1
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Jia Y, Oyken M, Kim RQ, Tjokrodirijo RTN, de Ru AH, Janssen APA, Hacker SM, van Veelen PA, Geurink PP, Sapmaz A. Development of Inhibitors, Probes, and PROTAC Provides a Complete Toolbox to Study PARK7 in the Living Cell. J Med Chem 2024. [PMID: 38713163 DOI: 10.1021/acs.jmedchem.3c02410] [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] [Indexed: 05/08/2024]
Abstract
The integration of diverse chemical tools like small-molecule inhibitors, activity-based probes (ABPs), and proteolysis targeting chimeras (PROTACs) advances clinical drug discovery and facilitates the exploration of various biological facets of targeted proteins. Here, we report the development of such a chemical toolbox for the human Parkinson disease protein 7 (PARK7/DJ-1) implicated in Parkinson's disease and cancers. By combining structure-guided design, miniaturized library synthesis, and high-throughput screening, we identified two potent compounds, JYQ-164 and JYQ-173, inhibiting PARK7 in vitro and in cells by covalently and selectively targeting its critical residue, Cys106. Leveraging JYQ-173, we further developed a cell-permeable Bodipy probe, JYQ-196, for covalent labeling of PARK7 in living cells and a first-in-class PARK7 degrader JYQ-194 that selectively induces its proteasomal degradation in human cells. Our study provides a valuable toolbox to enhance the understanding of PARK7 biology in cellular contexts and opens new opportunities for therapeutic interventions.
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Affiliation(s)
- Yuqing Jia
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, Zürich CH-8093, Switzerland
| | - Merve Oyken
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Robbert Q Kim
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Rayman T N Tjokrodirijo
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Antonius P A Janssen
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Stephan M Hacker
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Paul P Geurink
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Aysegul Sapmaz
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
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2
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Fuchs KJ, van de Meent M, Honders MW, Khatri I, Kester MGD, Koster EAS, Koutsoumpli G, de Ru AH, van Bergen CAM, van Veelen PA, ’t Hoen PAC, van Balen P, van den Akker EB, Veelken JH, Halkes CJM, Falkenburg JHF, Griffioen M. Expanding the repertoire reveals recurrent, cryptic, and hematopoietic HLA class I minor histocompatibility antigens. Blood 2024; 143:1856-1872. [PMID: 38427583 PMCID: PMC11076866 DOI: 10.1182/blood.2023022343] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/03/2024] Open
Abstract
ABSTRACT Allogeneic stem cell transplantation (alloSCT) is a curative treatment for hematological malignancies. After HLA-matched alloSCT, antitumor immunity is caused by donor T cells recognizing polymorphic peptides, designated minor histocompatibility antigens (MiHAs), that are presented by HLA on malignant patient cells. However, T cells often target MiHAs on healthy nonhematopoietic tissues of patients, thereby inducing side effects known as graft-versus-host disease. Here, we aimed to identify the dominant repertoire of HLA-I-restricted MiHAs to enable strategies to predict, monitor or modulate immune responses after alloSCT. To systematically identify novel MiHAs by genome-wide association screening, T-cell clones were isolated from 39 transplanted patients and tested for reactivity against 191 Epstein-Barr virus transformed B cell lines of the 1000 Genomes Project. By discovering 81 new MiHAs, we more than doubled the antigen repertoire to 159 MiHAs and demonstrated that, despite many genetic differences between patients and donors, often the same MiHAs are targeted in multiple patients. Furthermore, we showed that one quarter of the antigens are cryptic, that is translated from unconventional open reading frames, for example long noncoding RNAs, showing that these antigen types are relevant targets in natural immune responses. Finally, using single cell RNA-seq data, we analyzed tissue expression of MiHA-encoding genes to explore their potential role in clinical outcome, and characterized 11 new hematopoietic-restricted MiHAs as potential targets for immunotherapy. In conclusion, we expanded the repertoire of HLA-I-restricted MiHAs and identified recurrent, cryptic and hematopoietic-restricted antigens, which are fundamental to predict, follow or manipulate immune responses to improve clinical outcome after alloSCT.
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Affiliation(s)
- Kyra J. Fuchs
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marian van de Meent
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - M. Willy Honders
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Indu Khatri
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel G. D. Kester
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eva A. S. Koster
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Georgia Koutsoumpli
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A. C. ’t Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter van Balen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik B. van den Akker
- Center for Computational Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - J. Hendrik Veelken
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
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3
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de Rooij MA, Remst DF, van der Steen DM, Wouters AK, Hagedoorn RS, Kester MG, Meeuwsen MH, Wachsmann TL, de Ru AH, van Veelen PA, Verdegaal EM, Falkenburg JF, Heemskerk MH. Erratum: A library of cancer testis specific T cell receptors for T cell receptor gene therapy. Mol Ther Oncolytics 2023; 31:100738. [PMID: 37920174 PMCID: PMC10618812 DOI: 10.1016/j.omto.2023.100738] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
[This corrects the article DOI: 10.1016/j.omto.2022.11.007.].
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4
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Claushuis B, de Ru AH, Rotman SA, van Veelen PA, Dawson LF, Wren BW, Corver J, Smits WK, Hensbergen PJ. Revised Model for the Type A Glycan Biosynthetic Pathway in Clostridioides difficile Strain 630Δ erm Based on Quantitative Proteomics of cd0241- cd0244 Mutant Strains. ACS Infect Dis 2023; 9:2665-2674. [PMID: 37965964 PMCID: PMC10714395 DOI: 10.1021/acsinfecdis.3c00485] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/20/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
The bacterial flagellum is involved in a variety of processes including motility, adherence, and immunomodulation. In the Clostridioides difficile strain 630Δerm, the main filamentous component, FliC, is post-translationally modified with an O-linked Type A glycan structure. This modification is essential for flagellar function, since motility is seriously impaired in gene mutants with improper biosynthesis of the Type A glycan. The cd0240-cd0244 gene cluster encodes the Type A biosynthetic proteins, but the role of each gene, and the corresponding enzymatic activity, have not been fully elucidated. Using quantitative mass spectrometry-based proteomics analyses, we determined the relative abundance of the observed glycan variations of the Type A structure in cd0241, cd0242, cd0243, and cd0244 mutant strains. Our data not only confirm the importance of CD0241, CD0242, and CD0243 but, in contrast to previous data, also show that CD0244 is essential for the biosynthesis of the Type A modification. Combined with additional bioinformatic analyses, we propose a revised model for Type A glycan biosynthesis.
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Affiliation(s)
- Bart Claushuis
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Arnoud H. de Ru
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Sarah A. Rotman
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Peter A. van Veelen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Lisa F. Dawson
- Faculty
of Infectious and Tropical Diseases, London
School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Brendan W. Wren
- Faculty
of Infectious and Tropical Diseases, London
School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Jeroen Corver
- Department
of Medical Microbiology, Leiden University
Medical Center, Leiden 2333 ZA, The Netherlands
| | - Wiep Klaas Smits
- Department
of Medical Microbiology, Leiden University
Medical Center, Leiden 2333 ZA, The Netherlands
| | - Paul J. Hensbergen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
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5
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van den Bulk J, Verdegaal EM, van der Ploeg M, Visser M, Nunes JB, de Ru AH, Tjokrodirijo RT, Ijsselsteijn ME, Janssen NI, van der Breggen R, de Bruin L, de Kok P, Janssen GM, Ruano D, Kapiteijn EH, van Veelen PA, de Miranda NF, van der Burg SH. Neoantigen Targetability in Progressive Advanced Melanoma. Clin Cancer Res 2023; 29:4278-4288. [PMID: 37540567 PMCID: PMC10570682 DOI: 10.1158/1078-0432.ccr-23-1106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/23/2023] [Accepted: 08/02/2023] [Indexed: 08/06/2023]
Abstract
PURPOSE The availability of (neo)antigens and the infiltration of tumors by (neo)antigen-specific T cells are crucial factors in cancer immunotherapy. In this study, we aimed to investigate the targetability of (neo)antigens in advanced progessive melanoma and explore the potential for continued T-cell-based immunotherapy. EXPERIMENTAL DESIGN We examined a cohort of eight patients with melanoma who had sequential metastases resected at early and later time points. Antigen-presenting capacity was assessed using IHC and flow cytometry. T-cell infiltration was quantified through multiplex immunofluorescence. Whole-exome and RNA sequencing were conducted to identify neoantigens and assess the expression of neoantigens and tumor-associated antigens. Mass spectrometry was used to evaluate antigen presentation. Tumor recognition by autologous T cells was assessed by coculture assays with cell lines derived from the metastatic lesions. RESULTS We observed similar T-cell infiltration in paired early and later metastatic (LM) lesions. Although elements of the antigen-presenting machinery were affected in some LM lesions, both the early and later metastasis-derived cell lines were recognized by autologous T cells. At the genomic level, the (neo)antigen landscape was dynamic, but the (neo)antigen load was stable between paired lesions. CONCLUSIONS Our findings indicate that subsequently isolated tumors from patients with late-stage melanoma retain sufficient antigen-presenting capacity, T-cell infiltration, and a stable (neo)antigen load, allowing recognition of tumor cells by T cells. This indicates a continuous availability of T-cell targets in metastases occurring at different time points and supports further exploration of (neo)antigen-specific T-cell-based therapeutic approaches for advanced melanoma.
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Affiliation(s)
- Jitske van den Bulk
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Els M.E. Verdegaal
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Manon van der Ploeg
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Marten Visser
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Joana B. Nunes
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Arnoud H. de Ru
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Rayman T.N. Tjokrodirijo
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Natasja I. Janssen
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ruud van der Breggen
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Linda de Bruin
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Pita de Kok
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - George M.C. Janssen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ellen H.W. Kapiteijn
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter A. van Veelen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Sjoerd H. van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
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6
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Gan J, de Vries J, Akkermans JJLL, Mohammed Y, Tjokrodirijo RTN, de Ru AH, Kim RQ, Vargas DA, Pol V, Fasan R, van Veelen PA, Neefjes J, van Dam H, Ovaa H, Sapmaz A, Geurink PP. Cellular Validation of a Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2. ACS Chem Biol 2023; 18:2003-2013. [PMID: 37642399 PMCID: PMC10510154 DOI: 10.1021/acschembio.3c00227] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023]
Abstract
Ubiquitin thioesterase OTUB2, a cysteine protease from the ovarian tumor (OTU) deubiquitinase superfamily, is often overexpressed during tumor progression and metastasis. Development of OTUB2 inhibitors is therefore believed to be therapeutically important, yet potent and selective small-molecule inhibitors targeting OTUB2 are scarce. Here, we describe the development of an improved OTUB2 inhibitor, LN5P45, comprising a chloroacethydrazide moiety that covalently reacts to the active-site cysteine residue. LN5P45 shows outstanding target engagement and proteome-wide selectivity in living cells. Importantly, LN5P45 as well as other OTUB2 inhibitors strongly induce monoubiquitination of OTUB2 on lysine 31. We present a route to future OTUB2-related therapeutics and have shown that the OTUB2 inhibitor developed in this study can help to uncover new aspects of the related biology and open new questions regarding the understanding of OTUB2 regulation at the post-translational modification level.
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Affiliation(s)
- Jin Gan
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Jelle de Vries
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Jimmy J. L. L. Akkermans
- Department
of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center LUMC, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Yassene Mohammed
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Rayman T. N. Tjokrodirijo
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Arnoud H. de Ru
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Robbert Q. Kim
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - David A. Vargas
- Department
of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester, New York 14627, United States
| | - Vito Pol
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Rudi Fasan
- Department
of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester, New York 14627, United States
| | - Peter A. van Veelen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Jacques Neefjes
- Department
of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center LUMC, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Hans van Dam
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Huib Ovaa
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Aysegul Sapmaz
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Paul P. Geurink
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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7
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van Dinther M, Cunningham KT, Singh SP, White MPJ, Campion T, Ciancia C, van Veelen PA, de Ru AH, González-Prieto R, Mukundan A, Byeon CH, Staggers SR, Hinck CS, Hinck AP, Dijke PT, Maizels RM. CD44 acts as a coreceptor for cell-specific enhancement of signaling and regulatory T cell induction by TGM1, a parasite TGF-β mimic. Proc Natl Acad Sci U S A 2023; 120:e2302370120. [PMID: 37590410 PMCID: PMC10450677 DOI: 10.1073/pnas.2302370120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 02/10/2023] [Accepted: 06/25/2023] [Indexed: 08/19/2023] Open
Abstract
Long-lived parasites evade host immunity through highly evolved molecular strategies. The murine intestinal helminth, Heligmosomoides polygyrus, down-modulates the host immune system through release of an immunosuppressive TGF-β mimic, TGM1, which is a divergent member of the CCP (Sushi) protein family. TGM1 comprises 5 domains, of which domains 1-3 (D1/2/3) bind mammalian TGF-β receptors, acting on T cells to induce Foxp3+ regulatory T cells; however, the roles of domains 4 and 5 (D4/5) remain unknown. We noted that truncated TGM1, lacking D4/5, showed reduced potency. Combination of D1/2/3 and D4/5 as separate proteins did not alter potency, suggesting that a physical linkage is required and that these domains do not deliver an independent signal. Coprecipitation from cells treated with biotinylated D4/5, followed by mass spectrometry, identified the cell surface protein CD44 as a coreceptor for TGM1. Both full-length and D4/5 bound strongly to a range of primary cells and cell lines, to a greater degree than D1/2/3 alone, although some cell lines did not respond to TGM1. Ectopic expression of CD44 in nonresponding cells conferred responsiveness, while genetic depletion of CD44 abolished enhancement by D4/5 and ablated the ability of full-length TGM1 to bind to cell surfaces. Moreover, CD44-deficient T cells showed attenuated induction of Foxp3 by full-length TGM1, to levels similar to those induced by D1/2/3. Hence, a parasite protein known to bind two host cytokine receptor subunits has evolved a third receptor specificity, which serves to raise the avidity and cell type-specific potency of TGF-β signaling in mammalian cells.
