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Madunić K, Luijkx YMCA, Mayboroda OA, Janssen GMC, van Veelen PA, Strijbis K, Wennekes T, Lageveen-Kammeijer GSM, Wuhrer M. O-Glycomic and Proteomic Signatures of Spontaneous and Butyrate-Stimulated Colorectal Cancer Cell Line Differentiation. Mol Cell Proteomics 2023; 22:100501. [PMID: 36669592 PMCID: PMC9999233 DOI: 10.1016/j.mcpro.2023.100501] [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: 03/13/2022] [Revised: 01/08/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Gut microbiota of the gastrointestinal tract provide health benefits to the human host via bacterial metabolites. Bacterial butyrate has beneficial effects on intestinal homeostasis and is the preferred energy source of intestinal epithelial cells, capable of inducing differentiation. It was previously observed that changes in the expression of specific proteins as well as protein glycosylation occur with differentiation. In this study, specific mucin O-glycans were identified that mark butyrate-induced epithelial differentiation of the intestinal cell line CaCo-2 (Cancer Coli-2), by applying porous graphitized carbon nano-liquid chromatography with electrospray ionization tandem mass spectrometry. Moreover, a quantitative proteomic approach was used to decipher changes in the cell proteome. It was found that the fully differentiated butyrate-stimulated cells are characterized by a higher expression of sialylated O-glycan structures, whereas fucosylation is downregulated with differentiation. By performing an integrative approach, we generated hypotheses about the origin of the observed O-glycome changes. These insights pave the way for future endeavors to study the dynamic O-glycosylation patterns in the gut, either produced via cellular biosynthesis or through the action of bacterial glycosidases as well as the functional role of these patterns in homeostasis and dysbiosis at the gut-microbiota interface.
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Affiliation(s)
- K Madunić
- Center for Proteomics and Metabolomics, Leiden University, The Netherlands
| | - Y M C A Luijkx
- Department Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands; Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - O A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University, The Netherlands
| | - G M C Janssen
- Center for Proteomics and Metabolomics, Leiden University, The Netherlands
| | - P A van Veelen
- Center for Proteomics and Metabolomics, Leiden University, The Netherlands
| | - K Strijbis
- Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - T Wennekes
- Department Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | | | - M Wuhrer
- Center for Proteomics and Metabolomics, Leiden University, The Netherlands.
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2
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Venema WJ, Hiddingh S, Janssen GMC, Ossewaarde-van Norel J, van Loon ND, de Boer JH, van Veelen PA, Kuiper JJW. Retina-arrestin specific CD8+ T cells are not implicated in HLA-A29-positive birdshot chorioretinitis. Clin Immunol 2023; 247:109219. [PMID: 36581221 DOI: 10.1016/j.clim.2022.109219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND HLA-A29-positive birdshot chorioretinitis (BCR) is an inflammatory eye disorder that is generally assumed to be caused by an autoimmune response to HLA-A29-presented peptides from retinal arrestin (SAG), yet the epitopes recognized by CD8+ T cells from patients remain to be identified. OBJECTIVES The identification of natural ligands of SAG presented by HLA-A29. To quantify CD8+ T cells reactive to antigenic SAG peptides presented by HLA-A29 in patients and controls. METHODS We performed mass-spectrometry based immunopeptidomics of HLA-A29 of antigen-presenting cell lines from patients engineered to express SAG. MHC-I Dextramer technology was utilised to determine expansion of antigen-specific CD8+ T cells reactive to SAG peptides in complex with HLA-A29 in a cohort of BCR patients, HLA-A29-positive controls, and HLA-A29-negative controls. RESULTS We report on the naturally presented antigenic SAG peptides identified by sequencing the HLA-A29 immunopeptidome of antigen-presenting cells of patients. We show that the N-terminally extended SAG peptide precursors can be trimmed in vitro by the antigen-processing aminopeptidases ERAP1 and ERAP2. Unexpectedly, no enhanced antigen engagement by CD8+ T cells upon stimulation with SAG peptides was observed in patients or HLA-A29-positive controls. Multiplexed HLA-A29-peptide dextramer profiling of a case-control cohort revealed that CD8+ T cells specific for these SAG peptides were neither detectable in peripheral blood nor in eye biopsies of patients. CONCLUSIONS Collectively, these findings demonstrate that SAG is not a CD8+ T cell autoantigen and sharply contrast the paradigm in the pathogenesis of BCR. Therefore, the mechanism by which HLA-A29 is associated with BCR does not involve SAG.
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Affiliation(s)
- W J Venema
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - S Hiddingh
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - G M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - J Ossewaarde-van Norel
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - N Dam van Loon
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - J H de Boer
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - P A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - J J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands.
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3
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Tuerlings M, Janssen GMC, Boone I, van Hoolwerff M, Rodriguez Ruiz A, Houtman E, Suchiman HED, van der Wal RJP, Nelissen RGHH, Coutinho de Almeida R, van Veelen PA, Ramos YFM, Meulenbelt I. WWP2 confers risk to osteoarthritis by affecting cartilage matrix deposition via hypoxia associated genes. Osteoarthritis Cartilage 2023; 31:39-48. [PMID: 36208715 DOI: 10.1016/j.joca.2022.09.009] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/12/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVE To explore the co-expression network of the osteoarthritis (OA) risk gene WWP2 in articular cartilage and study cartilage characteristics when mimicking the effect of OA risk allele rs1052429-A on WWP2 expression in a human 3D in vitro model of cartilage. METHOD Co-expression behavior of WWP2 with genes expressed in lesioned OA articular cartilage (N = 35 samples) was explored. By applying lentiviral particle mediated WWP2 upregulation in 3D in vitro pellet cultures of human primary chondrocytes (N = 8 donors) the effects of upregulation on cartilage matrix deposition was evaluated. Finally, we transfected primary chondrocytes with miR-140 mimics to evaluate whether miR-140 and WWP2 are involved in similar pathways. RESULTS Upon performing Spearman correlations in lesioned OA cartilage, 98 highly correlating genes (|ρ| > 0.7) were identified. Among these genes, we identified GJA1, GDF10, STC2, WDR1, and WNK4. Subsequent upregulation of WWP2 on 3D chondrocyte pellet cultures resulted in a decreased expression of COL2A1 and ACAN and an increase in EPAS1 expression. Additionally, we observed a decreased expression of GDF10, STC2, and GJA1. Proteomics analysis identified 42 proteins being differentially expressed with WWP2 upregulation, which were enriched for ubiquitin conjugating enzyme activity. Finally, upregulation of miR-140 in 2D chondrocytes resulted in significant upregulation of WWP2 and WDR1. CONCLUSIONS Mimicking the effect of OA risk allele rs1052429-A on WWP2 expression initiates detrimental processes in the cartilage shown by a response in hypoxia associated genes EPAS1, GDF10, and GJA1 and a decrease in anabolic markers, COL2A1 and ACAN.
