1
|
Mishto M, Takala I, Bonfanti P, Liepe J. Proteasome isoforms in human thymi and mouse models. Immunol Lett 2024; 269:106899. [PMID: 39019403 DOI: 10.1016/j.imlet.2024.106899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/02/2024] [Accepted: 07/13/2024] [Indexed: 07/19/2024]
Abstract
The thymus is the organ where functional and self-tolerant T cells are selected through processes of positive and negative selection before migrating to the periphery. The antigenic peptides presented on MHC class I molecules of thymic epithelial cells (TECs) in the cortex and medulla of the thymus are key players in these processes. It has been theorized that these cells express different proteasome isoforms, which generate MHC class I immunopeptidomes with features that differentiate cortex and medulla, and hence positive and negative CD8+ T cell selection. This theory is largely based on mouse models and does not consider the large variety of noncanonical antigenic peptides that could be produced by proteasomes and presented on MHC class I molecules. Here, we review the multi-omics, biochemical and cellular studies carried out on mouse models and human thymi to investigate their content of proteasome isoforms, briefly summarize the implication that noncanonical antigenic peptide presentation in the thymus could have on CD8+ T cell repertoire and put these aspects in the larger framework of anatomical and immunological differences between these two species.
Collapse
Affiliation(s)
- Michele Mishto
- Molecular Immunology laboratory, the Francis Crick Institute, NW1 1AT London, United Kingdom; Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, United Kingdom.
| | - Iina Takala
- Research group of Quantitative System Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Paola Bonfanti
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom; Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Pears Building, London NW3 2PP, United Kingdom
| | - Juliane Liepe
- Research group of Quantitative System Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| |
Collapse
|
2
|
Schmalen A, Kammerl IE, Meiners S, Noessner E, Deeg CA, Hauck SM. A Lysine Residue at the C-Terminus of MHC Class I Ligands Correlates with Low C-Terminal Proteasomal Cleavage Probability. Biomolecules 2023; 13:1300. [PMID: 37759700 PMCID: PMC10527444 DOI: 10.3390/biom13091300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/10/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The majority of peptides presented by MHC class I result from proteasomal protein turnover. The specialized immunoproteasome, which is induced during inflammation, plays a major role in antigenic peptide generation. However, other cellular proteases can, either alone or together with the proteasome, contribute peptides to MHC class I loading non-canonically. We used an immunopeptidomics workflow combined with prediction software for proteasomal cleavage probabilities to analyze how inflammatory conditions affect the proteasomal processing of immune epitopes presented by A549 cells. The treatment of A549 cells with IFNγ enhanced the proteasomal cleavage probability of MHC class I ligands for both the constitutive proteasome and the immunoproteasome. Furthermore, IFNγ alters the contribution of the different HLA allotypes to the immunopeptidome. When we calculated the HLA allotype-specific proteasomal cleavage probabilities for MHC class I ligands, the peptides presented by HLA-A*30:01 showed characteristics hinting at a reduced C-terminal proteasomal cleavage probability independently of the type of proteasome. This was confirmed by HLA-A*30:01 ligands from the immune epitope database, which also showed this effect. Furthermore, two additional HLA allotypes, namely, HLA-A*03:01 and HLA-A*11:01, presented peptides with a markedly reduced C-terminal proteasomal cleavage probability. The peptides eluted from all three HLA allotypes shared a peptide binding motif with a C-terminal lysine residue, suggesting that this lysine residue impairs proteasome-dependent HLA ligand production and might, in turn, favor peptide generation by other cellular proteases.
