presentation, e.g. different subunits of MHC I molecules, the proteasome and tapasin, confirming the observed increase in cross-presentation efficacy in those cells. Further, several proteins were identified that were not previously associated with phagosomal functions. Hierarchical clustering of phagosomal proteins demonstrated that their acquisition to DC phagosomes is not only dependent on the duration of phagosome maturation but also on the activation state of DCs. Thus, our study provides a comprehensive overview of how DCs alter their phagosome composition in response to LPS, which has profound impact on the initiation of efficient immune responses.
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Affiliation(s)
- Anne-Marie Pauwels
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Anetta Härtlova
- ¶Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Julien Peltier
- ¶Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Yasmine Driege
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Griet Baudelet
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Priscille Brodin
- ‖Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Matthias Trost
- ¶Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Rudi Beyaert
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Eik Hoffmann
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium;; ‖Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, Lille, France
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11
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Myers SA, Rhoads A, Cocco AR, Peckner R, Haber AL, Schweitzer LD, Krug K, Mani DR, Clauser KR, Rozenblatt-Rosen O, Hacohen N, Regev A, Carr SA. Streamlined Protocol for Deep Proteomic Profiling of FAC-sorted Cells and Its Application to Freshly Isolated Murine Immune Cells. Mol Cell Proteomics 2019; 18:995-1009. [PMID: 30792265 DOI: 10.1074/mcp.ra118.001259] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/15/2019] [Indexed: 12/27/2022] Open
Abstract
Proteomic profiling describes the molecular landscape of proteins in cells immediately available to sense, transduce, and enact the appropriate responses to extracellular queues. Transcriptional profiling has proven invaluable to our understanding of cellular responses; however, insights may be lost as mounting evidence suggests transcript levels only moderately correlate with protein levels in steady state cells. Mass spectrometry-based quantitative proteomics is a well-suited and widely used analytical tool for studying global protein abundances. Typical proteomic workflows are often limited by the amount of sample input that is required for deep and quantitative proteome profiling. This is especially true if the cells of interest need to be purified by fluorescence-activated cell sorting (FACS) and one wants to avoid ex vivo culturing. To address this need, we developed an easy to implement, streamlined workflow that enables quantitative proteome profiling from roughly 2 μg of protein input per experimental condition. Utilizing a combination of facile cell collection from cell sorting, solid-state isobaric labeling and multiplexing of peptides, and small-scale fractionation, we profiled the proteomes of 12 freshly isolated, primary murine immune cell types. Analyzing half of the 3e5 cells collected per cell type, we quantified over 7000 proteins across 12 key immune cell populations directly from their resident tissues. We show that low input proteomics is precise, and the data generated accurately reflects many aspects of known immunology, while expanding the list of cell-type specific proteins across the cell types profiled. The low input proteomics methods we developed are readily adaptable and broadly applicable to any cell or sample types and should enable proteome profiling in systems previously unattainable.
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Affiliation(s)
- Samuel A Myers
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; §Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;.
| | - Andrew Rhoads
- ¶Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | - Alexandra R Cocco
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - Ryan Peckner
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - Adam L Haber
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; §Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | | | - Karsten Krug
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - D R Mani
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - Karl R Clauser
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - Orit Rozenblatt-Rosen
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; §Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Nir Hacohen
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; ‖Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215;; **Center for Cancer Immunology, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Aviv Regev
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; §Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;; ‡‡Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140
| | - Steven A Carr
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;.
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12
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Siau A, Huang X, Loh HP, Zhang N, Meng W, Sze SK, Renia L, Preiser P. Immunomic Identification of Malaria Antigens Associated With Protection in Mice. Mol Cell Proteomics 2019; 18:837-853. [PMID: 30718293 DOI: 10.1074/mcp.ra118.000997] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 01/22/2019] [Indexed: 11/06/2022] Open
Abstract
Efforts to develop vaccines against malaria represent a major research target. The observations that 1) sterile protection can be obtained when the host is exposed to live parasites and 2) the immunity against blood stage parasite is principally mediated by protective antibodies suggest that a protective vaccine is feasible. However, only a small number of proteins have been investigated so far and most of the Plasmodium proteome has yet to be explored. To date, only few immunodominant antigens have emerged for testing in clinical trials but no formulation has led to substantial protection in humans. The nature of parasite molecules associated with protection remains elusive. Here, immunomic screening of mice immune sera with different protection efficiencies against the whole parasite proteome allowed us to identify a large repertoire of antigens validated by screening a library expressing antigens. The calculation of weighted scores reflecting the likelihood of protection of each antigen using five predictive criteria derived from immunomic and proteomic data sets, highlighted a priority list of protective antigens. Altogether, the approach sheds light on conserved antigens across Plasmodium that are amenable to targeting by the host immune system upon merozoite invasion and blood stage development. Most of these antigens have preliminary protection data but have not been widely considered as candidate for vaccine trials, opening new perspectives that overcome the limited choice of immunodominant, poorly protective vaccines currently being the focus of malaria vaccine researches.