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Affiliation(s)
- M Tuerlings
- Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - G M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands.
| | - I Boone
- Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - M van Hoolwerff
- Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - A Rodriguez Ruiz
- Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - E Houtman
- Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - H E D Suchiman
- Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - R J P van der Wal
- Dept. Orthopaedics, Leiden University Medical Center, Leiden, the Netherlands.
| | - R G H H Nelissen
- Dept. Orthopaedics, Leiden University Medical Center, Leiden, the Netherlands.
| | - R Coutinho de Almeida
- Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - P A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands.
| | - Y F M Ramos
- Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - I Meulenbelt
- Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands.
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4
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Kissel T, Reijm S, Slot LM, Cavallari M, Wortel CM, Vergroesen RD, Stoeken-Rijsbergen G, Kwekkeboom JC, Kampstra A, Levarht E, Drijfhout JW, Bang H, Bonger KM, Janssen G, van Veelen PA, Huizinga T, Scherer HU, Reth M, Toes R. Antibodies and B cells recognising citrullinated proteins display a broad cross-reactivity towards other post-translational modifications. Ann Rheum Dis 2020; 79:472-480. [PMID: 32041746 DOI: 10.1136/annrheumdis-2019-216499] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [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: 10/18/2019] [Accepted: 01/17/2020] [Indexed: 11/04/2022]
Abstract
OBJECTIVE Autoantibodies against antigens carrying distinct post-translational modifications (PTMs), such as citrulline, homocitrulline or acetyllysine, are hallmarks of rheumatoid arthritis (RA). The relation between these anti-modified protein antibody (AMPA)-classes is poorly understood as is the ability of different PTM-antigens to activate B-cell receptors (BCRs) directed against citrullinated proteins (CP). Insights into the nature of PTMs able to activate such B cells are pivotal to understand the 'evolution' of the autoimmune response conceivable underlying the disease. Here, we investigated the cross-reactivity of monoclonal AMPA and the ability of different types of PTM-antigens to activate CP-reactive BCRs. METHODS BCR sequences from B cells isolated using citrullinated or acetylated antigens were used to produce monoclonal antibodies (mAb) followed by a detailed analysis of their cross-reactivity towards PTM-antigens. Ramos B-cell transfectants expressing CP-reactive IgG BCRs were generated and their activation on stimulation with PTM-antigens investigated. RESULTS Most mAbs were highly cross-reactive towards multiple PTMs, while no reactivity was observed to the unmodified controls. B cells carrying CP-reactive BCRs showed activation on stimulation with various types of PTM-antigens. CONCLUSIONS Our study illustrates that AMPA exhibit a high cross-reactivity towards at least two PTMs indicating that their recognition pattern is not confined to one type of modification. Furthermore, our data show that CP-reactive B cells are not only activated by citrullinated, but also by carbamylated and/or acetylated antigens. These data are vital for the understanding of the breach of B-cell tolerance against PTM-antigens and the possible contribution of these antigens to RA-pathogenesis.
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Affiliation(s)
- T Kissel
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - S Reijm
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - L M Slot
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - M Cavallari
- Department of Biology III (Molecular Immunology), Freiburg University, Freiburg, Germany
| | - C M Wortel
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - R D Vergroesen
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - G Stoeken-Rijsbergen
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - J C Kwekkeboom
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Asb Kampstra
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ewn Levarht
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - J W Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - H Bang
- Orgentec Diagnostika, Mainz, Germany
| | - K M Bonger
- Department of Biomolecular Chemistry and Synthetic Organic Chemistry, Radboud University, Nijmegen, The Netherlands
| | - Gmc Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - P A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Twj Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - H U Scherer
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - M Reth
- Department of Biology III (Molecular Immunology), Freiburg University, Freiburg, Germany
| | - Rem Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
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5
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Lubbers R, Oostindie SC, Dijkstra DJ, Parren PWHI, Verheul MK, Abendstein L, Sharp TH, de Ru A, Janssen GMC, van Veelen PA, van den Bremer ETJ, Bleijlevens B, de Kreuk BJ, Beurskens FJ, Trouw LA. Carbamylation reduces the capacity of IgG for hexamerization and complement activation. Clin Exp Immunol 2019; 200:1-11. [PMID: 31853959 PMCID: PMC7066385 DOI: 10.1111/cei.13411] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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] [Accepted: 12/11/2019] [Indexed: 02/06/2023] Open
Abstract
Carbamylation is a post‐translational modification that can be detected on a range of proteins, including immunoglobulin (Ig)G, in several clinical conditions. Carbamylated IgG (ca‐IgG) was reported to lose its capacity to trigger complement activation, but the mechanism remains unclear. Because C1q binds with high affinity to hexameric IgG, we analyzed whether carbamylation of IgG affects binding of C1q, hexamerization and complement‐dependent cytotoxicity (CDC). Synovial tissues of rheumatoid arthritis (RA) patients were analyzed for the presence of ca‐IgG in vivo. Synovial tissues from RA patients were analyzed for the presence of ca‐IgG using mass spectrometry (MS). Monomeric or hexameric antibodies were carbamylated in vitro and quality in solution was controlled. The capacity of ca‐IgG to activate complement was analyzed in enzyme‐linked immunosorbent (ELISAs) and cellular CDC assays. Using MS, we identified ca‐IgG to be present in the joints of RA patients. Using in vitro carbamylated antibodies, we observed that ca‐IgG lost its capacity to activate complement in both solid‐phase and CDC assays. Mixing ca‐IgG with non‐modified IgG did not result in effective inhibition of complement activation by ca‐IgG. Carbamylation of both monomeric IgG and preformed hexameric IgG greatly impaired the capacity to trigger complement activation. Furthermore, upon carbamylation, the preformed hexameric IgG dissociated into monomeric IgG in solution, indicating that carbamylation influences both hexamerization and C1q binding. In conclusion, ca‐IgG can be detected in vivo and has a strongly reduced capacity to activate complement which is, in part, mediated through a reduced ability to form hexamers.