Collapse
Affiliation(s)
- Adrian Schmalen
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, Martinsried, 82152 Planegg, Germany
- Core Facility—Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), 80939 Munich, Germany
| | - Ilona E. Kammerl
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians-University, Helmholtz Center Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Silke Meiners
- Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), 23845 Borstel, Germany
- Institute of Experimental Medicine, Christian-Albrechts University Kiel, 24118 Kiel, Germany
| | - Elfriede Noessner
- Immunoanalytics Research Group—Tissue Control of Immunocytes, Helmholtz Center Munich, 81377 Munich, Germany
| | - Cornelia A. Deeg
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, Martinsried, 82152 Planegg, Germany
| | - Stefanie M. Hauck
- Core Facility—Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), 80939 Munich, Germany
| |
Collapse
|
3
|
Trougakos IP, Stamatelopoulos K, Terpos E, Tsitsilonis OE, Aivalioti E, Paraskevis D, Kastritis E, Pavlakis GN, Dimopoulos MA. Insights to SARS-CoV-2 life cycle, pathophysiology, and rationalized treatments that target COVID-19 clinical complications. J Biomed Sci 2021; 28:9. [PMID: 33435929 PMCID: PMC7801873 DOI: 10.1186/s12929-020-00703-5] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/23/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Gaining further insights into SARS-CoV-2 routes of infection and the underlying pathobiology of COVID-19 will support the design of rational treatments targeting the life cycle of the virus and/or the adverse effects (e.g., multi-organ collapse) that are triggered by COVID-19-mediated adult respiratory distress syndrome (ARDS) and/or other pathologies. MAIN BODY COVID-19 is a two-phase disease being marked by (phase 1) increased virus transmission and infection rates due to the wide expression of the main infection-related ACE2, TMPRSS2 and CTSB/L human genes in tissues of the respiratory and gastrointestinal tract, as well as by (phase 2) host- and probably sex- and/or age-specific uncontrolled inflammatory immune responses which drive hyper-cytokinemia, aggressive inflammation and (due to broad organotropism of SARS-CoV-2) collateral tissue damage and systemic failure likely because of imbalanced ACE/ANGII/AT1R and ACE2/ANG(1-7)/MASR axes signaling. CONCLUSION Here we discuss SARS-CoV-2 life cycle and a number of approaches aiming to suppress viral infection rates or propagation; increase virus antigen presentation in order to activate a robust and durable adaptive immune response from the host, and/or mitigate the ARDS-related "cytokine storm" and collateral tissue damage that triggers the severe life-threatening complications of COVID-19.
Collapse
Affiliation(s)
- Ioannis P Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, 15784, Athens, Greece.
| | - Kimon Stamatelopoulos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, 11528, Athens, Greece
| | - Evangelos Terpos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, 11528, Athens, Greece
| | - Ourania E Tsitsilonis
- Department of Animal and Human Physiology, Faculty of Biology, National and Kapodistrian University of Athens, 15784, Athens, Greece
| | - Evmorfia Aivalioti
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, 11528, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 11527, Athens, Greece
| | - Efstathios Kastritis
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, 11528, Athens, Greece
| | - George N Pavlakis
- Human Retrovirus Section, National Cancer Institute, Frederick, MD, 21702, USA
| | - Meletios A Dimopoulos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, 11528, Athens, Greece.
| |
Collapse
|
4
|
Gkogkou E, Barnasas G, Vougas K, Trougakos IP. Expression profiling meta-analysis of ACE2 and TMPRSS2, the putative anti-inflammatory receptor and priming protease of SARS-CoV-2 in human cells, and identification of putative modulators. Redox Biol 2020; 36:101615. [PMID: 32863223 PMCID: PMC7311357 DOI: 10.1016/j.redox.2020.101615] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/29/2020] [Accepted: 06/18/2020] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has resulted in hundreds of thousands of deaths worldwide. While the majority of people with COVID-19 won't require hospitalization, those who do may experience severe life-threatening complications, including acute respiratory distress syndrome. SARS-CoV-2 infects human cells by binding to the cellular surface protein angiotensin-converting enzyme 2 (ACE2); in addition, the cellular transmembrane serine protease 2 (TMPRSS2) is needed for priming of the spike (S) protein of the virus. Virus entry may also depend on the activity of the endosomal/lysosomal cysteine proteases cathepsin B, L (CTSB, CTSL) although their activity is likely dispensable. Given that the uncertainty of how COVID-19 kills, hampers doctors' ability to choose treatments the need for a deep understanding of COVID-19 biology is urgent. Herein, we performed an expression profiling meta-analysis of ACE2, TMPRSS2 and CTSB/L genes (and proteins) in public repository databases and found that all are widely expressed in human tissues; also, the ACE2 and TMPRSS2 genes tend to be co-regulated. The ACE2 and TMPRSS genes expression is (among others) suppressed by TNF, and is induced by pro-inflammatory conditions including obesity, Barrett's esophagus, stomach infection by helicobacter pylori, diabetes, autoimmune diseases and oxidized LDL; by exercise, as well as by growth factors, viruses' infections, cigarette smoke, interferons and androgens. Regarding currently investigated therapies interferon-beta induced ACE2 gene expression in bronchial epithelial cells, while chloroquine tends to upregulate CTSB/L genes. Finally, we analyzed KEGG pathways modulated by ACE2, TMPRSS2 and CTSB/L and probed DrugBank for drugs that target modules of the affected pathways. Our data indicate possible novel high-risk groups for COVID-19; provide a rich resource for future investigations of its pathogenesis and highlight the therapeutic challenges we face.