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Affiliation(s)
- Maarten van Dinther
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden2300 RC, The Netherlands
| | - Kyle T. Cunningham
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Shashi Prakash Singh
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Madeleine P. J. White
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Tiffany Campion
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Claire Ciancia
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Román González-Prieto
- Andalusian Center for Molecular Biology and Regenerative Medicine, Universidad de Sevilla - CSIC - Universidad Pablo de Olavide, 41092Sevilla, Spain
- Department of Cell Biology, Faculty of Biology, University of Sevilla, 41013Sevilla, Spain
| | - Ananya Mukundan
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15260
| | - Chang-Hyeock Byeon
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15260
| | - Sophia R. Staggers
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15260
| | - Cynthia S. Hinck
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15260
| | - Andrew P. Hinck
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15260
| | - Peter ten Dijke
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden2300 RC, The Netherlands
| | - Rick M. Maizels
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, GlasgowG12 8TA, United Kingdom
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8
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Claushuis B, Cordfunke RA, de Ru AH, Otte A, van Leeuwen HC, Klychnikov OI, van Veelen PA, Corver J, Drijfhout JW, Hensbergen PJ. In-Depth Specificity Profiling of Endopeptidases Using Dedicated Mix-and-Split Synthetic Peptide Libraries and Mass Spectrometry. Anal Chem 2023; 95:11621-11631. [PMID: 37495545 PMCID: PMC10413326 DOI: 10.1021/acs.analchem.3c01215] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023]
Abstract
Proteases comprise the class of enzymes that catalyzes the hydrolysis of peptide bonds, thereby playing a pivotal role in many aspects of life. The amino acids surrounding the scissile bond determine the susceptibility toward protease-mediated hydrolysis. A detailed understanding of the cleavage specificity of a protease can lead to the identification of its endogenous substrates, while it is also essential for the design of inhibitors. Although many methods for protease activity and specificity profiling exist, none of these combine the advantages of combinatorial synthetic libraries, i.e., high diversity, equimolar concentration, custom design regarding peptide length, and randomization, with the sensitivity and detection power of mass spectrometry. Here, we developed such a method and applied it to study a group of bacterial metalloproteases that have the unique specificity to cleave between two prolines, i.e., Pro-Pro endopeptidases (PPEPs). We not only confirmed the prime-side specificity of PPEP-1 and PPEP-2, but also revealed some new unexpected peptide substrates. Moreover, we have characterized a new PPEP (PPEP-3) that has a prime-side specificity that is very different from that of the other two PPEPs. Importantly, the approach that we present in this study is generic and can be extended to investigate the specificity of other proteases.
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Affiliation(s)
- Bart Claushuis
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Robert A. Cordfunke
- Department
of Immunology, Leiden University Medical
Center, Leiden, 2333 ZA, The Netherlands
| | - Arnoud H. de Ru
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Annemarie Otte
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Hans C. van Leeuwen
- Department
of CBRN Protection, Netherlands Organization
for Applied Scientific Research TNO, Rijswijk, 2280 AA, The Netherlands
| | - Oleg I. Klychnikov
- Department
of Biochemistry, Moscow State University, Moscow 119991, Russian Federation
| | - Peter A. van Veelen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Jeroen Corver
- Department
of Medical Microbiology, Leiden University
Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Jan W. Drijfhout
- Department
of Immunology, Leiden University Medical
Center, Leiden, 2333 ZA, The Netherlands
| | - Paul J. Hensbergen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden, 2333 ZA, The Netherlands
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9
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Salas-Lloret D, Jansen NS, Nagamalleswari E, van der Meulen C, Gracheva E, de Ru AH, Otte HAM, van Veelen PA, Pichler A, Goedhart J, Vertegaal AC, González-Prieto R. SUMO-activated target traps (SATTs) enable the identification of a comprehensive E3-specific SUMO proteome. Sci Adv 2023; 9:eadh2073. [PMID: 37531430 PMCID: PMC10396300 DOI: 10.1126/sciadv.adh2073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023]
Abstract
Ubiquitin and ubiquitin-like conjugation cascades consist of dedicated E1, E2, and E3 enzymes with E3s providing substrate specificity. Mass spectrometry-based approaches have enabled the identification of more than 6500 SUMO2/3 target proteins. The limited number of SUMO E3s provides the unique opportunity to systematically study E3 substrate wiring. We developed SUMO-activated target traps (SATTs) and systematically identified substrates for eight different SUMO E3s, PIAS1, PIAS2, PIAS3, PIAS4, NSMCE2, ZNF451, LAZSUL (ZNF451-3), and ZMIZ2. SATTs enabled us to identify 427 SUMO1 and 961 SUMO2/3 targets in an E3-specific manner. We found pronounced E3 substrate preference. Quantitative proteomics enabled us to measure substrate specificity of E3s, quantified using the SATT index. Furthermore, we developed the Polar SATTs web-based tool to browse the dataset in an interactive manner. Overall, we uncover E3-to-target wiring of 1388 SUMO substrates, highlighting unique and overlapping sets of substrates for eight different SUMO E3 ligases.
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Affiliation(s)
- Daniel Salas-Lloret
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Nicolette S. Jansen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Coen van der Meulen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Ekaterina Gracheva
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - H. Anne Marie Otte
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Andrea Pichler
- Max Plank Institute for Immunobiology and Epigenetics, Freiburg, Germany
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | | | | | - Román González-Prieto
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-CSIC-Universidad-Pablo de Olavide, Sevilla, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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10
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de Rooij MA, Remst DF, van der Steen DM, Wouters AK, Hagedoorn RS, Kester MG, Meeuwsen MH, Wachsmann TL, de Ru AH, van Veelen PA, Verdegaal EM, Falkenburg JF, Heemskerk MH. A library of cancer testis specific T cell receptors for T cell receptor gene therapy. Mol Ther Oncolytics 2023; 28:1-14. [PMID: 36589698 PMCID: PMC9792401 DOI: 10.1016/j.omto.2022.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
To increase the number of cancer patients that can be treated with T cell receptor (TCR) gene therapy, we aimed to identify a set of high-affinity cancer-specific TCRs targeting different melanoma-associated antigens (MAGEs). In this study, peptides derived from MAGE genes with tumor-specific expression pattern were identified by human leukocyte antigen (HLA) peptidomics. Next, peptide-HLA tetramers were generated, and used to sort MAGE-specific CD8+ T cell clones from the allogeneic (allo) HLA repertoire of healthy donors. To evaluate the clinical potential, most potent TCRs were sequenced, transferred into peripheral blood-derived CD8+ T cells, and tested for antitumor efficacy. In total we identified, seven MAGE-specific TCRs that effectively target MAGE-A1, MAGE-A3, MAGE-A6, and MAGE-A9 in the context of HLA-A∗01:01, -A∗02:01, -A∗03:01, -B∗07:02, -B∗35:01, or -C∗07:02. TCR gene transfer into CD8⁺ T cells resulted in efficient reactivity against a variety of different tumor types, while no cross-reactivity was detected. In addition, major in vivo antitumor effects of MAGE-A1 specific TCR engineered CD8⁺ T cells were observed in the orthotopic xenograft model for established multiple myeloma. The identification of seven MAGE-specific TCRs expands the pool of cancer patients eligible for TCR gene therapy and increases possibilities for personalized TCR gene therapy.
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Affiliation(s)
- Marije A.J. de Rooij
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Dennis F.G. Remst
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Dirk M. van der Steen
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Anne K. Wouters
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Renate S. Hagedoorn
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Michel G.D. Kester
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Miranda H. Meeuwsen
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Tassilo L.A. Wachsmann
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Els M.E. Verdegaal
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - J.H. Frederik Falkenburg
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Mirjam H.M. Heemskerk
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
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11
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Meeuwsen MH, Wouters AK, Wachsmann TLA, Hagedoorn RS, Kester MGD, Remst DFG, van der Steen DM, de Ru AH, van Hees EP, Kremer M, Griffioen M, van Veelen PA, Falkenburg JHF, Heemskerk MHM. Broadly applicable TCR-based therapy for multiple myeloma targeting the immunoglobulin J chain. J Hematol Oncol 2023; 16:16. [PMID: 36850001 PMCID: PMC9969645 DOI: 10.1186/s13045-023-01408-6] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/09/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND The immunoglobulin J chain (Jchain) is highly expressed in the majority of multiple myeloma (MM), and Jchain-derived peptides presented in HLA molecules may be suitable antigens for T-cell therapy of MM. METHODS Using immunopeptidomics, we identified Jchain-derived epitopes presented by MM cells, and pHLA tetramer technology was used to isolate Jchain-specific T-cell clones. RESULTS We identified T cells specific for Jchain peptides presented in HLA-A1, -A24, -A3, and -A11 that recognized and lysed JCHAIN-positive MM cells. TCRs of the most promising T-cell clones were sequenced, cloned into retroviral vectors, and transferred to CD8 T cells. Jchain TCR T cells recognized target cells when JCHAIN and the appropriate HLA restriction alleles were expressed, while JCHAIN or HLA-negative cells, including healthy subsets, were not recognized. Patient-derived JCHAIN-positive MM samples were also lysed by Jchain TCR T cells. In a preclinical in vivo model for established MM, Jchain-A1, -A24, -A3, and -A11 TCR T cells strongly eradicated MM cells, which resulted in 100-fold lower tumor burden in Jchain TCR versus control-treated mice. CONCLUSIONS We identified TCRs targeting Jchain-derived peptides presented in four common HLA alleles. All four TCRs demonstrated potent preclinical anti-myeloma activity, encouraging further preclinical testing and ultimately clinical development.
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Affiliation(s)
- Miranda H Meeuwsen
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Anne K Wouters
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Tassilo L A Wachsmann
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Renate S Hagedoorn
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Michel G D Kester
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Dennis F G Remst
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Dirk M van der Steen
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Els P van Hees
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Martijn Kremer
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - J H Frederik Falkenburg
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
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12
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Treffers EE, Tas A, Scholte FEM, de Ru AH, Snijder EJ, van Veelen PA, van Hemert MJ. The alphavirus nonstructural protein 2 NTPase induces a host translational shut-off through phosphorylation of eEF2 via cAMP-PKA-eEF2K signaling. PLoS Pathog 2023; 19:e1011179. [PMID: 36848386 PMCID: PMC9997916 DOI: 10.1371/journal.ppat.1011179] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 03/09/2023] [Accepted: 02/03/2023] [Indexed: 03/01/2023] Open
Abstract
Chikungunya virus (CHIKV) is a reemerging alphavirus. Since 2005, it has infected millions of people during outbreaks in Africa, Asia, and South/Central America. CHIKV replication depends on host cell factors at many levels and is expected to have a profound effect on cellular physiology. To obtain more insight into host responses to infection, stable isotope labeling with amino acids in cell culture and liquid chromatography-tandem mass spectrometry were used to assess temporal changes in the cellular phosphoproteome during CHIKV infection. Among the ~3,000 unique phosphorylation sites analyzed, the largest change in phosphorylation status was measured on residue T56 of eukaryotic elongation factor 2 (eEF2), which showed a >50-fold increase at 8 and 12 h p.i. Infection with other alphaviruses (Semliki Forest, Sindbis and Venezuelan equine encephalitis virus (VEEV)) triggered a similarly strong eEF2 phosphorylation. Expression of a truncated form of CHIKV or VEEV nsP2, containing only the N-terminal and NTPase/helicase domains (nsP2-NTD-Hel), sufficed to induce eEF2 phosphorylation, which could be prevented by mutating key residues in the Walker A and B motifs of the NTPase domain. Alphavirus infection or expression of nsP2-NTD-Hel resulted in decreased cellular ATP levels and increased cAMP levels. This did not occur when catalytically inactive NTPase mutants were expressed. The wild-type nsP2-NTD-Hel inhibited cellular translation independent of the C-terminal nsP2 domain, which was previously implicated in directing the virus-induced host shut-off for Old World alphaviruses. We hypothesize that the alphavirus NTPase activates a cellular adenylyl cyclase resulting in increased cAMP levels, thus activating PKA and subsequently eukaryotic elongation factor 2 kinase. This in turn triggers eEF2 phosphorylation and translational inhibition. We conclude that the nsP2-driven increase of cAMP levels contributes to the alphavirus-induced shut-off of cellular protein synthesis that is shared between Old and New World alphaviruses. MS Data are available via ProteomeXchange with identifier PXD009381.
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Affiliation(s)
- Emmely E. Treffers
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Ali Tas
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Florine E. M. Scholte
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric J. Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A. van Veelen
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Martijn J. van Hemert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
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13
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van Amerongen RA, Tuit S, Wouters AK, van de Meent M, Siekman SL, Meeuwsen MH, Wachsmann TLA, Remst DFG, Hagedoorn RS, van der Steen DM, de Ru AH, Verdegaal EME, van Veelen PA, Falkenburg JHF, Heemskerk MHM. PRAME and CTCFL-reactive TCRs for the treatment of ovarian cancer. Front Immunol 2023; 14:1121973. [PMID: 37026005 PMCID: PMC10070997 DOI: 10.3389/fimmu.2023.1121973] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/06/2023] [Indexed: 04/08/2023] Open
Abstract
Recurrent disease emerges in the majority of patients with ovarian cancer (OVCA). Adoptive T-cell therapies with T-cell receptors (TCRs) targeting tumor-associated antigens (TAAs) are considered promising solutions for less-immunogenic 'cold' ovarian tumors. In order to treat a broader patient population, more TCRs targeting peptides derived from different TAAs binding in various HLA class I molecules are essential. By performing a differential gene expression analysis using mRNA-seq datasets, PRAME, CTCFL and CLDN6 were selected as strictly tumor-specific TAAs, with high expression in ovarian cancer and at least 20-fold lower expression in all healthy tissues of risk. In primary OVCA patient samples and cell lines we confirmed expression and identified naturally expressed TAA-derived peptides in the HLA class I ligandome. Subsequently, high-avidity T-cell clones recognizing these peptides were isolated from the allo-HLA T-cell repertoire of healthy individuals. Three PRAME TCRs and one CTCFL TCR of the most promising T-cell clones were sequenced, and transferred to CD8+ T cells. The PRAME TCR-T cells demonstrated potent and specific antitumor reactivity in vitro and in vivo. The CTCFL TCR-T cells efficiently recognized primary patient-derived OVCA cells, and OVCA cell lines treated with demethylating agent 5-aza-2'-deoxycytidine (DAC). The identified PRAME and CTCFL TCRs are promising candidates for the treatment of patients with ovarian cancer, and are an essential addition to the currently used HLA-A*02:01 restricted PRAME TCRs. Our selection of differentially expressed genes, naturally expressed TAA peptides and potent TCRs can improve and broaden the use of T-cell therapies for patients with ovarian cancer or other PRAME or CTCFL expressing cancers.