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Affiliation(s)
- R Lubbers
- Department Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - S C Oostindie
- Genmab, Utrecht, the Netherlands.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - D J Dijkstra
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - P W H I Parren
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands.,Lava Therapeutics, Utrecht, the Netherlands
| | - M K Verheul
- Department Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - L Abendstein
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - T H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - A de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - G M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - P A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | | | | | - L A Trouw
- Department Rheumatology, Leiden University Medical Center, Leiden, the Netherlands.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
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6
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McLaughlin RJ, de Haan A, Zaldumbide A, de Koning EJ, de Ru AH, van Veelen PA, van Lummel M, Roep BO. Human islets and dendritic cells generate post-translationally modified islet autoantigens. Clin Exp Immunol 2016; 185:133-40. [PMID: 26861694 DOI: 10.1111/cei.12775] [Citation(s) in RCA: 30] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/15/2016] [Accepted: 02/07/2016] [Indexed: 12/14/2022] Open
Abstract
The initiation of type 1 diabetes (T1D) requires a break in peripheral tolerance. New insights into neoepitope formation indicate that post-translational modification of islet autoantigens, for example via deamidation, may be an important component of disease initiation or exacerbation. Indeed, deamidation of islet autoantigens increases their binding affinity to the T1D highest-risk human leucocyte antigen (HLA) haplotypes HLA-DR3/DQ2 and -DR4/DQ8, increasing the chance that T cells reactive to deamidated autoantigens can be activated upon T cell receptor ligation. Here we investigated human pancreatic islets and inflammatory and tolerogenic human dendritic cells (DC and tolDC) as potential sources of deamidated islet autoantigens and examined whether deamidation is altered in an inflammatory environment. Islets, DC and tolDC contained tissue transglutaminase, the key enzyme responsible for peptide deamidation, and enzyme activity increased following an inflammatory insult. Islets treated with inflammatory cytokines were found to contain deamidated insulin C-peptide. DC, heterozygous for the T1D highest-risk DQ2/8, pulsed with native islet autoantigens could present naturally processed deamidated neoepitopes. HLA-DQ2 or -DQ8 homozygous DC did not present deamidated islet peptides. This study identifies both human islets and DC as sources of deamidated islet autoantigens and implicates inflammatory activation of tissue transglutaminase as a potential mechanism for islet and DC deamidation.
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Affiliation(s)
- R J McLaughlin
- Department of Immunohematology and Blood Transfusion, Leiden, the Netherlands
| | - A de Haan
- Department of Immunohematology and Blood Transfusion, Leiden, the Netherlands
| | - A Zaldumbide
- Department of Molecular Cell Biology, Leiden, the Netherlands
| | - E J de Koning
- Department of Nephrology, Leiden University Medical Center, Leiden, the Netherlands
| | - A H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden, the Netherlands
| | - P A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden, the Netherlands
| | - M van Lummel
- Department of Immunohematology and Blood Transfusion, Leiden, the Netherlands
| | - B O Roep
- Department of Immunohematology and Blood Transfusion, Leiden, the Netherlands.,Department of Diabetes Immunology, Diabetes and Metabolism Research Institute at the Beckman Research Institute of the City of Hope, Duarte, CA, USA
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7
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Eichmann M, de Ru A, van Veelen PA, Peakman M, Kronenberg-Versteeg D. Identification and characterisation of peptide binding motifs of six autoimmune disease-associated human leukocyte antigen-class I molecules including HLA-B*39:06. ACTA ACUST UNITED AC 2014; 84:378-88. [PMID: 25154780 DOI: 10.1111/tan.12413] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/14/2014] [Accepted: 07/08/2014] [Indexed: 11/26/2022]
Abstract
Research on CD8 T cell-mediated inflammatory diseases requires a better understanding of target epitopes and the constraints placed upon these by major histocompatibility complex (MHC) class I binding restrictions, especially those that relate to predisposing alleles. We used linear trap quadrupole fourier transform (LTQ-FT) tandem mass spectrometry to identify naturally processed and presented peptides eluted from the MHC-negative myeloid leukaemia cell line K562 transfected with specific MHC class I genes. We provide information on the peptidome of HLA-B*39:06, which is associated with the autoimmune disease type 1 diabetes, and extend the analysis to include a further five human leukocyte antigen (HLA) alleles (HLA-A*02:01/-A*11:01/-A*24:02/-B*18:01/-B*38:01) studied under identical experimental conditions. We identified a total of 3095 individual peptides with a mascot score ≥40 (HLA-A*02:01 = 569 peptides, -A*11:01 = 904, A*24:02 = 257, -B*18:01 = 615, -B*38:01 = 453, -B*39:06 = 297). Peptides had a preferential length of nine amino acids and originated mainly from cytoplasmic or nuclear proteins. Eluted peptides revealed a strong binding motif with binding anchor positions at position 2 (P2) and the C-terminus (PΩ). Peptides eluted from HLA-A*02:01 showed a P2 preference for leucine (62% of total peptides have Leu at P2) and PΩ preference for valine (49%). Similar data are provided for HLA-A*11:01 (P2:Thr, 29%; PΩ:Lys, 49%), -A*24:02 (P2:Tyr, 78%; PΩ:Phe, 41%), -B*18:01 (P2:Glu, 77%; PΩ:Tyr, 32%), -B*38:01 (P2:His, 51%; PΩ:Leu, 45%) and -B*39:06 (P2:Arg/His, 24%; PΩ:Ala, 64%). This work thus gives an overview of the naturally processed and presented repertoire of several common and autoimmune disease-related HLA alleles, which may be useful in studying autoreactive CD8 T cell responses and the role of HLA in disease susceptibility.
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Affiliation(s)
- M Eichmann
- Department of Immunobiology, King's College London, London, UK
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8
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Rombouts Y, Willemze A, van Beers JJBC, Shi J, Kerkman PF, Janssen GMC, van Veelen PA, Zaldumbide A, Hoeben RC, Pruijn GJ, Deelder AM, Wolbink G, Rispens T, García-Vallejo JJ, van Kooyk Y, Huizinga TWJ, Wuhrer M, Trouw LA, Scherer HU, Toes REM. A1.45 Hyperglycosylation of ACPA-IGG variable domains modulates reactivity to citrullinated antigens. Ann Rheum Dis 2014. [DOI: 10.1136/annrheumdis-2013-205124.44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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9
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Shi J, Janssen GMC, van Veelen PA, Cerami A, Huizinga TWJ, Toes RE, Trouw LA. The ‘Senshu’ method often used to detect citrullinated proteins does not discriminate between citrullination and carbamylation. Ann Rheum Dis 2012. [DOI: 10.1136/annrheumdis-2011-201234.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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10
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Kessler JH, Bres-Vloemans SA, van Veelen PA, de Ru A, Huijbers IJG, Camps M, Mulder A, Offringa R, Drijfhout JW, Leeksma OC, Ossendorp F, Melief CJM. BCR-ABL fusion regions as a source of multiple leukemia-specific CD8+ T-cell epitopes. Leukemia 2006; 20:1738-50. [PMID: 16932347 DOI: 10.1038/sj.leu.2404354] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
For immunotherapy of residual disease in patients with Philadelphia-positive leukemias, the BCR-ABL fusion regions are attractive disease-specific T-cell targets. We analyzed these regions for the prevalence of cytotoxic T lymphocyte (CTL) epitopes by an advanced reverse immunology procedure. Seventeen novel BCR-ABL fusion peptides were identified to bind efficiently to the human lymphocyte antigen (HLA)-A68, HLA-B51, HLA-B61 or HLA-Cw4 HLA class I molecules. Comprehensive enzymatic digestion analysis showed that 10 out of the 28 HLA class I binding fusion peptides were efficiently excised after their C-terminus by the proteasome, which is an essential requirement for efficient cell surface expression. Therefore, these peptides are prime vaccine candidates. The other peptides either completely lacked C-terminal liberation or were only inefficiently excised by the proteasome, rendering them inappropriate or less suitable for inclusion in a vaccine. CTL raised against the properly processed HLA-B61 epitope AEALQRPVA from the BCR-ABL e1a2 fusion region, expressed in acute lymphoblastic leukemia (ALL), specifically recognized ALL tumor cells, proving cell surface presentation of this epitope, its applicability for immunotherapy and underlining the accuracy of our epitope identification strategy. Our study provides a reliable basis for the selection of optimal peptides to be included in immunotherapeutic BCR-ABL vaccines against leukemia.