Collapse
Affiliation(s)
- Eirini Gkogkou
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Athens, 15784, Greece
| | - Grigoris Barnasas
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Athens, 15784, Greece
| | - Konstantinos Vougas
- Genomics and Proteomics Research Units, Center of Basic Research II, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece; DeepMed IO Ltd, 49 Peter St. Manchester, M2 3NG, UK
| | - Ioannis P Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Athens, 15784, Greece.
| |
Collapse
|
5
|
Kumar A, Suryadevara NC, Wolf KJ, Wilson JT, Di Paolo RJ, Brien JD, Joyce S. Heterotypic immunity against vaccinia virus in an HLA-B*07:02 transgenic mousepox infection model. Sci Rep 2020; 10:13167. [PMID: 32759969 PMCID: PMC7406653 DOI: 10.1038/s41598-020-69897-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/13/2020] [Indexed: 12/25/2022] Open
Abstract
Vaccination with vaccinia virus (VACV) elicits heterotypic immunity to smallpox, monkeypox, and mousepox, the mechanistic basis for which is poorly understood. It is generally assumed that heterotypic immunity arises from the presentation of a wide array of VACV-derived, CD8+ T cell epitopes that share homology with other poxviruses. Herein this assumption was tested using a large panel of VACV-derived peptides presented by HLA-B*07:02 (B7.2) molecules in a mousepox/ectromelia virus (ECTV)-infection, B7.2 transgenic mouse model. Most dominant epitopes recognized by ECTV- and VACV-reactive CD8+ T cells overlapped significantly without altering immunodominance hierarchy. Further, several epitopes recognized by ECTV-reactive CD8+ T cells were not recognized by VACV-reactive CD8+ T cells, and vice versa. In one instance, the lack of recognition owed to a N72K variation in the ECTV C4R70–78 variant of the dominant VACV B8R70–78 epitope. C4R70–78 does not bind to B7.2 and, hence, it was neither immunogenic nor antigenic. These findings provide a mechanistic basis for VACV vaccination-induced heterotypic immunity which can protect against Variola and Monkeypox disease. The understanding of how cross-reactive responses develop is essential for the rational design of a subunit-based vaccine that would be safe, and effectively protect against heterologous infection.
Collapse
Affiliation(s)
- Amrendra Kumar
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Centre, Nashville, TN, USA
| | - Naveen Chandra Suryadevara
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Centre, Nashville, TN, USA
| | - Kyle J Wolf
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - John T Wilson
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Richard J Di Paolo
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - James D Brien
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Sebastian Joyce
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA. .,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Centre, Nashville, TN, USA.
| |
Collapse
|
6
|
Friedrich M, Jasinski-Bergner S, Lazaridou MF, Subbarayan K, Massa C, Tretbar S, Mueller A, Handke D, Biehl K, Bukur J, Donia M, Mandelboim O, Seliger B. Tumor-induced escape mechanisms and their association with resistance to checkpoint inhibitor therapy. Cancer Immunol Immunother 2019; 68:1689-1700. [PMID: 31375885 DOI: 10.1007/s00262-019-02373-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 07/28/2019] [Indexed: 12/19/2022]
Abstract
Immunotherapy aims to activate the immune system to fight cancer in a very specific and targeted manner. Despite the success of different immunotherapeutic strategies, in particular antibodies directed against checkpoints as well as adoptive T-cell therapy, the response of patients is limited in different types of cancers. This attributes to escape of the tumor from immune surveillance and development of acquired resistances during therapy. In this review, the different evasion and resistance mechanisms that limit the efficacy of immunotherapies targeting tumor-associated antigens presented by major histocompatibility complex molecules on the surface of the malignant cells are summarized. Overcoming these escape mechanisms is a great challenge, but might lead to a better clinical outcome of patients and is therefore currently a major focus of research.
Collapse
Affiliation(s)
- Michael Friedrich
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Simon Jasinski-Bergner
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Maria-Filothei Lazaridou
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Karthikeyan Subbarayan
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Chiara Massa
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Sandy Tretbar
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Anja Mueller
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Diana Handke
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Katharina Biehl
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Jürgen Bukur
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Marco Donia
- Department of Oncology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Ofer Mandelboim
- Department of Immunology, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany.
| |
Collapse
|
7
|
Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTL responses. Nat Commun 2019; 10:2846. [PMID: 31253788 PMCID: PMC6599079 DOI: 10.1038/s41467-019-10661-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/24/2019] [Indexed: 11/08/2022] Open
Abstract
The magnitude of T cell responses to infection is a function of the naïve T cell repertoire combined with the context and duration of antigen presentation. Using mass spectrometry, we identify and quantify 21 class 1 MHC-restricted influenza A virus (IAV)-peptides following either direct or cross-presentation. All these peptides, including seven novel epitopes, elicit T cell responses in infected C57BL/6 mice. Directly presented IAV epitopes maintain their relative abundance across distinct cell types and reveal a broad range of epitope abundances. In contrast, cross-presented epitopes are more uniform in abundance. We observe a clear disparity in the abundance of the two key immunodominant IAV antigens, wherein direct infection drives optimal nucleoprotein (NP)366–374 presentation, while cross-presentation is optimal for acid polymerase (PA)224–233 presentation. The study demonstrates how assessment of epitope abundance in both modes of antigen presentation is necessary to fully understand the immunogenicity and response magnitude to T cell epitopes. CTL responses are critical in protection against pathogens. Here, using mass spectrometry and flow cytometry, the authors characterize the kinetics of influenza A virus class I MHC epitopes cross-presented in professional antigen presenting cells and identify new epitopes that elicit T cell responses in infected mice.