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Affiliation(s)
| | - Sander Tuit
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Anne K. Wouters
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Marian van de Meent
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Sterre L. Siekman
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Miranda H. Meeuwsen
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Dennis F. G. Remst
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Renate S. Hagedoorn
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Els M. E. Verdegaal
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Mirjam H. M. Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
- *Correspondence: Mirjam H. M. Heemskerk,
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Hos BJ, Tondini E, Camps MG, Rademaker W, van den Bulk J, Ruano D, Janssen GM, de Ru AH, van den Elsen PJ, de Miranda NF, van Veelen PA, Ossendorp F. Cancer-specific T helper shared and neo-epitopes uncovered by expression of the MHC class II master regulator CIITA. Cell Rep 2022; 41:111680. [DOI: 10.1016/j.celrep.2022.111680] [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: 11/23/2022] Open
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15
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van der Pan K, Kassem S, Khatri I, de Ru AH, Janssen GMC, Tjokrodirijo RTN, al Makindji F, Stavrakaki E, de Jager AL, Naber BAE, de Laat IF, Louis A, van den Bossche WBL, Vogelezang LB, Balvers RK, Lamfers MLM, van Veelen PA, Orfao A, van Dongen JJM, Teodosio C, Díez P. Quantitative proteomics of small numbers of closely-related cells: Selection of the optimal method for a clinical setting. Front Med (Lausanne) 2022; 9:997305. [PMID: 36237552 PMCID: PMC9553008 DOI: 10.3389/fmed.2022.997305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Mass spectrometry (MS)-based proteomics profiling has undoubtedly increased the knowledge about cellular processes and functions. However, its applicability for paucicellular sample analyses is currently limited. Although new approaches have been developed for single-cell studies, most of them have not (yet) been standardized and/or require highly specific (often home-built) devices, thereby limiting their broad implementation, particularly in non-specialized settings. To select an optimal MS-oriented proteomics approach applicable in translational research and clinical settings, we assessed 10 different sample preparation procedures in paucicellular samples of closely-related cell types. Particularly, five cell lysis protocols using different chemistries and mechanical forces were combined with two sample clean-up techniques (C18 filter- and SP3-based), followed by tandem mass tag (TMT)-based protein quantification. The evaluation was structured in three phases: first, cell lines from hematopoietic (THP-1) and non-hematopoietic (HT-29) origins were used to test the approaches showing the combination of a urea-based lysis buffer with the SP3 bead-based clean-up system as the best performer. Parameters such as reproducibility, accessibility, spatial distribution, ease of use, processing time and cost were considered. In the second phase, the performance of the method was tested on maturation-related cell populations: three different monocyte subsets from peripheral blood and, for the first time, macrophages/microglia (MAC) from glioblastoma samples, together with T cells from both tissues. The analysis of 50,000 cells down to only 2,500 cells revealed different protein expression profiles associated with the distinct cell populations. Accordingly, a closer relationship was observed between non-classical monocytes and MAC, with the latter showing the co-expression of M1 and M2 macrophage markers, although pro-tumoral and anti-inflammatory proteins were more represented. In the third phase, the results were validated by high-end spectral flow cytometry on paired monocyte/MAC samples to further determine the sensitivity of the MS approach selected. Finally, the feasibility of the method was proven in 194 additional samples corresponding to 38 different cell types, including cells from different tissue origins, cellular lineages, maturation stages and stimuli. In summary, we selected a reproducible, easy-to-implement sample preparation method for MS-based proteomic characterization of paucicellular samples, also applicable in the setting of functionally closely-related cell populations.
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Affiliation(s)
- Kyra van der Pan
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Sara Kassem
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Indu Khatri
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Leiden Computational Biology Center, LUMC, Leiden, Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, LUMC, Leiden, Netherlands
| | | | | | - Fadi al Makindji
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | | | - Anniek L. de Jager
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Brigitta A. E. Naber
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Inge F. de Laat
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Alesha Louis
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | | | | | | | | | | | - Alberto Orfao
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain
- Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Jacques J. M. van Dongen
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain
- Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- *Correspondence: Jacques J. M. van Dongen
| | - Cristina Teodosio
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain
- Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Paula Díez
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain
- Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
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16
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van Amerongen RA, Hagedoorn RS, Remst DFG, Assendelft DC, van der Steen DM, Wouters AK, van de Meent M, Kester MGD, de Ru AH, Griffioen M, van Veelen PA, Falkenburg JHF, Heemskerk MHM. WT1-specific TCRs directed against newly identified peptides install antitumor reactivity against acute myeloid leukemia and ovarian carcinoma. J Immunother Cancer 2022; 10:jitc-2021-004409. [PMID: 35728869 PMCID: PMC9214430 DOI: 10.1136/jitc-2021-004409] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 05/23/2022] [Indexed: 12/24/2022] Open
Abstract
Background Transcription factor Wilms’ tumor gene 1 (WT1) is an ideal tumor target based on its expression in a wide range of tumors, low-level expression in normal tissues and promoting role in cancer progression. In clinical trials, WT1 is targeted using peptide-based or dendritic cell-based vaccines and T-cell receptor (TCR)-based therapies. Antitumor reactivities were reported, but T-cell reactivity is hampered by self-tolerance to WT1 and limited number of WT1 peptides, which were thus far selected based on HLA peptide binding algorithms. Methods In this study, we have overcome both limitations by searching in the allogeneic T-cell repertoire of healthy donors for high-avidity WT1-specific T cells, specific for WT1 peptides derived from the HLA class I associated ligandome of primary leukemia and ovarian carcinoma samples. Results Using broad panels of malignant cells and healthy cell subsets, T-cell clones were selected that demonstrated potent and specific anti-WT1 T-cell reactivity against five of the eight newly identified WT1 peptides. Notably, T-cell clones for WT1 peptides previously used in clinical trials lacked reactivity against tumor cells, suggesting limited processing and presentation of these peptides. The TCR sequences of four T-cell clones were analyzed and TCR gene transfer into CD8+ T cells installed antitumor reactivity against WT1-expressing solid tumor cell lines, primary acute myeloid leukemia (AML) blasts, and ovarian carcinoma patient samples. Conclusions Our approach resulted in a set of naturally expressed WT1 peptides and four TCRs that are promising candidates for TCR gene transfer strategies in patients with WT1-expressing tumors, including AML and ovarian carcinoma.
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Affiliation(s)
- Rosa A van Amerongen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Renate S Hagedoorn
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dennis F G Remst
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Danique C Assendelft
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dirk M van der Steen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Anne K Wouters
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marian van de Meent
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel G D Kester
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
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17
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Laghmouchi A, Kester MGD, Hoogstraten C, Hageman L, de Klerk W, Huisman W, Koster EAS, de Ru AH, van Balen P, Klobuch S, van Veelen PA, Falkenburg JHF, Jedema I. Promiscuity of Peptides Presented in HLA-DP Molecules from Different Immunogenicity Groups Is Associated With T-Cell Cross-Reactivity. Front Immunol 2022; 13:831822. [PMID: 35251023 PMCID: PMC8888658 DOI: 10.3389/fimmu.2022.831822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 12/08/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
In the context of HLA-DP-mismatched allogeneic stem cell transplantation, mismatched HLA-DP alleles can provoke profound allo-HLA-DP-specific immune responses from the donor T-cell repertoire leading to graft-versus-leukemia effect and/or graft-versus-host disease in the patient. The magnitude of allo-HLA-DP-specific immune responses has been shown to depend on the specific HLA-DP disparity between donor and patient and the immunogenicity of the mismatched HLA-DP allele(s). HLA-DP peptidome clustering (DPC) was developed to classify the HLA-DP molecules based on similarities and differences in their peptide-binding motifs. To investigate a possible categorization of HLA-DP molecules based on overlap of presented peptides, we identified and compared the peptidomes of the thirteen most frequently expressed HLA-DP molecules. Our categorization based on shared peptides was in line with the DPC classification. We found that the HLA-DP molecules within the previously defined groups DPC-1 or DPC-3 shared the largest numbers of presented peptides. However, the HLA-DP molecules in DPC-2 segregated into two subgroups based on the overlap in presented peptides. Besides overlap in presented peptides within the DPC groups, a substantial number of peptides was also found to be shared between HLA-DP molecules from different DPC groups, especially for groups DPC-1 and -2. The functional relevance of these findings was illustrated by demonstration of cross-reactivity of allo-HLA-DP-reactive T-cell clones not only against HLA-DP molecules within one DPC group, but also across different DPC groups. The promiscuity of peptides presented in various HLA-DP molecules and the cross-reactivity against different HLA-DP molecules demonstrate that these molecules cannot be strictly categorized in immunogenicity groups.
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Affiliation(s)
- Aicha Laghmouchi
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Michel G D Kester
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Conny Hoogstraten
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Lois Hageman
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Wendy de Klerk
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Wesley Huisman
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Eva A S Koster
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Peter van Balen
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Sebastian Klobuch
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Inge Jedema
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
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18
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Meeuwsen MH, Wouters AK, Jahn L, Hagedoorn RS, Kester MG, Remst DF, Morton LT, van der Steen DM, Kweekel C, de Ru AH, Griffioen M, van Veelen PA, Falkenburg JF, Heemskerk MH. A broad and systematic approach to identify B cell malignancy-targeting TCRs for multi-antigen-based T cell therapy. Mol Ther 2022; 30:564-578. [PMID: 34371177 PMCID: PMC8821929 DOI: 10.1016/j.ymthe.2021.08.010] [Citation(s) in RCA: 4] [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] [Received: 12/16/2020] [Revised: 03/01/2021] [Accepted: 07/20/2021] [Indexed: 02/04/2023] Open
Abstract
CAR T cell therapy has shown great promise for the treatment of B cell malignancies. However, antigen-negative escape variants often cause disease relapse, necessitating the development of multi-antigen-targeting approaches. We propose that a T cell receptor (TCR)-based strategy would increase the number of potential antigenic targets, as peptides from both intracellular and extracellular proteins can be recognized. Here, we aimed to isolate a broad range of promising TCRs targeting multiple antigens for treatment of B cell malignancies. As a first step, 28 target genes for B cell malignancies were selected based on gene expression profiles. Twenty target peptides presented in human leukocyte antigen (HLA)-A∗01:01, -A∗24:02, -B∗08:01, or -B∗35:01 were identified from the immunopeptidome of B cell malignancies and used to form peptide-HLA (pHLA)-tetramers for T cell isolation. Target-peptide-specific CD8 T cells were isolated from HLA-mismatched healthy donors and subjected to a stringent stepwise selection procedure to ensure potency and eliminate cross-reactivity. In total, five T cell clones specific for FCRL5 in HLA-A∗01:01, VPREB3 in HLA-A∗24:02, and BOB1 in HLA-B∗35:01 recognized B cell malignancies. For all three specificities, TCR gene transfer into CD8 T cells resulted in cytokine production and efficient killing of multiple B cell malignancies. In conclusion, using this systematic approach we successfully identified three promising TCRs for T cell therapy against B cell malignancies.
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Affiliation(s)
- Miranda H. Meeuwsen
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands,Corresponding author: Miranda H. Meeuwsen, Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
| | - Anne K. Wouters
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Lorenz Jahn
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands,Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Renate S. Hagedoorn
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Michel G.D. Kester
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Dennis F.G. Remst
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Laura T. Morton
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Dirk M. van der Steen
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Christiaan Kweekel
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | | | - Mirjam H.M. Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands,Corresponding author: Mirjam H.M. Heemskerk, Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
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19
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Hensbergen PJ, de Ru AH, Friggen AH, Corver J, Smits WK, van Veelen PA. New insights into the Type A glycan modification of Clostridioides difficile flagellar protein flagellin C by phosphoproteomics analysis. J Biol Chem 2022; 298:101622. [PMID: 35065968 PMCID: PMC8861647 DOI: 10.1016/j.jbc.2022.101622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/12/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/16/2022] Open
Abstract
The type A glycan modification found in human pathogen Clostridioides difficile consists of a monosaccharide (GlcNAc) that is linked to an N-methylated threonine through a phosphodiester bond. This structure has previously been described on the flagellar protein flagellin C of several C. difficile strains and is important for bacterial motility. The study of post-translational modifications often relies on some type of enrichment strategy; however, a procedure for enrichment of this modification has not yet been demonstrated. In this study, we show that an approach that is commonly used in phosphoproteomics, Fe3+-immobilized metal affinity chromatography, also enriches for peptides with this unique post-translational modification. Using LC–MS/MS analyses of immobilized metal affinity chromatography–captured tryptic peptides, we observed not only type A-modified C. difficile flagellin peptides but also a variety of truncated/modified type A structures on these peptides. Using an elaborate set of mass spectrometry analyses, we demonstrate that one of these modifications consists of a type A structure containing a phosphonate (2-aminoethylphosphonate), a modification that is rarely observed and has hitherto not been described in C. difficile. In conclusion, we show that a common enrichment strategy results in reliable identification of peptides carrying a type A glycan modification, and that the results obtained can be used to advance models about its biosynthesis.