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MESH Headings
- Amino Acid Sequence
- CD8-Positive T-Lymphocytes/immunology
- Cancer Vaccines/immunology
- Cell Line, Tumor
- Epitope Mapping/methods
- Epitopes, T-Lymphocyte/immunology
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/immunology
- Fusion Proteins, bcr-abl/metabolism
- HLA-A Antigens/immunology
- HLA-A Antigens/metabolism
- HLA-A2 Antigen
- HLA-B Antigens/immunology
- HLA-B Antigens/metabolism
- HLA-B51 Antigen
- HLA-C Antigens/immunology
- HLA-C Antigens/metabolism
- Humans
- Immunotherapy/methods
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/immunology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy
- Molecular Sequence Data
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Peptide Fragments/metabolism
- Protein Binding/immunology
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Affiliation(s)
- J H Kessler
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands.
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11
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Langedijk JPM, van Veelen PA, Schaaper WMM, de Ru AH, Meloen RH, Hulst MM. A structural model of pestivirus E(rns) based on disulfide bond connectivity and homology modeling reveals an extremely rare vicinal disulfide. J Virol 2002; 76:10383-92. [PMID: 12239315 PMCID: PMC136578 DOI: 10.1128/jvi.76.20.10383-10392.2002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2002] [Accepted: 07/02/2002] [Indexed: 11/20/2022] Open
Abstract
E(rns) is a pestivirus envelope glycoprotein and is the only known viral surface protein with RNase activity. E(rns) is a disulfide-linked homodimer of 100 kDa; it is found on the surface of pestivirus-infected cells and is secreted into the medium. In this study, the disulfide arrangement of the nine cysteines present in the mature dimer was established by analysis of the proteolytically cleaved protein. Fragments were obtained after digestion with multiple proteolytic enzymes and subsequently analyzed by liquid chromatography-electrospray ionization mass spectrometry. The analysis demonstrates which cysteine is involved in dimerization and reveals an extremely rare vicinal disulfide bridge of unknown function. With the assistance of the disulfide arrangement, a three-dimensional model was built by homology modeling based on the alignment with members of the Rh/T2/S RNase family. Compared to these other RNase family members, E(rns) shows an N-terminal truncation, a large insertion of a cystine-rich region, and a C-terminal extension responsible for membrane translocation. The homology to mammalian RNase 6 supports a possible role of E(rns) in B-cell depletion.
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Affiliation(s)
- J P M Langedijk
- Pepscan Systems Inc., Edelhertweg 15, PO Box 2098, 8203 AB Lelystad, The Netherlands.
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12
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Hiemstra HS, Schloot NC, van Veelen PA, Willemen SJ, Franken KL, van Rood JJ, de Vries RR, Chaudhuri A, Behan PO, Drijfhout JW, Roep BO. Cytomegalovirus in autoimmunity: T cell crossreactivity to viral antigen and autoantigen glutamic acid decarboxylase. Proc Natl Acad Sci U S A 2001; 98:3988-91. [PMID: 11274421 PMCID: PMC31166 DOI: 10.1073/pnas.071050898] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Antigens of pathogenic microbes that mimic autoantigens are thought to be responsible for the activation of autoreactive T cells. Viral infections have been associated with the development of the neuroendocrine autoimmune diseases type 1 diabetes and stiff-man syndrome, but the mechanism is unknown. These diseases share glutamic acid decarboxylase (GAD65) as a major autoantigen. We screened synthetic peptide libraries dedicated to bind to HLA-DR3, which predisposes to both diseases, using clonal CD4(+) T cells reactive to GAD65 isolated from a prediabetic stiff-man syndrome patient. Here we show that these GAD65-specific T cells crossreact with a peptide of the human cytomegalovirus (hCMV) major DNA-binding protein. This peptide was identified after database searching with a recognition pattern that had been deduced from the library studies. Furthermore, we showed that hCMV-derived epitope can be naturally processed by dendritic cells and recognized by GAD65 reactive T cells. Thus, hCMV may be involved in the loss of T cell tolerance to autoantigen GAD65 by a mechanism of molecular mimicry leading to autoimmunity.
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Affiliation(s)
- H S Hiemstra
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, P. O. Box 9600, NL-2300 RC Leiden, The Netherlands
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13
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Kessler JH, Beekman NJ, Bres-Vloemans SA, Verdijk P, van Veelen PA, Kloosterman-Joosten AM, Vissers DC, ten Bosch GJ, Kester MG, Sijts A, Wouter Drijfhout J, Ossendorp F, Offringa R, Melief CJ. Efficient identification of novel HLA-A(*)0201-presented cytotoxic T lymphocyte epitopes in the widely expressed tumor antigen PRAME by proteasome-mediated digestion analysis. J Exp Med 2001; 193:73-88. [PMID: 11136822 PMCID: PMC2195886 DOI: 10.1084/jem.193.1.73] [Citation(s) in RCA: 186] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We report the efficient identification of four human histocompatibility leukocyte antigen (HLA)-A(*)0201-presented cytotoxic T lymphocyte (CTL) epitopes in the tumor-associated antigen PRAME using an improved "reverse immunology" strategy. Next to motif-based HLA-A(*)0201 binding prediction and actual binding and stability assays, analysis of in vitro proteasome-mediated digestions of polypeptides encompassing candidate epitopes was incorporated in the epitope prediction procedure. Proteasome cleavage pattern analysis, in particular determination of correct COOH-terminal cleavage of the putative epitope, allows a far more accurate and selective prediction of CTL epitopes. Only 4 of 19 high affinity HLA-A(*)0201 binding peptides (21%) were found to be efficiently generated by the proteasome in vitro. This approach avoids laborious CTL response inductions against high affinity binding peptides that are not processed and limits the number of peptides to be assayed for binding. CTL clones induced against the four identified epitopes (VLDGLDVLL, PRA(100-108); SLYSFPEPEA, PRA(142-151); ALYVDSLFFL, PRA(300-309); and SLLQHLIGL, PRA(425-433)) lysed melanoma, renal cell carcinoma, lung carcinoma, and mammary carcinoma cell lines expressing PRAME and HLA-A(*)0201. This indicates that these epitopes are expressed on cancer cells of diverse histologic origin, making them attractive targets for immunotherapy of cancer.