Collapse
|
8
|
Athanasopoulou S, Chondrogianni N, Santoro A, Asimaki K, Delitsikou V, Voutetakis K, Fabbri C, Pietruszka B, Kaluza J, Franceschi C, Gonos ES. Beneficial Effects of Elderly Tailored Mediterranean Diet on the Proteasomal Proteolysis. Front Physiol 2018; 9:457. [PMID: 29765333 PMCID: PMC5938393 DOI: 10.3389/fphys.2018.00457] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/13/2018] [Indexed: 12/22/2022] Open
Abstract
Aging is a multifactorial process characterized by the accumulation of proteins undergoing oxidative modifications, either due to enhanced levels of oxidative stress or due to their decreased clearance; both facts are related to the establishment of chronic inflammatory processes. These processes are directly associated with functional and structural modifications of a key cellular component, namely the proteasome. In this study, levels of oxidized proteins, along with proteasome and immunoproteasome composition and activity on a selected group of 120 elderly volunteers were analyzed before and after the administration of a specific dietary protocol, based on an elderly tailored Mediterranean diet (the "NU-AGE diet"). A significant negative correlation between levels of oxidized/carbonylated proteins and proteasome function was confirmed, both before and after intervention. Furthermore, it was demonstrated that subgroups of non-frail subjects and women receive a greater benefit after the intervention, concerning specifically the proteasome content and activity. These data highlight the putative beneficial effects of Mediterranean diet on the major cellular proteolytic mechanism, the proteasome, in elderly people.
Collapse
Affiliation(s)
- Sophia Athanasopoulou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Niki Chondrogianni
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- C.I.G. Interdepartmental Centre “L. Galvani”, University of Bologna, Bologna, Italy
| | - Konstantina Asimaki
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Vasiliki Delitsikou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Konstantinos Voutetakis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Cristina Fabbri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- C.I.G. Interdepartmental Centre “L. Galvani”, University of Bologna, Bologna, Italy
| | - Barbara Pietruszka
- Department of Human Nutrition, Warsaw University of Life Sciences – SGGW, Warsaw, Poland
| | - Joanna Kaluza
- Department of Human Nutrition, Warsaw University of Life Sciences – SGGW, Warsaw, Poland
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- Institute of Neurological Sciences (IRCCS), Bologna, Italy
| | - Efstathios S. Gonos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| |
Collapse
|
9
|
Chong C, Marino F, Pak H, Racle J, Daniel RT, Müller M, Gfeller D, Coukos G, Bassani-Sternberg M. High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome. Mol Cell Proteomics 2018; 17:533-548. [PMID: 29242379 PMCID: PMC5836376 DOI: 10.1074/mcp.tir117.000383] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/12/2017] [Indexed: 12/11/2022] Open
Abstract
Comprehensive knowledge of the human leukocyte antigen (HLA) class-I and class-II peptides presented to T-cells is crucial for designing innovative therapeutics against cancer and other diseases. However methodologies for their purification for mass-spectrometry analysis have been a major limitation. We designed a novel high-throughput, reproducible and sensitive method for sequential immuno-affinity purification of HLA-I and -II peptides from up to 96 samples in a plate format, suitable for both cell lines and tissues. Our methodology drastically reduces sample-handling and can be completed within five hours. We challenged our methodology by extracting HLA peptides from multiple replicates of tissues (n = 7) and cell lines (n = 21, 108 cells per replicate), which resulted in unprecedented depth, sensitivity and high reproducibility (Pearson correlations up to 0.98 and 0.97 for HLA-I and HLA-II). Because of the method's achieved sensitivity, even single measurements of peptides purified from 107 B-cells resulted in the identification of more than 1700 HLA-I and 2200 HLA-II peptides. We demonstrate the feasibility of performing drug-screening by using ovarian cancer cells treated with interferon gamma (IFNγ). Our analysis revealed an augmented presentation of chymotryptic-like and longer ligands associated with IFNγ induced changes of the antigen processing and presentation machinery. This straightforward method is applicable for basic and clinical applications.