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Affiliation(s)
- Paul J Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Annemieke H Friggen
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Jeroen Corver
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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20
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Lippold S, Knaupp A, de Ru AH, Tjokrodirijo RTN, van Veelen PA, van Puijenbroek E, de Taeye SW, Reusch D, Vidarsson G, Wuhrer M, Schlothauer T, Falck D. Fc gamma receptor IIIb binding of individual antibody proteoforms resolved by affinity chromatography-mass spectrometry. MAbs 2021; 13:1982847. [PMID: 34674601 PMCID: PMC8726612 DOI: 10.1080/19420862.2021.1982847] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Indexed: 12/25/2022] Open
Abstract
The crystallizable fragment (Fc) of immunoglobulin G (IgG) activates key immunological responses by interacting with Fc gamma receptors (FcɣR). FcɣRIIIb contributes to neutrophil activation and is involved in antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP). These processes present important mechanisms-of-actions of therapeutic antibodies. The very low affinity of IgG toward FcɣRIIIb (KD ~ 10 µM) is a technical challenge for interaction studies. Additionally, the interaction is strongly dependent on IgG glycosylation, a major contributor to proteoform heterogeneity. We developed an affinity chromatography–mass spectrometry (AC-MS) assay for analyzing IgG-FcɣRIIIb interactions in a proteoform-resolved manner. This proved to be well suited to study low-affinity interactions. The applicability and selectivity of the method were demonstrated on a panel of nine different IgG monoclonal antibodies (mAbs), including no-affinity, low-affinity and high-affinity Fc-engineered or glycoengineered mAbs. Thereby, we could reproduce reported affinity rankings of different IgG glycosylation features and IgG subclasses. Additional post-translational modifications (IgG1 Met252 oxidation, IgG3 hinge-region O-glycosylation) showed no effect on FcɣRIIIb binding. Interestingly, we observed indications of an effect of the variable domain sequence on the Fc-binding that deserves further attention. Our new AC-MS method is a powerful tool for expanding knowledge on structure–function relationships of the IgG-FcɣRIIIb interaction. Hence, this assay may substantially improve the efficiency of assessing critical quality attributes of therapeutic mAbs with respect to an important aspect of neutrophil activation.
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Affiliation(s)
- Steffen Lippold
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander Knaupp
- Pharma Research and Early Development, Roche Innovation Center, Munich, Germany
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rayman T N Tjokrodirijo
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Steven W de Taeye
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam Umc, University of Amsterdam, Amsterdam, The Netherlands
| | - Dietmar Reusch
- Pharma Technical Development, Roche Innovation Center, Munich, Germany
| | - Gestur Vidarsson
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam Umc, University of Amsterdam, Amsterdam, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tilman Schlothauer
- Pharma Research and Early Development, Roche Innovation Center, Munich, Germany.,Biological Technologies, Genentech Inc, South San Francisco, USA
| | - David Falck
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
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21
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Uribe ML, Martín-Nieto J, Quereda C, Rubio-Fernández M, Cruces J, Janssen GMC, de Ru AH, van Veelen PA, Hensbergen PJ. Retinal Proteomics of a Mouse Model of Dystroglycanopathies Reveals Molecular Alterations in Photoreceptors. J Proteome Res 2021; 20:3268-3277. [PMID: 34027671 PMCID: PMC8280732 DOI: 10.1021/acs.jproteome.1c00126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Mutations in the POMT1 gene, encoding a protein O-mannosyltransferase
essential for α-dystroglycan
(α-DG) glycosylation, are frequently observed in a group of
rare congenital muscular dystrophies, collectively known as dystroglycanopathies.
However, it is hitherto unclear whether the effects seen in affected
patients can be fully ascribed to α-DG hypoglycosylation. To
study this, here we used comparative mass spectrometry-based proteomics
and immunofluorescence microscopy and investigated the changes in
the retina of mice in which Pomt1 is specifically
knocked out in photoreceptor cells. Our results demonstrate significant
proteomic changes and associated structural alteration in photoreceptor
cells of Pomt1 cKO mice. In addition to the effects
related to impaired α-DG O-mannosylation, we
observed morphological alterations in the outer segment that are associated
with dysregulation of a relatively understudied POMT1 substrate (KIAA1549),
BBSome proteins, and retinal stress markers. In conclusion, our study
provides new hypotheses to explain the phenotypic changes that are
observed in the retina of patients with dystroglycanopathies.
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Affiliation(s)
- Mary Luz Uribe
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.,Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03080 Alicante, Spain
| | - José Martín-Nieto
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03080 Alicante, Spain.,Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, 03080 Alicante, Spain
| | - Cristina Quereda
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03080 Alicante, Spain
| | - Marcos Rubio-Fernández
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, 03080 Alicante, Spain
| | - Jesús Cruces
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Universidad Autónoma de Madrid, 28029 Madrid, Spain
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Paul J Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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22
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Rodrigues JG, Duarte HO, Gomes C, Balmaña M, Martins ÁM, Hensbergen PJ, de Ru AH, Lima J, Albergaria A, van Veelen PA, Wuhrer M, Gomes J, Reis CA. Terminal α2,6-sialylation of epidermal growth factor receptor modulates antibody therapy response of colorectal cancer cells. Cell Oncol (Dordr) 2021; 44:835-850. [PMID: 33847896 DOI: 10.1007/s13402-021-00606-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 10/08/2020] [Accepted: 03/26/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The epidermal growth factor receptor (EGFR) is a key protein involved in cancer development. Monoclonal antibodies targeting EGFR are approved for the treatment of metastatic colorectal cancer (CRC). Despite the beneficial clinical effects observed in subgroups of patients, the acquisition of resistance to treatment remains a major concern. Protein N-glycosylation of cellular receptors is known to regulate physiological processes leading to activation of downstream signaling pathways. In the present study, the role of EGFR-specific terminal ⍺2,6-sialylation was analyzed in modulation of the malignant phenotype of CRC cells and their resistance to monoclonal antibody Cetuximab-based therapy. METHODS Glycoengineered CRC cell models with specific sialyltransferase ST6GAL1 expression levels were applied to evaluate EGFR activation, cell surface glycosylation and therapeutic response to Cetuximab. RESULTS Glycoproteomic analysis revealed EGFR as a major target of ST6Gal1-mediated ⍺2,6-sialylation in a glycosite-specific manner. Mechanistically, CRC cells with increased ST6Gal1 expression and displaying terminal ⍺2,6-sialylation showed a marked resistance to Cetuximab-induced cytotoxicity. Moreover, we found that this resistance was accompanied by downregulation of EGFR expression and its activation. CONCLUSIONS Our data indicate that EGFR ⍺2,6-sialylation is a key factor in modulating the susceptibility of CRC cells to antibody targeted therapy, thereby disclosing a potential novel biomarker and providing key molecular information for tailor made anti-cancer strategies.
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Affiliation(s)
- Joana G Rodrigues
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313, Porto, Portugal
| | - Henrique O Duarte
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313, Porto, Portugal
| | - Catarina Gomes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135, Porto, Portugal
| | - Meritxell Balmaña
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135, Porto, Portugal.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030, Vienna, Austria
| | - Álvaro M Martins
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135, Porto, Portugal
| | - Paul J Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jorge Lima
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135, Porto, Portugal.,Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - André Albergaria
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135, Porto, Portugal.,Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Joana Gomes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135, Porto, Portugal.
| | - Celso A Reis
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135, Porto, Portugal. .,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313, Porto, Portugal. .,Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.
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23
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de Waard AA, Verkerk T, Jongsma MLM, Hoefakker K, Sethumadhavan S, Gerke C, Bliss S, Kong X, Janssen GMC, de Ru AH, Claas FHJ, Mulder A, Tampé R, van Veelen PA, Halenius A, Spaapen RM. PAKC: A novel panel of HLA class I antigen presentation machinery knockout cells from the same genetic origin. Eur J Immunol 2021; 51:734-737. [PMID: 33275281 PMCID: PMC7986913 DOI: 10.1002/eji.202048599] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 09/30/2020] [Accepted: 11/27/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Antonius A de Waard
- Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands.,Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Tamara Verkerk
- Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands.,Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Marlieke L M Jongsma
- Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands.,Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, The Netherlands
| | - Kelly Hoefakker
- Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands.,Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Sunesh Sethumadhavan
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Carolin Gerke
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sophie Bliss
- Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands.,Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Xiangrui Kong
- Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands.,Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, LUMC, Leiden, The Netherlands
| | | | - Arend Mulder
- Department of Immunology, LUMC, Leiden, The Netherlands
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | | | - Anne Halenius
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Robbert M Spaapen
- Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands.,Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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24
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de Waard AA, Verkerk T, Hoefakker K, van der Steen DM, Jongsma ML, Melamed Kadosh D, Bliss S, de Ru AH, Admon A, van Veelen PA, Griffioen M, Heemskerk MH, Spaapen RM. Healthy cells functionally present TAP-independent SSR1 peptides: implications for selection of clinically relevant antigens. iScience 2021; 24:102051. [PMID: 33554062 PMCID: PMC7847959 DOI: 10.1016/j.isci.2021.102051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/11/2020] [Revised: 11/27/2020] [Accepted: 01/07/2021] [Indexed: 01/02/2023] Open
Abstract
Tumors with an impaired transporter associated with antigen processing (TAP) present several endoplasmic reticulum-derived self-antigens on HLA class I (HLA-I) which are absent on healthy cells. Selection of such TAP-independent antigens for T cell-based immunotherapy should include analysis of their expression on healthy cells to prevent therapy-induced adverse toxicities. However, it is unknown how the absence of clinically relevant antigens on healthy cells needs to be validated. Here, we monitored TAP-independent antigen presentation on various healthy cells after establishing a T cell tool recognizing a TAP-independent signal sequence receptor 1-derived antigen. We found that most but not all healthy cells present this antigen under normal and inflammatory conditions, indicating that TAP-independent antigen presentation is a variable phenomenon. Our data emphasize the necessity of extensive testing of a wide variety of healthy cell types to define clinically relevant TAP-independent antigens that can be safely targeted by immunotherapy. The ER-resident SSR1 holds an antigenic peptide that is processed independently of TAP TAP-independent peptide presentation is functional in healthy cell types TAP-independent SSR1-derived antigen presentation varies between healthy cells This exposes safety and efficacy risks of clinical TAP-independent peptide targeting
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Affiliation(s)
- Antonius A. de Waard
- Department of Immunopathology, Sanquin Research, Amsterdam, CX 1066, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, CX 1066, The Netherlands
| | - Tamara Verkerk
- Department of Immunopathology, Sanquin Research, Amsterdam, CX 1066, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, CX 1066, The Netherlands
| | - Kelly Hoefakker
- Department of Immunopathology, Sanquin Research, Amsterdam, CX 1066, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, CX 1066, The Netherlands
| | | | - Marlieke L.M. Jongsma
- Department of Immunopathology, Sanquin Research, Amsterdam, CX 1066, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, CX 1066, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, ZA 2333, The Netherlands
| | | | - Sophie Bliss
- Department of Immunopathology, Sanquin Research, Amsterdam, CX 1066, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, CX 1066, The Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, LUMC, Leiden, ZA 2333, The Netherlands
| | - Arie Admon
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, LUMC, Leiden, ZA 2333, The Netherlands
| | | | | | - Robbert M. Spaapen
- Department of Immunopathology, Sanquin Research, Amsterdam, CX 1066, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, CX 1066, The Netherlands
- Corresponding author
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25
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Duarte HO, Rodrigues JG, Gomes C, Hensbergen PJ, Ederveen ALH, de Ru AH, Mereiter S, Polónia A, Fernandes E, Ferreira JA, van Veelen PA, Santos LL, Wuhrer M, Gomes J, Reis CA. ST6Gal1 targets the ectodomain of ErbB2 in a site-specific manner and regulates gastric cancer cell sensitivity to trastuzumab. Oncogene 2021; 40:3719-3733. [PMID: 33947960 PMCID: PMC8154592 DOI: 10.1038/s41388-021-01801-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 11/13/2020] [Revised: 03/22/2021] [Accepted: 04/14/2021] [Indexed: 02/03/2023]
Abstract
The clinical performance of the therapeutic monoclonal antibody trastuzumab in the treatment of ErbB2-positive unresectable gastric cancer (GC) is severely hampered by the emergence of molecular resistance. Trastuzumab's target epitope is localized within the extracellular domain of the oncogenic cell surface receptor tyrosine kinase (RTK) ErbB2, which is known to undergo extensive N-linked glycosylation. However, the site-specific glycan repertoire of ErbB2, as well as the detailed molecular mechanisms through which specific aberrant glycan signatures functionally impact the malignant features of ErbB2-addicted GC cells, including the acquisition of trastuzumab resistance, remain elusive. Here, we demonstrate that ErbB2 is modified with both α2,6- and α2,3-sialylated glycan structures in GC clinical specimens. In-depth mass spectrometry-based glycomic and glycoproteomic analysis of ErbB2's ectodomain disclosed a site-specific glycosylation profile in GC cells, in which the ST6Gal1 sialyltransferase specifically targets ErbB2 N-glycosylation sites occurring within the receptor's trastuzumab-binding domain. Abrogation of ST6Gal1 expression reshaped the cellular and ErbB2-specific glycomes, expanded the cellular half-life of the ErbB2 receptor, and sensitized ErbB2-dependent GC cells to trastuzumab-induced cytotoxicity through the stabilization of ErbB dimers at the cell membrane, and the decreased activation of both ErbB2 and EGFR RTKs. Overall, our data demonstrates that ST6Gal1-mediated aberrant α2,6-sialylation actively tunes the resistance of ErbB2-driven GC cells to trastuzumab.