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MESH Headings
- Amino Acid Sequence
- Antigen Presentation
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/metabolism
- Base Sequence
- Cell Line, Transformed
- Cysteine Endopeptidases/metabolism
- Cytotoxicity, Immunologic
- DNA Primers/genetics
- Epitopes/genetics
- Epitopes/metabolism
- HLA-A Antigens/metabolism
- Humans
- Molecular Sequence Data
- Multienzyme Complexes/metabolism
- Proteasome Endopeptidase Complex
- Protein Binding
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- T-Lymphocytes, Cytotoxic/immunology
- Tumor Cells, Cultured
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Affiliation(s)
- J H Kessler
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.
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14
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van Hall T, van Bergen J, van Veelen PA, Kraakman M, Heukamp LC, Koning F, Melief CJ, Ossendorp F, Offringa R. Identification of a novel tumor-specific CTL epitope presented by RMA, EL-4, and MBL-2 lymphomas reveals their common origin. J Immunol 2000; 165:869-77. [PMID: 10878361 DOI: 10.4049/jimmunol.165.2.869] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
C57BL/6 mice generate a vigorous H-2Db-restricted CTL response against murine leukemia virus (MuLV)-induced tumors. For many years it has been suggested that this response is directed to an MuLV-encoded peptide as well as to a nonviral tumor-associated peptide. Recently, a peptide from the leader sequence of gag was demonstrated to be the MuLV-derived epitope. Here we describe the molecular identification of the tumor-associated epitope. Furthermore, we show that the CTL response against this epitope can restrict the outgrowth of MuLV-induced tumors in vivo. The epitope is selectively presented by the MuLV-induced T cell tumors RBL-5, RMA, and MBL-2 as well as by the chemically induced T cell lymphoma EL-4. Intriguingly, these tumors share expression of the newly identified epitope because they represent variants of the same clonal tumor cell line, as evident from sequencing of the TCR alpha- and beta-chains, which proved to be identical. Our research shows that all sources of RBL-5, RMA, RMA-S, MBL-2, and EL-4 tumors are derived from a single tumor line, most likely EL-4.
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MESH Headings
- Adoptive Transfer
- Animals
- Antigen Presentation
- Binding Sites/immunology
- Cancer Vaccines/administration & dosage
- Cell Lineage/genetics
- Cell Lineage/immunology
- Epitopes, T-Lymphocyte/administration & dosage
- Epitopes, T-Lymphocyte/isolation & purification
- Epitopes, T-Lymphocyte/metabolism
- Friend murine leukemia virus
- Gene Expression Regulation/immunology
- Genes, T-Cell Receptor beta
- Leukemia, Experimental/immunology
- Leukemia, Experimental/metabolism
- Leukemia, Experimental/pathology
- Lymphoma, T-Cell/immunology
- Lymphoma, T-Cell/metabolism
- Lymphoma, T-Cell/pathology
- Mice
- Mice, Inbred C57BL
- Mice, Nude
- Moloney murine leukemia virus
- Oligopeptides/administration & dosage
- Oligopeptides/chemical synthesis
- Oligopeptides/immunology
- Oligopeptides/metabolism
- Rauscher Virus
- Sequence Analysis, Protein
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- T-Lymphocytes, Cytotoxic/pathology
- T-Lymphocytes, Cytotoxic/transplantation
- Thymoma/immunology
- Thymoma/metabolism
- Thymoma/pathology
- Tumor Cells, Cultured/transplantation
- Tumor Virus Infections/immunology
- Tumor Virus Infections/metabolism
- Tumor Virus Infections/pathology
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Affiliation(s)
- T van Hall
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
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15
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Krijgsveld J, Zaat SA, Meeldijk J, van Veelen PA, Fang G, Poolman B, Brandt E, Ehlert JE, Kuijpers AJ, Engbers GH, Feijen J, Dankert J. Thrombocidins, microbicidal proteins from human blood platelets, are C-terminal deletion products of CXC chemokines. J Biol Chem 2000; 275:20374-81. [PMID: 10877842 DOI: 10.1074/jbc.275.27.20374] [Citation(s) in RCA: 246] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antibacterial proteins are components of the innate immune system found in many organisms and produced by a variety of cell types. Human blood platelets contain a number of antibacterial proteins in their alpha-granules that are released upon thrombin activation. The present study was designed to purify these proteins obtained from human platelets and to characterize them chemically and biologically. Two antibacterial proteins were purified from platelet granules in a two-step protocol using cation exchange chromatography and continuous acid urea polyacrylamide gel electrophoresis and were designated thrombocidin (TC)-1 and TC-2. Characterization of these proteins using mass spectrometry and N-terminal sequencing revealed that TC-1 and TC-2 are variants of the CXC chemokines neutrophil-activating peptide-2 and connective tissue-activating peptide-III, respectively. TC-1 and TC-2 differ from these chemokines by a C-terminal truncation of 2 amino acids. Both TCs, but not neutrophil-activating peptide-2 and connective tissue-activating peptide-III, were bactericidal for Bacillus subtilis, Escherichia coli, Staphylococcus aureus, and Lactococcus lactis and fungicidal for Cryptococcus neoformans. Killing of B. subtilis by either TC appeared to be very rapid. Because TCs were unable to dissipate the membrane potential of L. lactis, the mechanism of TC-mediated killing most probably does not involve pore formation.