Collapse
Affiliation(s)
- Chloe Chong
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Fabio Marino
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - HuiSong Pak
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Julien Racle
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
- **Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Roy T Daniel
- ¶Service of Neurosurgery, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Markus Müller
- ‖Vital IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David Gfeller
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
- **Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - George Coukos
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland;
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| |
Collapse
|
10
|
Witkowski JM, Mikosik A, Bryl E, Fulop T. Proteodynamics in aging human T cells - The need for its comprehensive study to understand the fine regulation of T lymphocyte functions. Exp Gerontol 2017; 107:161-168. [PMID: 29038026 DOI: 10.1016/j.exger.2017.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/01/2017] [Accepted: 10/09/2017] [Indexed: 12/20/2022]
Abstract
Cellular life depends mostly on the creation, modification, interactions and destruction of proteins. This is true for every cell, including human T lymphocytes. One way these cells can ascertain the fidelity and at least partial functionality of their proteomes under constant attack of irreversible modulations (e.g., ROS- or glycation-dependent) is proteostasis. However, with cellular aging proteostasis progressively fails and proteostenosis (decreased amounts and functionalities of remaining proteins) occurs. There are several mechanisms involved in the modulation and protection of the proteome in the T cells which include mainly multiple layers of vesicle-bound and cytoplasmic proteases (e.g., lysosomal and proteasomal ones) acting mostly by degradation of obsolete and age-modified proteins. Recently it was shown that another not yet so widely known system consisting of obligatorily calcium-dependent cysteine proteases, the calpains and their inhibitor, the calpastatin serves in T cells as a dual switch, either activating or inactivating different proteins depending on intracellular conditions. Thus the proteolytic elimination of altered proteins as well as modulation of activity of those remaining leads to dynamic change of proteome composition and function (proteodynamics) in aging lymphocytes, so far in an almost unknown way. Aging T cell proteodynamics requires further comprehensive analysis of the resulting lysoproteomic patterns and their changes.
Collapse
Affiliation(s)
- Jacek M Witkowski
- Department of Pathophysiology, Medical University of Gdańsk, Poland.
| | - Anna Mikosik
- Department of Pathophysiology, Medical University of Gdańsk, Poland
| | - Ewa Bryl
- Department of Pathology and Experimental Rheumatology, Medical University of Gdańsk, Poland
| | - Tamas Fulop
- Centre for Aging Research, University of Sherbrooke, QC, Canada
| |
Collapse
|
11
|
Aronica E, Bauer S, Bozzi Y, Caleo M, Dingledine R, Gorter JA, Henshall DC, Kaufer D, Koh S, Löscher W, Louboutin JP, Mishto M, Norwood BA, Palma E, Poulter MO, Terrone G, Vezzani A, Kaminski RM. Neuroinflammatory targets and treatments for epilepsy validated in experimental models. Epilepsia 2017; 58 Suppl 3:27-38. [PMID: 28675563 DOI: 10.1111/epi.13783] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2017] [Indexed: 12/16/2022]
Abstract
A large body of evidence that has accumulated over the past decade strongly supports the role of inflammation in the pathophysiology of human epilepsy. Specific inflammatory molecules and pathways have been identified that influence various pathologic outcomes in different experimental models of epilepsy. Most importantly, the same inflammatory pathways have also been found in surgically resected brain tissue from patients with treatment-resistant epilepsy. New antiseizure therapies may be derived from these novel potential targets. An essential and crucial question is whether targeting these molecules and pathways may result in anti-ictogenesis, antiepileptogenesis, and/or disease-modification effects. Therefore, preclinical testing in models mimicking relevant aspects of epileptogenesis is needed to guide integrated experimental and clinical trial designs. We discuss the most recent preclinical proof-of-concept studies validating a number of therapeutic approaches against inflammatory mechanisms in animal models that could represent novel avenues for drug development in epilepsy. Finally, we suggest future directions to accelerate preclinical to clinical translation of these recent discoveries.