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Affiliation(s)
- Henrique O. Duarte
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP—Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226ICBAS—Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Joana G. Rodrigues
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP—Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226ICBAS—Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Catarina Gomes
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP—Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Paul J. Hensbergen
- grid.10419.3d0000000089452978Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands
| | - Agnes L. Hipgrave Ederveen
- grid.10419.3d0000000089452978Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands
| | - Arnoud H. de Ru
- grid.10419.3d0000000089452978Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands
| | - Stefan Mereiter
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP—Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal ,grid.4299.60000 0001 2169 3852Present Address: IMBA, Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna, Austria
| | - António Polónia
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP—Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP Diagnostics, Department of Pathology, IPATIMUP, University of Porto, Porto, Portugal
| | - Elisabete Fernandes
- grid.418711.a0000 0004 0631 0608Experimental Pathology and Therapeutics Group, IPO-Porto Research Center, Portuguese Institute of Oncology, Porto, Portugal
| | - José A. Ferreira
- grid.418711.a0000 0004 0631 0608Experimental Pathology and Therapeutics Group, IPO-Porto Research Center, Portuguese Institute of Oncology, Porto, Portugal
| | - Peter A. van Veelen
- grid.10419.3d0000000089452978Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands
| | - Lúcio L. Santos
- grid.418711.a0000 0004 0631 0608Experimental Pathology and Therapeutics Group, IPO-Porto Research Center, Portuguese Institute of Oncology, Porto, Portugal ,grid.418711.a0000 0004 0631 0608Department of Surgical Oncology, Portuguese Institute of Oncology, Porto, Portugal
| | - Manfred Wuhrer
- grid.10419.3d0000000089452978Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands
| | - Joana Gomes
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP—Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Celso A. Reis
- grid.5808.50000 0001 1503 7226i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP—Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226ICBAS—Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226Faculty of Medicine, University of Porto, Porto, Portugal
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26
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Lippold S, de Ru AH, Nouta J, van Veelen PA, Palmblad M, Wuhrer M, de Haan N. Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification. Beilstein J Org Chem 2020; 16:3038-3051. [PMID: 33363672 PMCID: PMC7736696 DOI: 10.3762/bjoc.16.253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 07/19/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
Glycoproteomic data are often very complex, reflecting the high structural diversity of peptide and glycan portions. The use of glycopeptide-centered glycoproteomics by mass spectrometry is rapidly evolving in many research areas, leading to a demand in reliable data analysis tools. In recent years, several bioinformatic tools were developed to facilitate and improve both the identification and quantification of glycopeptides. Here, a selection of these tools was combined and evaluated with the aim of establishing a robust glycopeptide detection and quantification workflow targeting enriched glycoproteins. For this purpose, a tryptic digest from affinity-purified immunoglobulins G and A was analyzed on a nano-reversed-phase liquid chromatography-tandem mass spectrometry platform with a high-resolution mass analyzer and higher-energy collisional dissociation fragmentation. Initial glycopeptide identification based on MS/MS data was aided by the Byonic software. Additional MS1-based glycopeptide identification relying on accurate mass and retention time differences using GlycopeptideGraphMS considerably expanded the set of confidently annotated glycopeptides. For glycopeptide quantification, the performance of LaCyTools was compared to Skyline, and GlycopeptideGraphMS. All quantification packages resulted in comparable glycosylation profiles but featured differences in terms of robustness and data quality control. Partial cysteine oxidation was identified as an unexpectedly abundant peptide modification and impaired the automated processing of several IgA glycopeptides. Finally, this study presents a semiautomated workflow for reliable glycoproteomic data analysis by the combination of software packages for MS/MS- and MS1-based glycopeptide identification as well as the integration of analyte quality control and quantification.
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Affiliation(s)
- Steffen Lippold
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Jan Nouta
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Noortje de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
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27
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Wojcik I, Sénard T, de Graaf EL, Janssen GMC, de Ru AH, Mohammed Y, van Veelen PA, Vidarsson G, Wuhrer M, Falck D. Site-Specific Glycosylation Mapping of Fc Gamma Receptor IIIb from Neutrophils of Individual Healthy Donors. Anal Chem 2020; 92:13172-13181. [PMID: 32886488 PMCID: PMC7547861 DOI: 10.1021/acs.analchem.0c02342] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/04/2020] [Indexed: 12/30/2022]
Abstract
Fc gamma receptors (FcγRs) translate antigen recognition by immunoglobulin G (IgG) into various immune responses. A better understanding of this key element of immunity promises novel insights into mechanisms of (auto-/allo-)immune diseases and more rationally designed antibody-based drugs. Glycosylation on both IgG and FcγR impacts their interaction dramatically. Regarding FcγR glycosylation profiling, major analytical challenges are associated with the presence of multiple glycosylation sites in close proximity and large structural heterogeneity. To address these challenges, we developed a straightforward and comprehensive analytical methodology to map FcγRIIIb glycosylation in primary human cells. After neutrophil isolation and immunoprecipitation, glycopeptides containing a single site each were generated by a dual-protease in-gel digestion. The complex mixture was resolved by liquid chromatography-tandem mass spectrometry (LC-MS/MS) providing information on the level of individual donors. In contrast to recently published alternatives for FcγRIIIb, we assessed its site-specific glycosylation in a single LC-MS/MS run and simultaneously determined the donor allotype. Studying FcγRIIIb derived from healthy donor neutrophils, we observed profound differences as compared to the soluble variant and the homologous FcγRIIIa on natural killer cells. This method will allow assessment of differences in FcγRIII glycosylation between individuals, cell types, subcellular locations, and pathophysiological conditions.
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Affiliation(s)
- Iwona Wojcik
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
- Glycoscience
Research Laboratory, Genos Ltd., Zagreb 10000, Croatia
| | - Thomas Sénard
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
| | - Erik L. de Graaf
- Department
of Experimental Immunohematology, Sanquin Research, and Landsteiner
Laboratory, Academic Medical Center, University
of Amsterdam, 1066 CX Amsterdam, The Netherlands
| | - George M. C. Janssen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
| | - Arnoud H. de Ru
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
| | - Yassene Mohammed
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
| | - Peter A. van Veelen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
| | - Gestur Vidarsson
- Department
of Experimental Immunohematology, Sanquin Research, and Landsteiner
Laboratory, Academic Medical Center, University
of Amsterdam, 1066 CX Amsterdam, The Netherlands
| | - Manfred Wuhrer
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
| | - David Falck
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
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28
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van Balen P, Kester MGD, de Klerk W, Crivello P, Arrieta-Bolaños E, de Ru AH, Jedema I, Mohammed Y, Heemskerk MHM, Fleischhauer K, van Veelen PA, Falkenburg JHF. Immunopeptidome Analysis of HLA-DPB1 Allelic Variants Reveals New Functional Hierarchies. J I 2020; 204:3273-3282. [DOI: 10.4049/jimmunol.2000192] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/13/2020] [Indexed: 01/22/2023]
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29
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Kemps PG, Zondag TC, Steenwijk EC, Andriessen Q, Borst J, Vloemans S, Roelen DL, Voortman LM, Verdijk RM, van Noesel CJM, Cleven AHG, Hawkins C, Lang V, de Ru AH, Janssen GMC, Haasnoot GW, Franken KLMC, van Eijk R, Solleveld-Westerink N, van Wezel T, Egeler RM, Beishuizen A, van Laar JAM, Abla O, van den Bos C, van Veelen PA, van Halteren AGS. Apparent Lack of BRAF V600E Derived HLA Class I Presented Neoantigens Hampers Neoplastic Cell Targeting by CD8 + T Cells in Langerhans Cell Histiocytosis. Front Immunol 2020; 10:3045. [PMID: 31998317 PMCID: PMC6967030 DOI: 10.3389/fimmu.2019.03045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 10/23/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022] Open
Abstract
Langerhans Cell Histiocytosis (LCH) is a neoplastic disorder of hematopoietic origin characterized by inflammatory lesions containing clonal histiocytes (LCH-cells) intermixed with various immune cells, including T cells. In 50-60% of LCH-patients, the somatic BRAF V600E driver mutation, which is common in many cancers, is detected in these LCH-cells in an otherwise quiet genomic landscape. Non-synonymous mutations like BRAF V600E can be a source of neoantigens capable of eliciting effective antitumor CD8+ T cell responses. This requires neopeptides to be stably presented by Human Leukocyte Antigen (HLA) class I molecules and sufficient numbers of CD8+ T cells at tumor sites. Here, we demonstrate substantial heterogeneity in CD8+ T cell density in n = 101 LCH-lesions, with BRAF V600E mutated lesions displaying significantly lower CD8+ T cell:CD1a+ LCH-cell ratios (p = 0.01) than BRAF wildtype lesions. Because LCH-lesional CD8+ T cell density had no significant impact on event-free survival, we investigated whether the intracellularly expressed BRAF V600E protein is degraded into neopeptides that are naturally processed and presented by cell surface HLA class I molecules. Epitope prediction tools revealed a single HLA class I binding BRAF V600E derived neopeptide (KIGDFGLATEK), which indeed displayed strong to intermediate binding capacity to HLA-A*03:01 and HLA-A*11:01 in an in vitro peptide-HLA binding assay. Mass spectrometry-based targeted peptidomics was used to investigate the presence of this neopeptide in HLA class I presented peptides isolated from several BRAF V600E expressing cell lines with various HLA genotypes. While the HLA-A*02:01 binding BRAF wildtype peptide KIGDFGLATV was traced in peptides isolated from all five cell lines expressing this HLA subtype, KIGDFGLATEK was not detected in the HLA class I peptidomes of two distinct BRAF V600E transduced cell lines with confirmed expression of HLA-A*03:01 or HLA-A*11:01. These data indicate that the in silico predicted HLA class I binding and proteasome-generated neopeptides derived from the BRAF V600E protein are not presented by HLA class I molecules. Given that the BRAF V600E mutation is highly prevalent in chemotherapy refractory LCH-patients who may qualify for immunotherapy, this study therefore questions the efficacy of immune checkpoint inhibitor therapy in LCH.
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Affiliation(s)
- Paul G Kemps
- Immunology Laboratory Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Timo C Zondag
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Eline C Steenwijk
- Immunology Laboratory Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Quirine Andriessen
- Immunology Laboratory Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Jelske Borst
- Immunology Laboratory Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Sandra Vloemans
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Dave L Roelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Robert M Verdijk
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Carel J M van Noesel
- Department of Pathology, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Arjen H G Cleven
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | - Cynthia Hawkins
- Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Veronica Lang
- Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Geert W Haasnoot
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Kees L M C Franken
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | - R Maarten Egeler
- Immunology Laboratory Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands.,Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Auke Beishuizen
- Department of Pediatric Oncology, Sophia Children's Hospital, Erasmus University Medical Center, Rotterdam, Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Jan A M van Laar
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Oussama Abla
- Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Cor van den Bos
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Department of Pediatric Oncology, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Astrid G S van Halteren
- Immunology Laboratory Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
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30
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Pirro M, Rombouts Y, Stella A, Neyrolles O, Burlet-Schiltz O, van Vliet SJ, de Ru AH, Mohammed Y, Wuhrer M, van Veelen PA, Hensbergen PJ. Characterization of Macrophage Galactose-type Lectin (MGL) ligands in colorectal cancer cell lines. Biochim Biophys Acta Gen Subj 2020; 1864:129513. [PMID: 31911241 DOI: 10.1016/j.bbagen.2020.129513] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/20/2019] [Accepted: 01/02/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND The Ca2+-dependent C-type lectin receptor Macrophage Galactose-type Lectin (MGL) is highly expressed by tolerogenic dendritic cells (DC) and macrophages. MGL exhibits a high binding specificity for terminal alpha- and beta-linked GalNAc residues found in Tn, sTn and LacdiNAc antigens. These glycan epitopes are often overexpressed in colorectal cancer (CRC), and, as such, MGL can be used to discriminate tumor from the corresponding healthy tissues. Moreover, the high expression of MGL ligands is associated with poor disease-free survival in stage III of CRC tumors. Nonetheless, the glycoproteins expressed by tumor cells that are recognized by MGL have hitherto remained elusive. METHODS Using a panel of three CRC cell lines (HCT116, HT29 and LS174T), recapitulating CRC diversity, we performed FACS staining and pull-down assays using a recombinant soluble form of MGL (and a mutant MGL as control) combined with mass spectrometry-based (glyco)proteomics. RESULTS HCT116 and HT29, but not LS174T, are high MGL-binding CRC cell lines. On these cells, the major cell surface binding proteins are receptors (e.g. MET, PTK7, SORL1, PTPRF) and integrins (ITGB1, ITGA3). From these proteins, several N- and/or O-glycopeptides were identified, of which some carried either a LacdiNAc or Tn epitope. CONCLUSIONS We have identified cell surface MGL-ligands on CRC cell lines. GENERAL SIGNIFICANCE Advances in (glyco)proteomics have led to identification of candidate key mediators of immune-evasion and tumor growth in CRC.
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Affiliation(s)
- Martina Pirro
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Yoann Rombouts
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Alexandre Stella
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sandra J van Vliet
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Paul J Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands.
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31
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Kampstra ASB, van Heemst J, Janssen GM, de Ru AH, van Lummel M, van Veelen PA, Toes REM. Ligandomes obtained from different HLA-class II-molecules are homologous for N- and C-terminal residues outside the peptide-binding cleft. Immunogenetics 2019; 71:519-530. [PMID: 31520135 PMCID: PMC6790208 DOI: 10.1007/s00251-019-01129-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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] [Received: 04/23/2019] [Accepted: 08/23/2019] [Indexed: 12/31/2022]
Abstract
Human CD4+ T lymphocytes play an important role in inducing potent immune responses. T cells are activated and stimulated by peptides presented in human leucocyte antigen (HLA)-class II molecules. These HLA-class II molecules typically present peptides of between 12 and 20 amino acids in length. The region that interacts with the HLA molecule, designated as the peptide-binding core, is highly conserved in the residues which anchor the peptide to the molecule. In addition, as these peptides are the product of proteolytic cleavages, certain conserved residues may be expected at the N- and C-termini outside the binding core. To study whether similar conserved residues are present in different cell types, potentially harbouring different proteolytic enzymes, the ligandomes of HLA-DRB1*03:01/HLA-DRB > 1 derived from two different cell types (dendritic cells and EBV-transformed B cells) were identified with mass spectrometry and the binding core and N- and C-terminal residues of a total of 16,568 peptides were analysed using the frequencies of the amino acids in the human proteome. Similar binding motifs were found as well as comparable conservations in the N- and C-terminal residues. Furthermore, the terminal conservations of these ligandomes were compared to the N- and C-terminal conservations of the ligandome acquired from dendritic cells homozygous for HLA-DRB1*04:01. Again, comparable conservations were evident with only minor differences. Taken together, these data show that there are conservations in the terminal residues of peptides, presumably the result of the activity of proteases involved in antigen processing.