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Affiliation(s)
- J Krijgsveld
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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16
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Sijts AJ, Standera S, Toes RE, Ruppert T, Beekman NJ, van Veelen PA, Ossendorp FA, Melief CJ, Kloetzel PM. MHC class I antigen processing of an adenovirus CTL epitope is linked to the levels of immunoproteasomes in infected cells. J Immunol 2000; 164:4500-6. [PMID: 10779750 DOI: 10.4049/jimmunol.164.9.4500] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Proteasomes are the major source for the generation of peptides bound by MHC class I molecules. To study the functional relevance of the IFN-gamma-inducible proteasome subunits low molecular mass protein 2 (LMP2), LMP7, and mouse embryonal cell (MEC) ligand 1 in Ag processing and concomitantly that of immunoproteasomes, we established the tetracycline-regulated mouse cell line MEC217, allowing the titrable formation of immunoproteasomes. Infection of MEC217 cells with Adenovirus type 5 (Ad5) and analysis of Ag presentation with Ad5-specific CTL showed that cells containing immunoproteasomes processed the viral early 1B protein (E1B)-derived epitope E1B192-200 with increased efficiency, thus allowing a faster detection of viral entry in induced cells. Importantly, optimal CTL activation was already achieved at submaximal immunosubunit expression. In contrast, digestion of E1B-polypeptide with purified proteasomes in vitro yielded E1B192-200 at quantities that were proportional to the relative contents of immunosubunits. Our data provide evidence that the IFN-gamma-inducible proteasome subunits, when present at relatively low levels as at initial stages of infection, already increase the efficiency of antigenic peptide generation and thereby enhance MHC class I Ag processing in infected cells.
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MESH Headings
- Adenoviruses, Human/genetics
- Adenoviruses, Human/immunology
- Adjuvants, Immunologic/physiology
- Amino Acid Sequence
- Animals
- Antigen Presentation/drug effects
- Antigen Presentation/genetics
- Cell Line
- Cysteine Endopeptidases/biosynthesis
- Cysteine Endopeptidases/immunology
- Cysteine Endopeptidases/metabolism
- Cysteine Endopeptidases/physiology
- Dose-Response Relationship, Immunologic
- Enzyme Induction/drug effects
- Enzyme Induction/genetics
- Enzyme Induction/immunology
- Epitopes, T-Lymphocyte/metabolism
- Histocompatibility Antigens Class I/metabolism
- Humans
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Molecular Sequence Data
- Multienzyme Complexes/biosynthesis
- Multienzyme Complexes/immunology
- Multienzyme Complexes/metabolism
- Multienzyme Complexes/physiology
- Peptide Biosynthesis/immunology
- Proteasome Endopeptidase Complex
- T-Lymphocytes, Cytotoxic/enzymology
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- T-Lymphocytes, Cytotoxic/virology
- Tetracycline/pharmacology
- Transfection
- Tumor Cells, Cultured
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Affiliation(s)
- A J Sijts
- Institute of Biochemistry, Charité, Humboldt University, Berlin, Germany
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17
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Beekman NJ, van Veelen PA, van Hall T, Neisig A, Sijts A, Camps M, Kloetzel PM, Neefjes JJ, Melief CJ, Ossendorp F. Abrogation of CTL epitope processing by single amino acid substitution flanking the C-terminal proteasome cleavage site. J Immunol 2000; 164:1898-905. [PMID: 10657639 DOI: 10.4049/jimmunol.164.4.1898] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CTL directed against the Moloney murine leukemia virus (MuLV) epitope SSWDFITV recognize Moloney MuLV-induced tumor cells, but do not recognize cells transformed by the closely related Friend MuLV. The potential Friend MuLV epitope has strong sequence homology with Moloney MuLV and only differs in one amino acid within the CTL epitope and one amino acid just outside the epitope. We now show that failure to recognize Friend MuLV-transformed tumor cells is based on a defect in proteasome-mediated processing of the Friend epitope which is due to a single amino acid substitution (N-->D) immediately flanking the C-terminal anchor residue of the epitope. Proteasome-mediated digestion analysis of a synthetic 26-mer peptide derived from the Friend sequence shows that cleavage takes place predominantly C-terminal of D, instead of V as is the case for the Moloney MuLV sequence. Therefore, the C terminus of the epitope is not properly generated. Epitope-containing peptide fragments extended with an additional C-terminal D are not efficiently translocated by TAP and do not show significant binding affinity to MHC class I-Kb molecules. Thus, a potential CTL epitope present in the Friend virus sequence is not properly processed and presented because of a natural flanking aspartic acid that obliterates the correct C-terminal cleavage site. This constitutes a novel way to subvert proteasome-mediated generation of proper antigenic peptide fragments.
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Affiliation(s)
- N J Beekman
- Department of Immunohematology, Leiden University Medical Center, Leiden, The Netherlands
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18
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Hiemstra HS, van Veelen PA, Geluk A, Schloot NC, de Vries RR, Ottenhoff TH, Roep BO, Drijfhout JW. Limitations of homology searching for identification of T-cell antigens with library derived mimicry epitopes. Vaccine 1999; 18:204-8. [PMID: 10506643 DOI: 10.1016/s0264-410x(99)00328-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mimicry epitopes that are recognized by T-cells can be identified through screening of synthetic peptide libraries. We have shown that these mimicry epitopes share sequence similarity with the corresponding natural epitopes and that mimicry sequences can be used for the definition of protein derived T-cell epitopes from databases. This can be done by either homology searching or pattern searching. Here we discuss the advantages and disadvantages of homology searching as an alternative for the generally applicable recognition pattern approach. We show that only for part of the library derived mimicry epitopes, the degree of similarity to the natural epitope may be high enough for successful homology searching in small databases.
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Affiliation(s)
- H S Hiemstra
- Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, Albinusdreef 2, P.O. box 9600, 2300 RC, Leiden, Netherlands
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19
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Hiemstra HS, van Veelen PA, Willemen SJ, Benckhuijsen WE, Geluk A, de Vries RR, Roep BO, Drijfhout JW. Quantitative determination of TCR cross-reactivity using peptide libraries and protein databases. Eur J Immunol 1999; 29:2385-91. [PMID: 10458750 DOI: 10.1002/(sici)1521-4141(199908)29:08<2385::aid-immu2385>3.0.co;2-b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A single T cell clone can be activated by many different peptides in the context of a particular HLA molecule. To quantify the number of peptides that can be recognized by a CD4(+) T cell clone, we screened a one-bead-one-peptide synthetic peptide library and a protein database for peptides that stimulate an HLA-DR3-restricted, human glutamic acid decarboxylase (GAD65)-reactive CD4(+) T cell clone. Both the library screening and the database analysis indicated that this T cell clone is able to recognize approximately 10(6) 11-mer peptides at low nanomolar concentration. Furthermore, we determined that the frequency of cross-reactivity increased only 1.5-3 times when the peptide concentration increased 10 times, in the range of 0.01 - 1 microM. These data imply that there is a considerable potential for T cell cross-reactivity and are useful for studies on the role of molecular mimicry in the etiology of T cell-mediated disease.