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Affiliation(s)
- Anthony Siau
- From the ‡Nanyang Technological University, School of Biological Sciences, Singapore;.
| | - Ximei Huang
- From the ‡Nanyang Technological University, School of Biological Sciences, Singapore;; From the ‡Nanyang Technological University, School of Biological Sciences, Singapore
| | - Han Ping Loh
- From the ‡Nanyang Technological University, School of Biological Sciences, Singapore;; From the ‡Nanyang Technological University, School of Biological Sciences, Singapore
| | - Neng Zhang
- From the ‡Nanyang Technological University, School of Biological Sciences, Singapore
| | - Wei Meng
- From the ‡Nanyang Technological University, School of Biological Sciences, Singapore
| | - Siu Kwan Sze
- From the ‡Nanyang Technological University, School of Biological Sciences, Singapore
| | - Laurent Renia
- §Singapore Immunology Network (SIgN), A*STAR, Biopolis, Singapore
| | - Peter Preiser
- From the ‡Nanyang Technological University, School of Biological Sciences, Singapore;.
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13
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Sanz-Bravo A, Alvarez-Navarro C, Martín-Esteban A, Barnea E, Admon A, López de Castro JA. Ranking the Contribution of Ankylosing Spondylitis-associated Endoplasmic Reticulum Aminopeptidase 1 (ERAP1) Polymorphisms to Shaping the HLA-B*27 Peptidome. Mol Cell Proteomics 2018; 17:1308-1323. [PMID: 29632046 DOI: 10.1074/mcp.ra117.000565] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/05/2018] [Indexed: 11/06/2022] Open
Abstract
The Endoplasmic reticulum aminopeptidase I (ERAP1) trims peptides to their optimal size for binding to Major Histocompatibility Complex class I proteins. The natural polymorphism of this enzyme is associated with ankylosing spondylitis (AS) in epistasis with the major risk factor for this disease, HLA-B*27, suggesting a direct relationship between AS and HLA-B*27-bound peptides. Three polymorphisms that affect peptide trimming protect from AS: K528R, D575N/R725Q, and Q730E. We characterized and ranked the effects of each mutation, and their various combinations, by quantitative comparisons of the HLA-B*27 peptidomes from cells expressing distinct ERAP1 variants. Five features were examined: peptide length, N-terminal flanking residues, N-terminal residues of the natural ligands, internal sequences and affinity for B*27:05. Polymorphism at residue 528 showed the largest influence, affecting all five features regardless of peptide length. D575N/R725Q showed a much smaller effect. Yet, when co-occurring with K528R, it further decreased ERAP1 activity. Polymorphism at residue 730 showed a significant influence on peptide length, because of distinct effects on trimming of nonamers compared with longer peptides. Accordingly, multiple features were affected by the Q730E mutation in a length-dependent way. The alterations induced in the B*27:05 peptidome by natural ERAP1 variants with different K528R/Q730E combinations reflected separate and additive effects of both mutations. Thus, the influence of ERAP1 on HLA-B*27 is very diverse at the population level, because of the multiplicity and complexity of ERAP1 variants, and to the distinct effects of their co-occurring polymorphisms, leading to significant modulation of disease risk among HLA-B*27-positive individuals.