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Affiliation(s)
- Arieke S B Kampstra
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Jurgen van Heemst
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - George M Janssen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H de Ru
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Menno van Lummel
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - René E M Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
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van Lummel M, Buis DTP, Ringeling C, de Ru AH, Pool J, Papadopoulos GK, van Veelen PA, Reijonen H, Drijfhout JW, Roep BO. Epitope Stealing as a Mechanism of Dominant Protection by HLA-DQ6 in Type 1 Diabetes. Diabetes 2019; 68:787-795. [PMID: 30626607 DOI: 10.2337/db18-0501] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 12/28/2018] [Indexed: 11/13/2022]
Abstract
The heterozygous DQ2/8 (DQA1*05:01-DQB1*02:01/DQA1*03:01-DQB1*03:02) genotype confers the highest risk in type 1 diabetes (T1D), whereas the DQ6/8 (DQA1*02:01-DQB1*06:02/DQA1*03:01-DQB1*03:02) genotype is protective. The mechanism of dominant protection by DQ6 (DQB1*06:02) is unknown. We tested the hypothesis that DQ6 interferes with peptide binding to DQ8 by competition for islet epitope ("epitope stealing") by analysis of the islet ligandome presented by HLA-DQ6/8 and -DQ8/8 on dendritic cells pulsed with islet autoantigens preproinsulin (PPI), GAD65, and IA-2, followed by competition assays using a newly established "epitope-stealing" HLA/peptide-binding assay. HLA-DQ ligandome analysis revealed a distinct DQ6 peptide-binding motif compared with the susceptible DQ2/8 molecules. PPI and IA-2 peptides were identified from DQ6, of DQ6/8 heterozygous dendritic cells, but no DQ8 islet peptides were retrieved. Insulin B6-23, a highly immunogenic CD4 T-cell epitope in patients with T1D, bound to both DQ6 and DQ8. Yet, binding of InsB6-23 to DQ8 was prevented by DQ6. We obtained first functional evidence of a mechanism of dominant protection from disease, in which HLA molecules associated with protection bind islet epitopes in a different, competing, HLA-binding register, leading to "epitope stealing" and conceivably diverting the immune response from islet epitopes presented by disease-susceptible HLA molecules in the absence of protective HLA.
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Affiliation(s)
- Menno van Lummel
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - David T P Buis
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Cherish Ringeling
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Jos Pool
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - George K Papadopoulos
- Laboratory of Biophysics, Biochemistry, Bioprocessing and Bioproducts, Faculty of Agricultural Technology, Technological Educational Institute of Epirus, Arta, Greece
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Helena Reijonen
- Department of Diabetes Immunology, Diabetes and Metabolism Research Institute at the Beckman Research Institute, City of Hope, Duarte, CA
| | - Jan W Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Bart O Roep
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
- Department of Diabetes Immunology, Diabetes and Metabolism Research Institute at the Beckman Research Institute, City of Hope, Duarte, CA
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Lee DIVD, Reijmers RM, Honders MW, Hagedoorn RS, Jong RMD, Kester MG, Steen DMVD, Ru AHD, Kweekel C, Jedema I, Veelken H, Heemskerk MM, Veelen PAV, Falkenburg JF, Griffioen M. Abstract A044: Mutated NPM1 as target for immunotherapy of acute myeloid leukemia. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-a044] [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] [Indexed: 11/16/2022]
Abstract
Abstract
The most frequent subtype of acute myeloid leukemia (AML) is defined by mutations in the nucleophosmin (NPM1) gene. Mutated NPM1 is an attractive target for immunotherapy, since it is an essential driver gene and 4 base pair frameshift insertions in exon 12 occur in 30-35% of AML, resulting in a novel C-terminal alternative reading frame of 11 amino acids. By searching in the HLA class I ligandome of primary AML, we identified multiple peptides derived from mutated NPM1. For one of these peptides, i.e., HLA-A*02:01-presented CLAVEEVSL, we searched for specific T-cells in AML patients and healthy individuals using peptide-MHC tetramers. Tetramer-positive CD8 T-cell clones were isolated and analyzed for reactivity against primary AML with mutated NPM1. From one selected clone with superior antitumor reactivity, we isolated the T-cell receptor (TCR) and demonstrated specific recognition and lysis of HLA-A*02:01-positive AML with mutated NPM1 in vitro after retroviral transfer to CD8 and CD4 T-cells. In vivo antitumor efficacy of TCR-transduced CD8 and CD4 T-cells was confirmed in immunodeficient mice engrafted with a human AML cell line expressing mutated NPM1. These data show that mutated NPM1-derived peptides are presented on AML and that CLAVEEVSL is a neoantigen that can be efficiently targeted on AML with mutated NPM1 by TCR gene transfer in a co-receptor independent fashion. Immunotherapy targeting mutated NPM1 may therefore contribute to treatment of AML.
Citation Format: Dyantha I. van der Lee, Rogier M. Reijmers, M. Willy Honders, Renate S. Hagedoorn, Rob. M. de Jong, Michel G.D. Kester, Dirk M. van der Steen, Arnoud H. de Ru, Christiaan Kweekel, Inge Jedema, Hendrik Veelken, Mirjam M. Heemskerk, Peter A. van Veelen, J.H. Frederik Falkenburg, Marieke Griffioen. Mutated NPM1 as target for immunotherapy of acute myeloid leukemia [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A044.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Inge Jedema
- Leiden University Medical Center, Leiden, The Netherlands
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van der Lee DI, Reijmers RM, Honders MW, Hagedoorn RS, de Jong RC, Kester MG, van der Steen DM, de Ru AH, Kweekel C, Bijen HM, Jedema I, Veelken H, van Veelen PA, Heemskerk MH, Falkenburg JHF, Griffioen M. Mutated nucleophosmin 1 as immunotherapy target in acute myeloid leukemia. J Clin Invest 2019; 129:774-785. [PMID: 30640174 DOI: 10.1172/jci97482] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [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: 09/15/2017] [Accepted: 11/06/2018] [Indexed: 12/15/2022] Open
Abstract
The most frequent subtype of acute myeloid leukemia (AML) is defined by mutations in the nucleophosmin 1 (NPM1) gene. Mutated NPM1 (ΔNPM1) is an attractive target for immunotherapy, since it is an essential driver gene and 4 bp frameshift insertions occur in the same hotspot in 30%-35% of AMLs, resulting in a C-terminal alternative reading frame of 11 aa. By searching the HLA class I ligandome of primary AMLs, we identified multiple ΔNPM1-derived peptides. For one of these peptides, HLA-A*02:01-binding CLAVEEVSL, we searched for specific T cells in healthy individuals using peptide-HLA tetramers. Tetramer-positive CD8+ T cells were isolated and analyzed for reactivity against primary AMLs. From one clone with superior antitumor reactivity, we isolated the T cell receptor (TCR) and demonstrated specific recognition and lysis of HLA-A*02:01-positive ΔNPM1 AML after retroviral transfer to CD8+ and CD4+ T cells. Antitumor efficacy of TCR-transduced T cells was confirmed in immunodeficient mice engrafted with a human AML cell line expressing ΔNPM1. In conclusion, the data show that ΔNPM1-derived peptides are presented on AML and that CLAVEEVSL is a neoantigen that can be efficiently targeted on AML by ΔNPM1 TCR gene transfer. Immunotherapy targeting ΔNPM1 may therefore contribute to treatment of AML.
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Affiliation(s)
| | | | | | | | | | | | | | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | | | | | | | | | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
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Bijen HM, Hassan C, Kester MGD, Janssen GMC, Hombrink P, de Ru AH, Drijfhout JW, Meiring HD, de Jong AP, Falkenburg JHF, Jimenez CR, Heemskerk MHM, van Veelen PA. Specific T Cell Responses against Minor Histocompatibility Antigens Cannot Generally Be Explained by Absence of Their Allelic Counterparts on the Cell Surface. Proteomics 2018; 18:e1700250. [PMID: 29251415 DOI: 10.1002/pmic.201700250] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 09/19/2017] [Revised: 11/22/2017] [Indexed: 12/20/2022]
Abstract
Allogeneic stem cell transplantation has emerged as immunotherapy in the treatment of a variety of hematological malignancies. Its efficacy depends on induction of graft versus leukemia by donor lymphocytes. Both graft versus leukemia and graft versus host disease are induced by T cells reactive against polymorphic peptides, called minor histocompatibility antigens (MiHA), which differ between patient and donor and are presented in the context of self-HLA (where HLA is human leukocyte antigen). The allelic counterpart (AC) of the MiHA is generally considered to be absent at the cell surface, based on the absence of immune responses directed against the AC. To study this in detail, we evaluate the recognition, HLA-binding affinity, and cell surface expression of three selected MiHA. By quantitative MS, we demonstrate the similarly abundant expression of both MiHA and AC at the cell surface. We conclude that the absent recognition of the AC cannot generally be explained by insufficient processing and presentation at the cell surface of the AC.
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Affiliation(s)
- Helena M Bijen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Chopie Hassan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel G D Kester
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pleun Hombrink
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Wouter Drijfhout
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hugo D Meiring
- Laboratory for Vaccine Research, Unit Research and Development, Netherlands Vaccine Institute, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Ad P de Jong
- Laboratory for Vaccine Research, Unit Research and Development, Netherlands Vaccine Institute, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Connie R Jimenez
- OncoProteomics Laboratory, Medical Oncology, VU Medical Center, Amsterdam, The Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
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36
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de Groot NG, Heijmans CMC, de Ru AH, Janssen GMC, Drijfhout JW, Otting N, Vangenot C, Doxiadis GGM, Koning F, van Veelen PA, Bontrop RE. A Specialist Macaque MHC Class I Molecule with HLA-B*27-like Peptide-Binding Characteristics. J Immunol 2017; 199:3679-3690. [PMID: 29021373 DOI: 10.4049/jimmunol.1700502] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 09/15/2017] [Indexed: 11/19/2022]
Abstract
In different macaque species, the MHC A2*05 gene is present in abundance, and its gene products are characterized by low cell-surface expression and a highly conserved peptide-binding cleft. We have characterized the peptide-binding motif of Mamu-A2*05:01, and elucidated the binding capacity for virus-derived peptides. The macaque A2*05 allotype prefers the basic amino acid arginine at the second position of the peptide, and hydrophobic and polar amino acids at the C-terminal end. These preferences are shared with HLA-B*27 and Mamu-B*008, molecules shown to be involved in elite control in human HIV type 1 and macaque SIV infections, respectively. In contrast, however, Mamu-A2*05 preferentially binds 8-mer peptides. Retention in the endoplasmic reticulum seems to be the cause of the lower cell-surface expression. Subsequent peptide-binding studies have illustrated that Mamu-A2*05:01 is able to bind SIV-epitopes known to evoke a strong CD8+ T cell response in the context of the Mamu-B*008 allotype in SIV-infected rhesus macaques. Thus, the macaque A2*05 gene encodes a specialized MHC class I molecule, and is most likely transported to the cell surface only when suitable peptides become available.
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Affiliation(s)
- Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands;
| | - Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - George M C Janssen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Jan W Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Christelle Vangenot
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland; and
| | - Gaby G M Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands
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Dekkers JS, Verheul MK, Stoop JN, Liu B, Ioan-Facsinay A, van Veelen PA, de Ru AH, Janssen GMC, Hegen M, Rapecki S, Huizinga TWJ, Trouw LA, Toes REM. Breach of autoreactive B cell tolerance by post-translationally modified proteins. Ann Rheum Dis 2017; 76:1449-1457. [DOI: 10.1136/annrheumdis-2016-210772] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/10/2017] [Accepted: 03/23/2017] [Indexed: 02/01/2023]
Abstract
ObjectivesOver 50% of patients with rheumatoid arthritis (RA) harbour a variety of anti-modified protein antibodies (AMPA) against different post-translationally modified (PTM) proteins, including anti-carbamylated protein (anti-CarP) antibodies. At present, it is unknown how AMPA are generated and how autoreactive B cell responses against PTM proteins are induced. Here we studied whether PTM foreign antigens can breach B cell tolerance towards PTM self-proteins.MethodsSerum reactivity towards five carbamylated proteins was determined for 160 patients with RA and 40 healthy individuals. Antibody cross-reactivity was studied by inhibition experiments. Mass spectrometry was performed to identify carbamylated self-proteins in human rheumatic joint tissue. Mice were immunised with carbamylated or non-modified (auto)antigens and analysed for autoantibody responses.ResultsWe show that anti-CarP antibodies in RA are highly cross-reactive towards multiple carbamylated proteins, including modified self-proteins and modified non-self-proteins. Studies in mice show that anti-CarP antibody responses recognising carbamylated self-proteins are induced by immunisation with carbamylated self-proteins and by immunisation with carbamylated proteins of non-self-origin. Similar to the data observed with sera from patients with RA, the murine anti-CarP antibody response was, both at the monoclonal level and the polyclonal level, highly cross-reactive towards multiple carbamylated proteins, including carbamylated self-proteins.ConclusionsSelf-reactive AMPA responses can be induced by exposure to foreign proteins containing PTM. These data show how autoreactive B cell responses against PTM self-proteins can be induced by exposure to PTM foreign proteins and provide new insights on the breach of autoreactive B cell tolerance.