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Affiliation(s)
- H S Hiemstra
- Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
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20
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Hiemstra HS, van Veelen PA, Schloot NC, Geluk A, van Meijgaarden KE, Willemen SJ, Leunissen JA, Benckhuijsen WE, Amons R, de Vries RR, Roep BO, Ottenhoff TH, Drijfhout JW. Definition of natural T cell antigens with mimicry epitopes obtained from dedicated synthetic peptide libraries. J Immunol 1998; 161:4078-82. [PMID: 9780178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Progress has recently been made in the use of synthetic peptide libraries for the identification of T cell-stimulating ligands. T cell epitopes identified from synthetic libraries are mimics of natural epitopes. Here we show how the mimicry epitopes obtained from synthetic peptide libraries enable unambiguous identification of natural T cell Ags. Synthetic peptide libraries were screened with Mycobacterium tuberculosis-reactive and -autoreactive T cell clones. In two cases, database homology searches with mimicry epitopes isolated from a dedicated synthetic peptide library allowed immediate identification of the natural antigenic protein. In two other cases, an amino acid pattern that reflected the epitope requirements of the T cell was determined by substitution and omission mixture analysis. Subsequently, the natural Ag was identified from databases using this refined pattern. This approach opens new perspectives for rapid and reliable Ag definition, representing a feasible alternative to the biochemical and genetic approaches described thus far.
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Affiliation(s)
- H S Hiemstra
- Department of Immunohematology and Blood Bank, Leiden University Medical Center, The Netherlands
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21
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van de Wal Y, Kooy YM, van Veelen PA, Peña SA, Mearin LM, Molberg O, Lundin KE, Sollid LM, Mutis T, Benckhuijsen WE, Drijfhout JW, Koning F. Small intestinal T cells of celiac disease patients recognize a natural pepsin fragment of gliadin. Proc Natl Acad Sci U S A 1998; 95:10050-4. [PMID: 9707598 PMCID: PMC21459 DOI: 10.1073/pnas.95.17.10050] [Citation(s) in RCA: 192] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Celiac disease is a common severe intestinal disease resulting from intolerance to dietary wheat gluten and related proteins. The large majority of patients expresses the HLA-DQ2 and/or DQ8 molecules, and gluten-specific HLA-DQ-restricted T cells have been found at the site of the lesion in the gut. The nature of peptides that are recognized by such T cells, however, has been unclear so far. We now report the identification of a gliadin-derived epitope that dominantly is recognized by intestinal gluten-specific HLA-DQ8-restricted T cells. The characterization of such epitopes is a key step toward the development of strategies to interfere in mechanisms involved in the pathogenesis of celiac disease.
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Affiliation(s)
- Y van de Wal
- Department of Immunohaematology and Bloodbank, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.
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22
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Li KW, van Minnen J, van Veelen PA, van der Greef J, Geraerts WP. Structure, localization and action of a novel inhibitory neuropeptide involved in the feeding of Lymnaea. Brain Res Mol Brain Res 1996; 37:267-72. [PMID: 8738160 DOI: 10.1016/0169-328x(95)00333-n] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A neuropeptide that strongly inhibits the spontaneous contractions of the oesophagus in Lymnaea has been characterized as GAPRFVamide. Direct mass spectrometry of nervous tissues and immunocytochemical studies show that the peptide is synthesized by neurones in the buccal ganglia and transported to the oesophagus via the dorso-buccal nerve. In accordance with the function of the peptide, immunoreactive fibres are detected within the muscle layer of the oesophagus. Finally, mass spectrometry reveals the presence of a number of unidentified peptides in the nerves that innervate the oesophagus, which suggests that oesophageal activities may be modified by multiple peptides.
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Affiliation(s)
- K W Li
- Graduate School Neurosciences Amsterdam, Research Institute Neurosciences, Vrije Universiteit, Faculty of Biology, The Netherlands
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23
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Li KW, Hoek RM, Smith F, Jiménez CR, van der Schors RC, van Veelen PA, Chen S, van der Greef J, Parish DC, Benjamin PR. Direct peptide profiling by mass spectrometry of single identified neurons reveals complex neuropeptide-processing pattern. J Biol Chem 1994; 269:30288-92. [PMID: 7982940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A novel strategy combining peptide fingerprinting of single neurons by matrix-assisted laser desorption ionization mass spectrometry, molecular cloning, peptide chemistry, and electrospray ionization mass spectrometry was used to study the intricate processing pattern of a preprohormone expressed in identified neurons, the neuroendocrine light yellow cells (LYCs) of the gastropod mollusc, Lymnaea stagnalis. The cDNA encoding the precursor, named prepro-LYCP (LYCPs, light yellow cell peptides), predicts a straightforward processing into three peptides, LYCP I, II, and III, at conventional dibasic processing sites flanking the peptide domains on the precursor. However, matrix-assisted laser desorption ionization mass spectrometry of single LYCs revealed trimmed variant peptides derived from LYCP I and II. The variants were much more abundant than the intact peptides, indicating that LYCP I and II serve as intermediates in a peptide-processing sequence. Using the molecular masses of the peptides as markers to guide their isolation by well established purification methods, the structural identities of the peptides could be confirmed by amino acid sequencing. Furthermore, matrix-assisted laser desorption ionization mass spectrometry could detect colocalization of a novel peptide with the LYCPs.
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Affiliation(s)
- K W Li
- Graduate School Neurosciences Amsterdam, Research Institute Neurosciences Vrije Universiteit, Faculty of Biology, The Netherlands
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24
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Li KW, Hoek RM, Smith F, Jiménez CR, van der Schors RC, van Veelen PA, Chen S, van der Greef J, Parish DC, Benjamin PR. Direct peptide profiling by mass spectrometry of single identified neurons reveals complex neuropeptide-processing pattern. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)43810-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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25
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Li KW, van Golen FA, van Minnen J, van Veelen PA, van der Greef J, Geraerts WP. Structural identification, neuronal synthesis, and role in male copulation of myomodulin-A of Lymnaea: a study involving direct peptide profiling of nervous tissue by mass spectrometry. Brain Res Mol Brain Res 1994; 25:355-8. [PMID: 7808235 DOI: 10.1016/0169-328x(94)90172-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We used a strategy combining immunodetection, peptide chemistry, and a novel method, direct peptide fingerprinting of neurons and small pieces of nerve by using matrix-assisted laser desorption ionization mass spectrometry, to structurally identify and localize the neuropeptide myomodulin-A in the mollusc, Lymnaea stagnalis. Lymnaea myomodulin appeared to be identical to Aplysia myomodulin-A and is produced by many central neurons, including neurons located in the ventral lobe of the right cerebral ganglion that innervate the penis complex via the penis nerve. Myomodulin-A could also be characterized from the penis complex, and physiological concentrations of the peptide enhanced the relaxation rate of electrically induced contractions of the penis retractor muscle in vitro in a dose-dependent fashion.