Collapse
Affiliation(s)
- Eleonora Aronica
- Department of (Neuro)Pathology, Academic Medical Center, Amsterdam, The Netherlands.,Swammerdam Institute for Life Sciences, Center for Neuroscience University of Amsterdam, Amsterdam, The Netherlands.,SEIN-Stichting Epilepsie Instellingen Nederland, Heemstede, The Netherlands
| | - Sebastian Bauer
- Department of Neurology, Philipps University, Marburg, Germany.,Department of Neurology, Epilepsy Center Frankfurt Rhine-Main, Goethe University, Frankfurt am Main, Germany
| | - Yuri Bozzi
- Neuroscience Institute, National Research Council (CNR), Pisa, Italy.,Laboratory of Molecular Neuropathology, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Matteo Caleo
- Neuroscience Institute, National Research Council (CNR), Pisa, Italy
| | - Raymond Dingledine
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia, U.S.A
| | - Jan A Gorter
- Swammerdam Institute for Life Sciences, Center for Neuroscience University of Amsterdam, Amsterdam, The Netherlands
| | - David C Henshall
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Daniela Kaufer
- Helen Wills Neuroscience Institute, UC Berkeley, Berkeley, California, U.S.A
| | - Sookyong Koh
- Department of Pediatrics, Emory University, Atlanta, Georgia, U.S.A
| | - Wolfgang Löscher
- Department of Pharmacology, Toxicology, and Pharmacy, University of Veterinary Medicine, Hannover, Germany
| | - Jean-Pierre Louboutin
- Department of Basic Medical Sciences, University of the West Indies, Kingston, Jamaica.,Gene Therapy Program, University of Pennsylvania, Philadelphia, Pennsylvania, U.S.A
| | - Michele Mishto
- Charite University Medicine Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Braxton A Norwood
- Department of Neurology, Philipps University, Marburg, Germany.,Neuroscience Division, Expesicor LLC, Kalispell, Montana, U.S.A
| | - Eleonora Palma
- Department of Physiology and Pharmacology, University of Rome La Sapienza, Rome, Italy
| | - Michael O Poulter
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Gaetano Terrone
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Annamaria Vezzani
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | | |
Collapse
|
12
|
Korovila I, Hugo M, Castro JP, Weber D, Höhn A, Grune T, Jung T. Proteostasis, oxidative stress and aging. Redox Biol 2017; 13:550-567. [PMID: 28763764 PMCID: PMC5536880 DOI: 10.1016/j.redox.2017.07.008] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 07/04/2017] [Accepted: 07/09/2017] [Indexed: 12/21/2022] Open
Abstract
The production of reactive species is an inevitable by-product of metabolism and thus, life itself. Since reactive species are able to damage cellular structures, especially proteins, as the most abundant macromolecule of mammalian cells, systems are necessary which regulate and preserve a functional cellular protein pool, in a process termed “proteostasis”. Not only the mammalian protein pool is subject of a constant turnover, organelles are also degraded and rebuild. The most important systems for these removal processes are the “ubiquitin-proteasomal system” (UPS), the central proteolytic machinery of mammalian cells, mainly responsible for proteostasis, as well as the “autophagy-lysosomal system”, which mediates the turnover of organelles and large aggregates. Many age-related pathologies and the aging process itself are accompanied by a dysregulation of UPS, autophagy and the cross-talk between both systems. This review will describe the sources and effects of oxidative stress, preservation of cellular protein- and organelle-homeostasis and the effects of aging on proteostasis in mammalian cells.
Collapse
Affiliation(s)
- Ioanna Korovila
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany
| | - Martín Hugo
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany
| | - José Pedro Castro
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; German Center for Diabetes Research (DZD), 85764 Muenchen-Neuherberg, Germany; Faculty of Medicine, Department of Biomedicine, University of Porto, 4200-319, Portugal; Institute for Innovation and Health Research (I3S), Aging and Stress Group, R. Alfredo Allen, 4200-135 Porto, Portugal
| | - Daniela Weber
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; NutriAct - Competence Cluster Nutrition Research Berlin-Potsdam, 14558 Nuthetal, Germany
| | - Annika Höhn
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; German Center for Diabetes Research (DZD), 85764 Muenchen-Neuherberg, Germany
| | - Tilman Grune
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; German Center for Diabetes Research (DZD), 85764 Muenchen-Neuherberg, Germany; German Center for Cardiovascular Research (DZHK), 10117 Berlin, Germany; NutriAct - Competence Cluster Nutrition Research Berlin-Potsdam, 14558 Nuthetal, Germany
| | - Tobias Jung
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; German Center for Cardiovascular Research (DZHK), 10117 Berlin, Germany.