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de Keijzer J, Mulder A, de Ru AH, van Soolingen D, van Veelen PA. Parallel reaction monitoring of clinical Mycobacterium tuberculosis lineages reveals pre-existent markers of rifampicin tolerance in the emerging Beijing lineage. J Proteomics 2016; 150:9-17. [PMID: 27576137 DOI: 10.1016/j.jprot.2016.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 02/21/2016] [Revised: 05/05/2016] [Accepted: 08/25/2016] [Indexed: 11/30/2022]
Abstract
The spread of multidrug resistant Mycobacterium tuberculosis is one of the major challenges in tuberculosis control. In Eurasia, the spread of multidrug resistant tuberculosis is driven by the M. tuberculosis Beijing genotype. In this study, we examined whether selective advantages are present in the proteome of Beijing isolates that contribute to the emergence of this genotype. To this end, we compared the proteome of M. tuberculosis Beijing to that of M. tuberculosis H37Rv, both in the presence and absence of the first-line antibiotic rifampicin. During rifampicin exposure, both M. tuberculosis genotypes express proteins belonging to the DosR dormancy regulon, which induces a metabolically hypoactive-, drug tolerant phenotype. However, these markers of rifampicin tolerance were already more abundant in the M. tuberculosis Beijing isolate prior to drug exposure. To determine whether the a priori high abundance of specific proteins contribute to the formation of antibiotic resistance in M. tuberculosis Beijing, we quantified the abundance of 33 selected proteins in 27 clinical isolates from the five most common M. tuberculosis lineages using parallel reaction monitoring. The observed pre-existing high abundance of dormancy proteins in Beijing strains provides an evolutionary advantage that allows these strains to persist for prolonged periods during rifampicin treatment. SIGNIFICANCE M. tuberculosis is the leading cause of death by a bacterial infection worldwide. Treatment-regimen to eradicate this pathogen make use of the first-line antibiotic rifampicin, which is considered to be the cornerstone of modern day anti-tuberculosis treatment. Despite the potency of rifampicin, there is an increasing occurrence of rifampicin resistant mutants in a specific cluster of M. tuberculosis, the Beijing genotype. Using both a data dependent acquisition and a targeted proteomic approach we identified markers of rifampicin tolerance to be high abundant in members of the M. tuberculosis Beijing genotype, already prior drug exposure. The identification of this M. tuberculosis Beijing specific trait will contribute to improved diagnostics and treatment of M. tuberculosis.
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Affiliation(s)
- Jeroen de Keijzer
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands.
| | - Arnout Mulder
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720, BA, The Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands; Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720, BA, The Netherlands; Departments of Pulmonary Diseases and Medical Microbiology, Radboud University Medical Center, Nijmegen, 6500, HB, The Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands; Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, 2300, RC, The Netherlands
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Heijs B, Holst S, Briaire-de Bruijn IH, van Pelt GW, de Ru AH, van Veelen PA, Drake RR, Mehta AS, Mesker WE, Tollenaar RA, Bovée JVMG, Wuhrer M, McDonnell LA. Multimodal Mass Spectrometry Imaging of N-Glycans and Proteins from the Same Tissue Section. Anal Chem 2016; 88:7745-53. [PMID: 27373711 DOI: 10.1021/acs.analchem.6b01739] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
On-tissue digestion matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) can be used to record spatially correlated molecular information from formalin-fixed, paraffin-embedded (FFPE) tissue sections. In this work, we present the in situ multimodal analysis of N-linked glycans and proteins from the same FFPE tissue section. The robustness and applicability of the method are demonstrated for several tumors, including epithelial and mesenchymal tumor types. Major analytical aspects, such as lateral diffusion of the analyte molecules and differences in measurement sensitivity due to the additional sample preparation methods, have been investigated for both N-glycans and proteolytic peptides. By combining the MSI approach with extract analysis, we were also able to assess which mass spectral peaks generated by MALDI-MSI could be assigned to unique N-glycan and peptide identities.
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Affiliation(s)
- Bram Heijs
- Center for Proteomics and Metabolomics, Leiden University Medical Center , Leiden, The Netherlands
| | - Stephanie Holst
- Center for Proteomics and Metabolomics, Leiden University Medical Center , Leiden, The Netherlands
| | | | - Gabi W van Pelt
- Department of Surgery, Leiden University Medical Center , Leiden, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center , Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center , Leiden, The Netherlands
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina , Charleston, South Carolina 29425, United States
| | - Anand S Mehta
- Department of Microbiology and Immunology, College of Medicine, Drexel University , Philadelphia, Pennsylvania 19129, United States
| | - Wilma E Mesker
- Department of Surgery, Leiden University Medical Center , Leiden, The Netherlands
| | - Rob A Tollenaar
- Department of Surgery, Leiden University Medical Center , Leiden, The Netherlands
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center , Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center , Leiden, The Netherlands
| | - Liam A McDonnell
- Center for Proteomics and Metabolomics, Leiden University Medical Center , Leiden, The Netherlands.,Department of Pathology, Leiden University Medical Center , Leiden, The Netherlands.,Fondazione Pisana per la Scienza ONLUS , Pisa, Italy
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de Keijzer J, Mulder A, de Haas PEW, de Ru AH, Heerkens EM, Amaral L, van Soolingen D, van Veelen PA. Thioridazine Alters the Cell-Envelope Permeability of Mycobacterium tuberculosis. J Proteome Res 2016; 15:1776-86. [PMID: 27068340 DOI: 10.1021/acs.jproteome.5b01037] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 11/30/2022]
Abstract
The increasing occurrence of multidrug resistant tuberculosis exerts a major burden on treatment of this infectious disease. Thioridazine, previously used as a neuroleptic, is active against extensively drug resistant tuberculosis when added to other second- and third-line antibiotics. By quantitatively studying the proteome of thioridazine-treated Mycobacterium tuberculosis, we discovered the differential abundance of several proteins that are involved in the maintenance of the cell-envelope permeability barrier. By assessing the accumulation of fluorescent dyes in mycobacterial cells over time, we demonstrate that long-term drug exposure of M. tuberculosis indeed increased the cell-envelope permeability. The results of the current study demonstrate that thioridazine induced an increase in cell-envelope permeability and thereby the enhanced uptake of compounds. These results serve as a novel explanation to the previously reported synergistic effects between thioridazine and other antituberculosis drugs. This new insight in the working mechanism of this antituberculosis compound could open novel perspectives of future drug-administration regimens in combinational therapy.
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Affiliation(s)
- Jeroen de Keijzer
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre (LUMC) , Leiden, 2300 RC The Netherlands
| | | | | | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre (LUMC) , Leiden, 2300 RC The Netherlands
| | | | - Leonard Amaral
- Travel Medicine of the CMDT, Institute of Hygiene and Tropical Medicine, Universidade Nova de Lisboa , Lisboa, 1349-008 Portugal
| | - Dick van Soolingen
- Departments of Pulmonary Diseases and Medical Microbiology, Radboud University Medical Centre , Nijmegen, 6500 HB The Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre (LUMC) , Leiden, 2300 RC The Netherlands
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de Keijzer J, Mulder A, de Beer J, de Ru AH, van Veelen PA, van Soolingen D. Mechanisms of Phenotypic Rifampicin Tolerance in Mycobacterium tuberculosis Beijing Genotype Strain B0/W148 Revealed by Proteomics. J Proteome Res 2016; 15:1194-204. [PMID: 26930559 DOI: 10.1021/acs.jproteome.5b01073] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [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: 01/09/2023]
Abstract
The "successful" Russian clone B0/W148 of Mycobacterium tuberculosis Beijing is well-known for its capacity to develop antibiotic resistance. During treatment, resistant mutants can occur that have inheritable resistance to specific antibiotics. Next to mutations, M. tuberculosis has several mechanisms that increase their tolerance to a variety of antibiotics. Insights in the phenotypic mechanisms that contribute to drug tolerance will increase our understanding of how antibiotic resistance develops in M. tuberculosis. In this study, we examined the (phospho)proteome dynamics in M. tuberculosis Beijing strain B0/W148 when exposed to a high dose of rifampicin; one of the most potent first-line antibiotics. A total of 2,534 proteins and 191 phosphorylation sites were identified, and revealed the differential regulation of DosR regulon proteins, which are necessary for the development of a dormant phenotype that is less susceptible to antibiotics. By examining independent phenotypic markers of dormancy, we show that persisters of in vitro rifampicin exposure entered a metabolically hypoactive state, which yields rifampicin and other antibiotics largely ineffective. These new insights in the role of protein regulation and post-translational modifications during the initial phase of rifampicin treatment reveal a shortcoming in the antituberculosis regimen that is administered to 8-9 million individuals annually.
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Affiliation(s)
- Jeroen de Keijzer
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC) , Leiden 2300 RC, The Netherlands
| | - Arnout Mulder
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM) , Bilthoven 3720 BA, The Netherlands
| | - Jessica de Beer
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM) , Bilthoven 3720 BA, The Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC) , Leiden 2300 RC, The Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC) , Leiden 2300 RC, The Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM) , Bilthoven 3720 BA, The Netherlands.,Departments of Pulmonary Diseases and Medical Microbiology, Radboud University Medical Center , Nijmegen 6500 HB, The Netherlands
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van Lummel M, van Veelen PA, de Ru AH, Janssen GMC, Pool J, Laban S, Joosten AM, Nikolic T, Drijfhout JW, Mearin ML, Aanstoot HJ, Peakman M, Roep BO. Dendritic Cells Guide Islet Autoimmunity through a Restricted and Uniquely Processed Peptidome Presented by High-Risk HLA-DR. J Immunol 2016; 196:3253-63. [PMID: 26944932 DOI: 10.4049/jimmunol.1501282] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 02/02/2016] [Indexed: 12/13/2022]
Abstract
Identifying T cell epitopes of islet autoantigens is important for understanding type 1 diabetes (T1D) immunopathogenesis and to design immune monitoring and intervention strategies in relationship to disease progression. Naturally processed T cell epitopes have been discovered by elution from HLA-DR4 of pulsed B lymphocytes. The designated professional APC directing immune responses is the dendritic cell (DC). To identify naturally processed epitopes, monocyte-derived DC were pulsed with preproinsulin (PPI), glutamic acid decarboxylase (65-kDa isoform; GAD65), and insulinoma-associated Ag-2 (IA-2), and peptides were eluted of HLA-DR3 and -DR4, which are associated with highest risk for T1D development. Proteome analysis confirmed uptake and processing of islet Ags by DC. PPI peptides generated by DC differed from those processed by B lymphocytes; PPI signal-sequence peptides were eluted from HLA-DR4 and -DR3/4 that proved completely identical to a primary target epitope of diabetogenic HLA-A2-restricted CD8 T cells. HLA-DR4 binding was confirmed. GAD65 peptides, eluted from HLA-DR3 and -DR4, encompassed two core regions overlapping the two most immunodominant and frequently studied CD4 T cell targets. GAD65 peptides bound to HLA-DR3. Strikingly, the IA-2 ligandome of HLA-DR was exclusively generated from the extracellular part of IA-2, whereas most previous immune studies have focused on intracellular IA-2 epitopes. The newly identified IA-2 peptides bound to HLA-DR3 and -DR4. Differential T cell responses were detected against the newly identified IA-2 epitopes in blood from T1D patients. The core regions to which DC may draw attention from autoreactive T cells are largely distinct and more restricted than are those of B cells. GAD65 peptides presented by DC focus on highly immunogenic T cell targets, whereas HLA-DR-binding peptides derived from IA-2 are distinct from the target regions of IA-2 autoantibodies.
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Affiliation(s)
- Menno van Lummel
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - George M C Janssen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Jos Pool
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Sandra Laban
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Antoinette M Joosten
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Tatjana Nikolic
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Jan W Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - M Luisa Mearin
- Department of Pediatrics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Henk J Aanstoot
- Diabeter, Center for Pediatric and Adolescent Diabetes Care and Research, 3011 TA Rotterdam, the Netherlands
| | - Mark Peakman
- Department of Immunobiology, School of Medicine, King's College London, London SE1 9RT, United Kingdom; and
| | - Bart O Roep
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; Department of Diabetes Immunology, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA 91010
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van Lummel M, van Veelen PA, de Ru AH, Pool J, Nikolic T, Laban S, Joosten A, Drijfhout JW, Gómez-Touriño I, Arif S, Aanstoot HJ, Peakman M, Roep BO. Discovery of a Selective Islet Peptidome Presented by the Highest-Risk HLA-DQ8trans Molecule. Diabetes 2016; 65:732-41. [PMID: 26718497 DOI: 10.2337/db15-1031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/17/2015] [Indexed: 11/13/2022]
Abstract
HLA-DQ2/8 heterozygous individuals are at far greater risk for type 1 diabetes (T1D) development by expressing HLA-DQ8trans on antigen-presenting cells compared with HLA-DQ2 or -DQ8 homozygous individuals. Dendritic cells (DC) initiate and shape adaptive immune responses by presenting HLA-epitope complexes to naïve T cells. To dissect the role of HLA-DQ8trans in presenting natural islet epitopes, we analyzed the islet peptidome of HLA-DQ2, -DQ8, and -DQ2/8 by pulsing DC with preproinsulin (PPI), IA-2, and GAD65. Quality and quantity of islet epitopes presented by HLA-DQ2/8 differed from -DQ2 or -DQ8. We identified two PPI epitopes solely processed and presented by HLA-DQ2/8 DC: an HLA-DQ8trans-binding signal-sequence epitope previously identified as CD8 T-cell epitope and a second epitope that we previously identified as CD4 T-cell epitope with increased binding to HLA-DQ8trans upon posttranslational modification. IA-2 epitopes retrieved from HLA-DQ2/8 and -DQ8 DC bound to HLA-DQ8cis/trans. No GAD65 epitopes were eluted from HLA-DQ. T-cell responses were detected against the novel islet epitopes in blood from patients with T1D but scantly detected in healthy donor subjects. We report the first PPI and IA-2 natural epitopes presented by highest-risk HLA-DQ8trans. The selective processing and presentation of HLA-DQ8trans-binding islet epitopes provides insight in the mechanism of excessive genetic risk imposed by HLA-DQ2/8 heterozygosity and may assist immune monitoring of disease progression and therapeutic intervention as well as provide therapeutic targets for immunotherapy in subjects at risk for T1D.