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Affiliation(s)
- K W Li
- Graduate School Neurosciences Amsterdam, Research Institute Neurosciences Vrije Universiteit, Faculty of Biology, Vrije Universiteit, The Netherlands
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Kostiainen R, Lasonder E, Bloemhoff W, van Veelen PA, Welling GW, Bruins AP. Characterization of a synthetic 37-residue fragment of a monoclonal antibody against herpes virus by capillary electrophoresis/electrospray (ionspray) mass spectrometry and 252Cf plasma desorption mass spectrometry. Biol Mass Spectrom 1994; 23:346-52. [PMID: 8038227 DOI: 10.1002/bms.1200230608] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A peptide comprising 37 amino acids of the antigen binding site of a monoclonal antibody directed against glycoprotein D of herpes simplex virus was synthesized. The synthetic peptide and the impurities formed in the synthesis were characterized by capillary electrophoresis/ionspray mass spectrometry and by 252Cf plasma desorption-time of flight mass spectrometry. The measured average molecular mass of the synthetic peptide was 4627.16 Da, which was only 0.08 Da higher than the calculated value (4627.08 Da). The plasma desorption mass spectrum of the synthetic peptide showed a protonated molecule at m/z 4624.1, which was 4 Da lower than the calculated one (4628.09 Da). The amino acid sequence of the peptide was confirmed in part by electrospray (ionspray) mass spectrometry using a high nozzle skimmer voltage difference. Five impurities were separated and identified by capillary electrophoresis/mass spectrometry and two of them also appeared in the plasma desorption mass spectrum.
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Affiliation(s)
- R Kostiainen
- University Centre for Pharmacy, Groningen, The Netherlands
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27
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Jiménez CR, van Veelen PA, Li KW, Wildering WC, Geraerts WP, Tjaden UR, van der Greef J. Neuropeptide expression and processing as revealed by direct matrix-assisted laser desorption ionization mass spectrometry of single neurons. J Neurochem 1994; 62:404-7. [PMID: 8263544 DOI: 10.1046/j.1471-4159.1994.62010404.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Neuropeptides were directly detected in single identified neurons and the neurohemal area of peptidergic (neuroendocrine) systems in the Lymnaea brain by using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The samples were placed in matrix solution and ruptured to allow mixing of cell contents with the matrix solution. After formation of matrix crystals, the analytes were analyzed by MALDI-MS. It was surprising that clean mass spectra were produced, displaying extreme sensitivity of detection. In one of the neuroendocrine systems studied, we could demonstrate for the first time, by comparing the peptide patterns of soma and of neurohemal axon terminals, that processing of the complex prohormone expressed in this system occurs entirely in the soma. In the other system studied, novel peptides could be detected in addition to peptides previously identified by conventional molecular biological and peptide chemical methods. Thus, complex peptide processing and expression patterns could be predicted that were not detected in earlier studies using conventional methods. As the first MALDI-MS study of direct peptide fingerprinting in the single neuron, these experiments demonstrate that MALDI-MS forms a new and valuable approach to the study of the synthesis and expression of bioactive peptides, with potential application to single-cell studies in vertebrates, including humans.
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Affiliation(s)
- C R Jiménez
- Graduate School Neurosciences Amsterdam, Research Institute Neurosciences, Vrije Universiteit, Faculty of Biology, The Netherlands
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van Veelen PA, Jiménez CR, Li KW, Wildering WC, Geraerts WPM, Tjaden UR, van der Greef J. Direct peptide profiling of single neurons by matrix-assisted laser desorption-ionization mass spectrometry. ACTA ACUST UNITED AC 1993. [DOI: 10.1002/oms.1210281229] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Otte SC, van de Meent EJ, van Veelen PA, Pundsnes AS, Amesz J. Identification of the major chlorosomal bacteriochlorophylls of the green sulfur bacteria Chlorobium vibrioforme and Chlorobium phaeovibrioides; their function in lateral energy transfer. Photosynth Res 1993; 35:159-169. [PMID: 24318682 DOI: 10.1007/bf00014746] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/1992] [Accepted: 08/18/1992] [Indexed: 06/02/2023]
Abstract
The chlorosomal bacteriochlorophyll (BChl) composition of the green sulfur bacteria Chlorobium vibrioforme and Chlorobium phaeovibrioides was investigated by means of normal-phase high-performance liquid chromatography. From both species a number of homologues was isolated, which were identified by absorption and (252)Cf-plasma desorption mass spectroscopy. Besides BChl d, C. vibrioforme contained a significant amount of BChl c, which may provide an explanation for the previous observation of at least two spectrally different pools of BChl in the chlorosomes of green sulfur bacteria (Otte et al. 1991). C. phaeovibrioides contained various homologues of BChl e only. Absorption spectra in acetone of BChl c, d and e, as well as bacteriopheophytin e are presented. No systematic differences were found for the various homologues of each pigment. In addition to farnesol, the mass spectra revealed the presence of various minor esterifying alcohols in both species, including phytol, oleol, cetol and 4-undecyl-2-furanmethanol, as well as an alcohol of low molecular mass, which is tentatively assumed to be decenol.
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Affiliation(s)
- S C Otte
- Department of Biophysics, Huygens Laboratory, University of Leiden, P.O. Box 9504, 2300 RA, Leiden, The Netherlands
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Abstract
The primary structure of human interleukin-3 contains two amino acid consensus sequences at Glutamate 22- Histidine 26 and Histidine 95-Histidine 98, that are characteristic for zinc binding proteins. Therefore, the hypothesis was tested that human interleukin-3 binds zinc specifically by either one or both sequences. Protein dotblotting, followed by probing with radioactive zinc demonstrated specific zinc binding of interleukin-3. Metal specificity was confirmed by competition experiments with 12 other divalent- and trivalent metal ions. Protease treatment combined with plasma desorption mass spectrometry was used to localize the zinc binding domain. Specific zinc binding was restricted to a fragment composed of Threonine 11-Lysine 28 and Asparagine 80-Lysine 100. It was found to decrease by a factor of five when either of these two amino acid stretches was missing. It is concluded that human interleukin-3 is a zinc binding protein. Interleukin-3 zinc binding capacity is largely determined by both moieties of the protein that contain the consensus sequences. In addition we propose that the zinc binding of hIL-3 is involved in (de)phosphorylation of the hIL-3 receptor.
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Affiliation(s)
- V Smit
- TNO Institute of Applied Radiobiology and Immunology, Rijswijk, The Netherlands
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van Veelen PA, Tjaden UR, van der Greef J, de With ND. Sequence-Informative fragmentation in an 8.9 kDa oligopeptide using plasma desorption mass spectrometry. ACTA ACUST UNITED AC 1991. [DOI: 10.1002/oms.1210260429] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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