| |
Collapse
|
13
|
Bergallo M, Loiacono E, Gambarino S, Vergano L, Tavormina P. Standard and immunoproteasome expression in pediatric tonsillectomy patients. Minerva Pediatr 2016; 72:159-162. [PMID: 27167592 DOI: 10.23736/s0026-4946.16.04463-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Pro-inflammatory cytokines including TNF-α and IFN-γ, play an important role during the recurrent tonsillitis illness and proteasome and immunoproteasome stimulation. METHODS mRNA expression analysis of proteasome and immunoproteasome subunits was performed by PBMC whole blood isolation from children tonsillectomy patients. Total RNA was extracted from PBMC and retro-transcribed in cDNA. A real-time PCR with TaqMan probe was then performed. RESULTS PBMC of children with tonsillectomy showed, a significantly increased expression of proteasome constitutive subunit β2 encoding (1.52±0.61 vs. 0.88±0.5, P<0.0001) compared to healthy controls (HC). The same results were observed for immunoproteasome inducible subunit LMP2 (2.55±1.95 vs. 0.73±0.49, P<0.001), LMP7 (1.94±1.18 vs. 0.79±0.41, P<0.001), MECL1 (1.97±1.20 vs. 0.79±0.41, P<0.001). No differences were observed for proteasome subunit β1. Conversely a significantly decreased expression of proteasome constitutive subunit β5 encoding mRNA (0.96±0.39 vs. 1.28±0.65, P=0.0291) was observed. CONCLUSIONS In children with recurrent tonsillitis was observed an increased expression of β2, the corresponding iPS, β1i and β5i compared to healthy controls. Contrariwise β5 subunit mRNA expression was significantly decreased.
Collapse
Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, School of Medicine, University of Turin, Turin, Italy - .,Laboratory of Cytoimmunodiagnostics, Regina Margherita Children's Hospital, Città della Salute e della Scienza, Turin, Italy -
| | - Elisa Loiacono
- Department of Public Health and Pediatric Sciences, School of Medicine, University of Turin, Turin, Italy.,Laboratory of Cytoimmunodiagnostics, Regina Margherita Children's Hospital, Città della Salute e della Scienza, Turin, Italy
| | - Stefano Gambarino
- Department of Public Health and Pediatric Sciences, School of Medicine, University of Turin, Turin, Italy.,Laboratory of Cytoimmunodiagnostics, Regina Margherita Children's Hospital, Città della Salute e della Scienza, Turin, Italy
| | - Luca Vergano
- Department of Public Health and Pediatric Sciences, School of Medicine, University of Turin, Turin, Italy.,Laboratory of Cytoimmunodiagnostics, Regina Margherita Children's Hospital, Città della Salute e della Scienza, Turin, Italy
| | - Paolo Tavormina
- Unit of Otorhinolaryngology, Regina Margherita Children's Hospital, Turin, Italy
| |
Collapse
|
14
|
Platteel ACM, Mishto M, Textoris-Taube K, Keller C, Liepe J, Busch DH, Kloetzel PM, Sijts AJAM. CD8(+) T cells of Listeria monocytogenes-infected mice recognize both linear and spliced proteasome products. Eur J Immunol 2016; 46:1109-18. [PMID: 26909514 DOI: 10.1002/eji.201545989] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 01/25/2016] [Accepted: 02/17/2016] [Indexed: 02/05/2023]
Abstract
CD8(+) T cells responding to infection recognize pathogen-derived epitopes presented by MHC class-I molecules. While most of such epitopes are generated by proteasome-mediated antigen cleavage, analysis of tumor antigen processing has revealed that epitopes may also derive from proteasome-catalyzed peptide splicing (PCPS). To determine whether PCPS contributes to epitope processing during infection, we analyzed the fragments produced by purified proteasomes from a Listeria monocytogenes polypeptide. Mass spectrometry identified a known H-2K(b) -presented linear epitope (LLO296-304 ) in the digests, as well as four spliced peptides that were trimmed by ERAP into peptides with in silico predicted H-2K(b) binding affinity. These spliced peptides, which displayed sequence similarity with LLO296-304 , bound to H-2K(b) molecules in cellular assays and one of the peptides was recognized by CD8(+) T cells of infected mice. This spliced epitope differed by one amino acid from LLO296-304 and double staining with LLO296-304 - and spliced peptide-folded MHC multimers showed that LLO296-304 and its spliced variant were recognized by the same CD8(+) T cells. Thus, PCPS multiplies the variety of peptides that is processed from an antigen and leads to the production of epitope variants that can be recognized by cross-reacting pathogen-specific CD8(+) T cells. Such mechanism may reduce the chances for pathogen immune evasion.