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Affiliation(s)
- Alejandro Sanz-Bravo
- From the ‡Centro de Biología Molecular Severo Ochoa (CSIC-UAM), 28049 Madrid, Spain
| | - Carlos Alvarez-Navarro
- §Instituto de Inmunología, Facultad de Medicina, Universidad Austral del Chile, and Escuela de Tecnología Médica, Facultad de Salud, Universidad Santo Tomás, Valdivia, Chile
| | | | - Eilon Barnea
- ¶Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Arie Admon
- ¶Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
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14
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Duhamel M, Rose M, Rodet F, Murgoci AN, Zografidou L, Régnier-Vigouroux A, Vanden Abeele F, Kobeissy F, Nataf S, Pays L, Wisztorski M, Cizkova D, Fournier I, Salzet M. Paclitaxel Treatment and Proprotein Convertase 1/3 (PC1/3) Knockdown in Macrophages is a Promising Antiglioma Strategy as Revealed by Proteomics and Cytotoxicity Studies. Mol Cell Proteomics 2018. [PMID: 29531019 DOI: 10.1074/mcp.ra117.000443] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
High grade gliomas are the most common brain tumors in adult. These tumors are characterized by a high infiltration in microglial cells and macrophages. The immunosuppressive tumor environment is known to orient immune cells toward a pro-tumoral and anti-inflammatory phenotype. Therefore, the current challenge for cancer therapy is to find a way to reorient macrophages toward an antitumoral phenotype. Previously, we demonstrated that macrophages secreted antitumoral factors when they were invalidated for the proprotein converstase 1/3 (PC1/3) and treated with LPS. However, achieving an activation of macrophages via LPS/TLR4/Myd88-dependent pathway appears yet unfeasible in cancer patients. On the contrary, the antitumor drug Paclitaxel is also known to activate the TLR4 MyD88-dependent signaling pathway and mimics LPS action. Therefore, we evaluated if PC1/3 knock-down (KD) macrophages could be activated by Paclitaxel and efficient against glioma. We report here that such a treatment of PC1/3 KD macrophages drove to the overexpression of proteins mainly involved in cytoskeleton rearrangement. In support of this finding, we found that these cells exhibited a Ca2+ increase after Paclitaxel treatment. This is indicative of a possible depolymerization of microtubules and may therefore reflect an activation of inflammatory pathways in macrophages. In such a way, we found that PC1/3 KD macrophages displayed a repression of the anti-inflammatory pathway STAT3 and secreted more pro-inflammatory cytokines. Extracellular vesicles isolated from these PC1/3 KD cells inhibited glioma growth. Finally, the supernatant collected from the coculture between glioma cells and PC1/3 KD macrophages contained more antitumoral factors. These findings unravel the potential value of a new therapeutic strategy combining Paclitaxel and PC1/3 inhibition to switch macrophages toward an antitumoral immunophenotype.
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Affiliation(s)
- Marie Duhamel
- From the ‡Inserm U-1192, Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), Université Lille 1, Cité Scientifique, 59655 Villeneuve D'Ascq, France;
| | - Mélanie Rose
- From the ‡Inserm U-1192, Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), Université Lille 1, Cité Scientifique, 59655 Villeneuve D'Ascq, France.,§Oncovet Clinical Research (OCR), SIRIC ONCOLille, Villeneuve d'Ascq, France
| | - Franck Rodet
- From the ‡Inserm U-1192, Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), Université Lille 1, Cité Scientifique, 59655 Villeneuve D'Ascq, France
| | - Adriana Natalia Murgoci
- From the ‡Inserm U-1192, Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), Université Lille 1, Cité Scientifique, 59655 Villeneuve D'Ascq, France.,§§Institute of Neuroimmunology, Slovak Academy of Sciences, 845 10, Bratislava, Slovak Republic
| | - Lea Zografidou
- ¶Johannes Gutenberg-Universität Mainz, Johann-Joachim-Becher-Weg 15, D-55128 Mainz, Germany
| | - Anne Régnier-Vigouroux
- ¶Johannes Gutenberg-Universität Mainz, Johann-Joachim-Becher-Weg 15, D-55128 Mainz, Germany
| | - Fabien Vanden Abeele
- ‖Inserm U-1003, Equipe labellisée par la Ligue Nationale contre le cancer, Laboratory of Excellence, Ion Channels Science and Therapeutics, Université Lille 1, Cité Scientifique, 59655 Villeneuve d'Ascq, France
| | - Firas Kobeissy
- **Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, 1107 2020 Beirut, Lebanon
| | - Serge Nataf
- ‡‡Inserm U-1060, CarMeN Laboratory, Banque de Tissus et de Cellules des Hospices Civils de Lyon, Université Lyon-1, Hôpital Edouard Herriot, 69437 Lyon cedex 03, France
| | - Laurent Pays
- ‡‡Inserm U-1060, CarMeN Laboratory, Banque de Tissus et de Cellules des Hospices Civils de Lyon, Université Lyon-1, Hôpital Edouard Herriot, 69437 Lyon cedex 03, France
| | - Maxence Wisztorski
- From the ‡Inserm U-1192, Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), Université Lille 1, Cité Scientifique, 59655 Villeneuve D'Ascq, France
| | - Dasa Cizkova
- §§Institute of Neuroimmunology, Slovak Academy of Sciences, 845 10, Bratislava, Slovak Republic
| | - Isabelle Fournier
- From the ‡Inserm U-1192, Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), Université Lille 1, Cité Scientifique, 59655 Villeneuve D'Ascq, France
| | - Michel Salzet
- From the ‡Inserm U-1192, Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), Université Lille 1, Cité Scientifique, 59655 Villeneuve D'Ascq, France
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