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Affiliation(s)
- Menno van Lummel
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Jos Pool
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Tatjana Nikolic
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Sandra Laban
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Antoinette Joosten
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Jan W Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Iria Gómez-Touriño
- Department of Immunobiology, School of Medicine, King's College London, London, U.K
| | - Sefina Arif
- Department of Immunobiology, School of Medicine, King's College London, London, U.K
| | - Henk J Aanstoot
- Diabeter, Center for Pediatric and Adolescent Diabetes Care and Research, Rotterdam, the Netherlands
| | - Mark Peakman
- Department of Immunobiology, School of Medicine, King's College London, London, U.K
| | - Bart O Roep
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands Department of Diabetes Immunology, Diabetes & Metabolism Research Institute at the Beckman Research Institute of City of Hope, Duarte, CA
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Hoelen H, Zaldumbide A, van Leeuwen WF, Torfs ECW, Engelse MA, Hassan C, Lebbink RJ, de Koning EJ, Resssing ME, de Ru AH, van Veelen PA, Hoeben RC, Roep BO, Wiertz EJHJ. Proteasomal Degradation of Proinsulin Requires Derlin-2, HRD1 and p97. PLoS One 2015; 10:e0128206. [PMID: 26107514 PMCID: PMC4479611 DOI: 10.1371/journal.pone.0128206] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 04/24/2015] [Indexed: 01/28/2023] Open
Abstract
Patients with type 1 diabetes (T1D) suffer from beta-cell destruction by CD8+ T-cells that have preproinsulin as an important target autoantigen. It is of great importance to understand the molecular mechanism underlying the processing of preproinsulin into these CD8+ T-cell epitopes. We therefore studied a pathway that may contribute to the production of these antigenic peptides: degradation of proinsulin via ER associated protein degradation (ERAD). Analysis of the MHC class I peptide ligandome confirmed the presentation of the most relevant MHC class I-restricted diabetogenic epitopes in our cells: the signal peptide-derived sequence A15-A25 and the insulin B-chain epitopes H29-A38 and H34-V42. We demonstrate that specific silencing of Derlin-2, p97 and HRD1 by shRNAs increases steady state levels of proinsulin. This indicates that these ERAD constituents are critically involved in proinsulin degradation and may therefore also play a role in subsequent antigen generation. These ERAD proteins therefore represent interesting targets for novel therapies aiming at the reduction and possibly also prevention of beta-cell directed auto-immune reactions in T1D.
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Affiliation(s)
- Hanneke Hoelen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Arnaud Zaldumbide
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Wouter F. van Leeuwen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ellen C. W. Torfs
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marten A. Engelse
- Department of Nephrology, Leiden University Medical Center, Leiden, The Netherlands
| | - Chopie Hassan
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eelco J. de Koning
- Department of Nephrology, Leiden University Medical Center, Leiden, The Netherlands
| | - Maaike E. Resssing
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H. de Ru
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A. van Veelen
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Rob C. Hoeben
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Bart O. Roep
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Emmanuel J. H. J. Wiertz
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail:
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45
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Treffers EE, Tas A, Scholte FE, Van MN, Heemskerk MT, de Ru AH, Snijder EJ, van Hemert MJ, van Veelen PA. Temporal SILAC-based quantitative proteomics identifies host factors involved in chikungunya virus replication. Proteomics 2015; 15:2267-80. [DOI: 10.1002/pmic.201400581] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/12/2015] [Accepted: 03/06/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Emmely E. Treffers
- Molecular Virology Laboratory; Department of Medical Microbiology; Leiden University Medical Center; ZA Leiden The Netherlands
- Department of Immunohematology and Blood transfusion; Leiden University Medical Center; ZA Leiden The Netherlands
| | - Ali Tas
- Molecular Virology Laboratory; Department of Medical Microbiology; Leiden University Medical Center; ZA Leiden The Netherlands
| | - Florine E.M. Scholte
- Molecular Virology Laboratory; Department of Medical Microbiology; Leiden University Medical Center; ZA Leiden The Netherlands
| | - Myrthe N. Van
- Molecular Virology Laboratory; Department of Medical Microbiology; Leiden University Medical Center; ZA Leiden The Netherlands
| | - Matthias T. Heemskerk
- Molecular Virology Laboratory; Department of Medical Microbiology; Leiden University Medical Center; ZA Leiden The Netherlands
| | - Arnoud H. de Ru
- Department of Immunohematology and Blood transfusion; Leiden University Medical Center; ZA Leiden The Netherlands
| | - Eric J. Snijder
- Molecular Virology Laboratory; Department of Medical Microbiology; Leiden University Medical Center; ZA Leiden The Netherlands
| | - Martijn J. van Hemert
- Molecular Virology Laboratory; Department of Medical Microbiology; Leiden University Medical Center; ZA Leiden The Netherlands
| | - Peter A. van Veelen
- Department of Immunohematology and Blood transfusion; Leiden University Medical Center; ZA Leiden The Netherlands
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46
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Hombrink P, Hassan C, Kester MGD, Jahn L, Pont MJ, de Ru AH, van Bergen CAM, Griffioen M, Falkenburg JHF, van Veelen PA, Heemskerk MHM. Identification of Biological Relevant Minor Histocompatibility Antigens within the B-lymphocyte-Derived HLA-Ligandome Using a Reverse Immunology Approach. Clin Cancer Res 2015; 21:2177-86. [PMID: 25589627 DOI: 10.1158/1078-0432.ccr-14-2188] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/28/2014] [Indexed: 11/16/2022]
Abstract
PURPOSE T-cell recognition of minor histocompatibility antigens (MiHA) not only plays an important role in the beneficial graft-versus-leukemia (GVL) effect of allogeneic stem cell transplantation (allo-SCT) but also mediates serious GVH complications associated with allo-SCT. Using a reverse immunology approach, we aim to develop a method enabling the identification of T-cell responses directed against predefined antigens, with the goal to select those MiHAs that can be used clinically in combination with allo-SCT. EXPERIMENTAL DESIGN In this study, we used a recently developed MiHA selection algorithm to select candidate MiHAs within the HLA-presented ligandome of transformed B cells. From the HLA-presented ligandome that predominantly consisted of monomorphic peptides, 25 polymorphic peptides with a clinically relevant allele frequency were selected. By high-throughput screening, the availability of high-avidity T cells specific for these MiHA candidates in different healthy donors was analyzed. RESULTS With the use of MHC multimer enrichment, analyses of expanded T cells by combinatorial coding MHC multimer flow cytometry, and subsequent single-cell cloning, positive T-cell clones directed to two new MiHA: LB-CLYBL-1Y and LB-TEP1-1S could be demonstrated, indicating the immunogenicity of these two MiHAs. CONCLUSIONS The biologic relevance of MiHA LB-CLYBL-1Y was demonstrated by the detection of LB-CLYBL-1Y-specific T cells in a patient suffering from acute myeloid leukemia (AML) that experienced an anti-leukemic response after treatment with allo-SCT.
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Affiliation(s)
- Pleun Hombrink
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Chopie Hassan
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Michel G D Kester
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lorenz Jahn
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Margot J Pont
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands.
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47
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Heijs B, Carreira RJ, Tolner EA, de Ru AH, van den Maagdenberg AMJM, van Veelen PA, McDonnell LA. Comprehensive Analysis of the Mouse Brain Proteome Sampled in Mass Spectrometry Imaging. Anal Chem 2015; 87:1867-75. [DOI: 10.1021/ac503952q] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Bram Heijs
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Ricardo J. Carreira
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Else A. Tolner
- Department
of Neurology, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Arnoud H. de Ru
- Department
of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Arn M. J. M. van den Maagdenberg
- Department
of Neurology, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
- Department
of Human Genetics, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Peter A. van Veelen
- Department
of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Liam A. McDonnell
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
- Fondazione Pisana
per la Scienza ONLUS, Pisa, 56121 Italy
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48
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Hassan C, Chabrol E, Jahn L, Kester MGD, de Ru AH, Drijfhout JW, Rossjohn J, Falkenburg JHF, Heemskerk MHM, Gras S, van Veelen PA. Naturally processed non-canonical HLA-A*02:01 presented peptides. J Biol Chem 2014; 290:2593-603. [PMID: 25505266 DOI: 10.1074/jbc.m114.607028] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Human leukocyte antigen (HLA) class I molecules generally present peptides (p) of 8 to 11 amino acids (aa) in length. Although an increasing number of examples with lengthy (>11 aa) peptides, presented mostly by HLA-B alleles, have been reported. Here we characterize HLA-A*02:01 restricted, in addition to the HLA-B*0702 and HLA-B*4402 restricted, lengthy peptides (>11 aa) arising from the B-cell ligandome. We analyzed a number of 15-mer peptides presented by HLA-A*02:01, and confirmed pHLA-I formation by HLA folding and thermal stability assays. Surprisingly the binding affinity and stability of the 15-mer epitopes in complex with HLA-A*02:01 were comparable with the values observed for canonical length (8 to 11 aa) HLA-A*02:01-restricted peptides. We solved the structures of two 15-mer epitopes in complex with HLA-A*02:01, within which the peptides adopted distinct super-bulged conformations. Moreover, we demonstrate that T-cells can recognize the 15-mer peptides in the context of HLA-A*02:01, indicating that these 15-mer peptides represent immunogenic ligands. Collectively, our data expand our understanding of longer epitopes in the context of HLA-I, highlighting that they are not limited to the HLA-B family, but can bind the ubiquitous HLA-A*02:01 molecule, and play an important role in T-cell immunity.
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Affiliation(s)
- Chopie Hassan
- From the Departments of Immunohematology and Blood Transfusion and
| | - Eric Chabrol
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton 3800, Australia
| | - Lorenz Jahn
- Hematology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Michel G D Kester
- Hematology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Arnoud H de Ru
- From the Departments of Immunohematology and Blood Transfusion and
| | - Jan W Drijfhout
- From the Departments of Immunohematology and Blood Transfusion and
| | - Jamie Rossjohn
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton 3800, Australia, the ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Australia, and the Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, Wales, United Kingdom
| | | | | | - Stephanie Gras
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton 3800, Australia, the ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Australia, and
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49
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Hassan C, Kester MGD, Oudgenoeg G, de Ru AH, Janssen GMC, Drijfhout JW, Spaapen RM, Jiménez CR, Heemskerk MHM, Falkenburg JHF, van Veelen PA. Accurate quantitation of MHC-bound peptides by application of isotopically labeled peptide MHC complexes. J Proteomics 2014; 109:240-4. [PMID: 25050860 DOI: 10.1016/j.jprot.2014.07.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [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: 03/05/2014] [Revised: 07/03/2014] [Accepted: 07/09/2014] [Indexed: 11/30/2022]
Abstract
Knowledge of the accurate copy number of HLA class I presented ligands is important in fundamental and clinical immunology. Currently, the best copy number determinations are based on mass spectrometry, employing single reaction monitoring (SRM) in combination with a known amount of isotopically labeled peptide. The major drawback of this approach is that the losses during sample pretreatment, i.e. immunopurification and filtration steps, are not well defined and must, therefore, be estimated. In addition, such losses can vary for individual peptides. Therefore, we developed a new approach in which isotopically labeled peptide-MHC monomers (hpMHC) are prepared and added directly after cell lysis, i.e. before the usual sample processing. Using this approach, all losses during sample processing can be accounted for and allows accurate determination of specific MHC class I-presented ligands. Our study pinpoints the immunopurification step as the origin of the rather extreme losses during sample pretreatment and offers a solution to account for these losses. Obviously, this has important implications for accurate HLA-ligand quantitation. The strategy presented here can be used to obtain a reliable view of epitope copy number and thus allows improvement of vaccine design and strategies for immunotherapy.
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Affiliation(s)
- Chopie Hassan
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel G D Kester
- Department of Hematology, Laboratory of Experimental hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Gideon Oudgenoeg
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - George M C Janssen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan W Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Robbert M Spaapen
- Department of Cell Biology II, The Netherlands Cancer Institute (NKI-AVL), Amsterdam, The Netherlands
| | - Connie R Jiménez
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Laboratory of Experimental hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - J H Frederik Falkenburg
- Department of Hematology, Laboratory of Experimental hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands.
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50
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de Keijzer J, de Haas PE, de Ru AH, van Veelen PA, van Soolingen D. Disclosure of selective advantages in the "modern" sublineage of the Mycobacterium tuberculosis Beijing genotype family by quantitative proteomics. Mol Cell Proteomics 2014; 13:2632-45. [PMID: 25022876 DOI: 10.1074/mcp.m114.038380] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Mycobacterium tuberculosis Beijing genotype, consisting of the more ancient (atypical) and modern (typical) emerging sublineage, is one of the most prevalent and genetically conserved genotype families and has often been associated with multidrug resistance. In this study, we employed a 2D-LC-FTICR MS approach, combined with dimethylation of tryptic peptides, to systematically compare protein abundance levels of ancient and modern Beijing strains and identify differences that could be associated with successful spread of the modern sublineage. The data is available via ProteomeXchange using the identifier PXD000931. Despite the highly uniform protein abundance ratios in both sublineages, we identified four proteins as differentially regulated between both sublineages, which could explain the apparent increased adaptation of the modern Beijing strains. These proteins are; Rv0450c/MmpL4, Rv1269c, Rv3137, and Rv3283/sseA. Transcriptional and functional analysis of these proteins in a large cohort of 29 Beijing strains showed that the mRNA levels of Rv0450c/MmpL4 are significantly higher in modern Beijing strains, whereas we also provide evidence that Rv3283/sseA is less abundant in the modern Beijing sublineage. Our findings provide a possible explanation for the increased virulence and success of the modern Beijing sublineage. In addition, in the established dataset of 1817 proteins, we demonstrate the pre-existence of several, possibly unique, antibiotic efflux pumps in the proteome of the Beijing strains. This may reflect an increased ability of Beijing strains to escape exposure to antituberculosis drugs.
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Affiliation(s)
- Jeroen de Keijzer
- From the ‡Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre (LUMC), Leiden, 2300 RC, The Netherlands;
| | - Petra E de Haas
- §Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720 BA, The Netherlands
| | - Arnoud H de Ru
- From the ‡Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre (LUMC), Leiden, 2300 RC, The Netherlands
| | - Peter A van Veelen
- From the ‡Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre (LUMC), Leiden, 2300 RC, The Netherlands
| | - Dick van Soolingen
- §Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720 BA, The Netherlands; ¶Departments of Pulmonary Diseases and Medical Microbiology, Radboud University Medical Centre, Nijmegen, 6500 HB, The Netherlands
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