Collapse
Affiliation(s)
- Anouk C M Platteel
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Michele Mishto
- Institut für Biochemie, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Interdepartmental Centre "Luigi Galvani" for Bioinformatics, Biophysics and Biocomplexity (CIG), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | | | - Christin Keller
- Institut für Biochemie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Juliane Liepe
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, UK
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, TU Munich, Munich, Germany
| | - Peter M Kloetzel
- Institut für Biochemie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Alice J A M Sijts
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
15
|
Becker HJ, Kondo E, Shimabukuro-Vornhagen A, Theurich S, von Bergwelt-Baildon MS. Processing and MHC class II presentation of exogenous soluble antigen involving a proteasome-dependent cytosolic pathway in CD40-activated B cells. Eur J Haematol 2015; 97:166-74. [DOI: 10.1111/ejh.12699] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Hans Jiro Becker
- Cologne Interventional Immunology; Cologne University Hospital; Cologne Germany
| | - Eisei Kondo
- Department of General Medicine; Okayama University Graduate School of Medicine; Dentistry and Pharmaceutical Sciences; Okayama Japan
| | | | - Sebastian Theurich
- Cologne Interventional Immunology; Cologne University Hospital; Cologne Germany
- Max Planck Institute for Metabolism Research; Cologne Germany
| | | |
Collapse
|
16
|
Textoris-Taube K, Keller C, Liepe J, Henklein P, Sidney J, Sette A, Kloetzel PM, Mishto M. The T210M Substitution in the HLA-a*02:01 gp100 Epitope Strongly Affects Overall Proteasomal Cleavage Site Usage and Antigen Processing. J Biol Chem 2015; 290:30417-28. [PMID: 26507656 DOI: 10.1074/jbc.m115.695189] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Indexed: 01/01/2023] Open
Abstract
MHC class I-restricted epitopes, which carry a tumor-specific mutation resulting in improved MHC binding affinity, are preferred T cell receptor targets in innovative adoptive T cell therapies. However, T cell therapy requires efficient generation of the selected epitope. How such mutations may affect proteasome-mediated antigen processing has so far not been studied. Therefore, we analyzed by in vitro experiments the effect on antigen processing and recognition of a T210M exchange, which previously had been introduced into the melanoma gp100209-217 tumor epitope to improve the HLA-A*02:01 binding and its immunogenicity. A quantitative analysis of the main steps of antigen processing shows that the T210M exchange affects proteasomal cleavage site usage within the mutgp100201-230 polypeptide, leading to the generation of an unique set of cleavage products. The T210M substitution qualitatively affects the proteasome-catalyzed generation of spliced and non-spliced peptides predicted to bind HLA-A or -B complexes. The T210M substitution also induces an enhanced production of the mutgp100209-217 epitope and its N-terminally extended peptides. The T210M exchange revealed no effect on ERAP1-mediated N-terminal trimming of the precursor peptides. However, mutant N-terminally extended peptides exhibited significantly increased HLA-A*02:01 binding affinity and elicited CD8(+) T cell stimulation in vitro similar to the wtgp100209-217 epitope. Thus, our experiments demonstrate that amino acid exchanges within an epitope can result in the generation of an altered peptide pool with new antigenic peptides and in a wider CD8(+) T cell response also towards N-terminally extended versions of the minimal epitope.
Collapse
Affiliation(s)
- Kathrin Textoris-Taube
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Christin Keller
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Juliane Liepe
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom, and
| | - Petra Henklein
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | - Peter M Kloetzel
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany,
| | - Michele Mishto
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany,
| |
Collapse
|
17
|
Giampieri E, De Cecco M, Remondini D, Sedivy J, Castellani G. Active Degradation Explains the Distribution of Nuclear Proteins during Cellular Senescence. PLoS One 2015; 10:e0118442. [PMID: 26115222 PMCID: PMC4483236 DOI: 10.1371/journal.pone.0118442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 01/16/2015] [Indexed: 11/19/2022] Open
Abstract
The amount of cellular proteins is a crucial parameter that is known to vary between cells as a function of the replicative passages, and can be important during physiological aging. The process of protein degradation is known to be performed by a series of enzymatic reactions, ranging from an initial step of protein ubiquitination to their final fragmentation by the proteasome. In this paper we propose a stochastic dynamical model of nuclear proteins concentration resulting from a balance between a constant production of proteins and their degradation by a cooperative enzymatic reaction. The predictions of this model are compared with experimental data obtained by fluorescence measurements of the amount of nuclear proteins in murine tail fibroblast (MTF) undergoing cellular senescence. Our model provides a three-parameter stationary distribution that is in good agreement with the experimental data even during the transition to the senescent state, where the nuclear protein concentration changes abruptly. The estimation of three parameters (cooperativity, saturation threshold, and maximal velocity of the reaction), and their evolution during replicative passages shows that only the maximal velocity varies significantly. Based on our modeling we speculate the reduction of functionality of the protein degradation mechanism as a possible competitive inhibition of the proteasome.
Collapse
Affiliation(s)
- Enrico Giampieri
- Department of Physics and Astronomy, Bologna University, Bologna, Italy and INFN Bologna
- * E-mail:
| | - Marco De Cecco
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics, Brown University, Providence, RI, USA
| | - Daniel Remondini
- Department of Physics and Astronomy, Bologna University, Bologna, Italy and INFN Bologna
| | - John Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics, Brown University, Providence, RI, USA
| | - Gastone Castellani
- Department of Physics and Astronomy, Bologna University, Bologna, Italy and INFN Bologna
| |
Collapse
|