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Admon A. The biogenesis of the immunopeptidome. Semin Immunol 2023; 67:101766. [PMID: 37141766 DOI: 10.1016/j.smim.2023.101766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.
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Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Israel.
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2
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Elizalde-Díaz JP, Miranda-Narváez CL, Martínez-Lazcano JC, Martínez-Martínez E. The relationship between chronic immune response and neurodegenerative damage in long COVID-19. Front Immunol 2022; 13:1039427. [PMID: 36591299 PMCID: PMC9800881 DOI: 10.3389/fimmu.2022.1039427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
In the past two years, the world has faced the pandemic caused by the severe acute respiratory syndrome 2 coronavirus (SARS-CoV-2), which by August of 2022 has infected around 619 million people and caused the death of 6.55 million individuals globally. Although SARS-CoV-2 mainly affects the respiratory tract level, there are several reports, indicating that other organs such as the heart, kidney, pancreas, and brain can also be damaged. A characteristic observed in blood serum samples of patients suffering COVID-19 disease in moderate and severe stages, is a significant increase in proinflammatory cytokines such as interferon-α (IFN-α), interleukin-1β (IL-1β), interleukin-2 (IL-2), interleukin-6 (IL-6) and interleukin-18 (IL-18), as well as the presence of autoantibodies against interferon-α (IFN-α), interferon-λ (IFN-λ), C-C motif chemokine ligand 26 (CCL26), CXC motif chemokine ligand 12 (CXCL12), family with sequence similarity 19 (chemokine (C-C motif)-like) member A4 (FAM19A4), and C-C motif chemokine ligand 1 (CCL1). Interestingly, it has been described that the chronic cytokinemia is related to alterations of blood-brain barrier (BBB) permeability and induction of neurotoxicity. Furthermore, the generation of autoantibodies affects processes such as neurogenesis, neuronal repair, chemotaxis and the optimal microglia function. These observations support the notion that COVID-19 patients who survived the disease present neurological sequelae and neuropsychiatric disorders. The goal of this review is to explore the relationship between inflammatory and humoral immune markers and the major neurological damage manifested in post-COVID-19 patients.
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Affiliation(s)
- José Pedro Elizalde-Díaz
- Laboratory of Cell Communication & Extracellular Vesicles, Division of Basic Science, Instituto Nacional de Medicina Genómica, Ciudad de México, Mexico
| | - Clara Leticia Miranda-Narváez
- Laboratorio de Neurofarmacología Molecular y Nanotecnología, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Ciudad de México, Mexico
| | - Juan Carlos Martínez-Lazcano
- Laboratorio de Neurofarmacología Molecular y Nanotecnología, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Ciudad de México, Mexico
| | - Eduardo Martínez-Martínez
- Laboratory of Cell Communication & Extracellular Vesicles, Division of Basic Science, Instituto Nacional de Medicina Genómica, Ciudad de México, Mexico
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3
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Single-Cell Proteomics: The Critical Role of Nanotechnology. Int J Mol Sci 2022; 23:ijms23126707. [PMID: 35743151 PMCID: PMC9224324 DOI: 10.3390/ijms23126707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/24/2022] Open
Abstract
In single-cell analysis, biological variability can be attributed to individual cells, their specific state, and the ability to respond to external stimuli, which are determined by protein abundance and their relative alterations. Mass spectrometry (MS)-based proteomics (e.g., SCoPE-MS and SCoPE2) can be used as a non-targeted method to detect molecules across hundreds of individual cells. To achieve high-throughput investigation, novel approaches in Single-Cell Proteomics (SCP) are needed to identify and quantify proteins as accurately as possible. Controlling sample preparation prior to LC-MS analysis is critical, as it influences sensitivity, robustness, and reproducibility. Several nanotechnological approaches have been developed for the removal of cellular debris, salts, and detergents, and to facilitate systematic sample processing at the nano- and microfluidic scale. In addition, nanotechnology has enabled high-throughput proteomics analysis, which have required the improvement of software tools, such as DART-ID or DO-MS, which are also fundamental for addressing key biological questions. Single-cell proteomics has many applications in nanomedicine and biomedical research, including advanced cancer immunotherapies or biomarker characterization, among others; and novel methods allow the quantification of more than a thousand proteins while analyzing hundreds of single cells.
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Juanes-Velasco P, Landeira-Viñuela A, García-Vaquero ML, Lecrevisse Q, Herrero R, Ferruelo A, Góngora R, Corrales F, Rivas JDL, Lorente JA, Hernández ÁP, Fuentes M. SARS-CoV-2 Infection Triggers Auto-Immune Response in ARDS. Front Immunol 2022; 13:732197. [PMID: 35154090 PMCID: PMC8831226 DOI: 10.3389/fimmu.2022.732197] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/06/2022] [Indexed: 12/15/2022] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a severe pulmonary disease, which is one of the major complications in COVID-19 patients. Dysregulation of the immune system and imbalances in cytokine release and immune cell activation are involved in SARS-CoV-2 infection. Here, the inflammatory, antigen, and auto-immune profile of patients presenting COVID-19-associated severe ARDS has been analyzed using functional proteomics approaches. Both, innate and humoral responses have been characterized through acute-phase protein network and auto-antibody signature. Severity and sepsis by SARS-CoV-2 emerged to be correlated with auto-immune profiles of patients and define their clinical progression, which could provide novel perspectives in therapeutics development and biomarkers of COVID-19 patients. Humoral response in COVID-19 patients’ profile separates with significant differences patients with or without ARDS. Furthermore, we found that this profile can be correlated with COVID-19 severity and results more common in elderly patients.
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Affiliation(s)
- Pablo Juanes-Velasco
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Marina L García-Vaquero
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Quentin Lecrevisse
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Raquel Herrero
- Department of Critical Care Medicine, Hospital Universitario de Getafe, Madrid, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Investigación Carlos III, Madrid, Spain.,Fundación de Investigación Biomédica del Hospital Universitario de Getafe, Madrid, Spain
| | - Antonio Ferruelo
- Fundación de Investigación Biomédica del Hospital Universitario de Getafe, Madrid, Spain
| | - Rafael Góngora
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, National Center for Biotechnology, Consejo Superior de Investigaciones Científicas, Madrid, Spain.,PROTEORED-ISCIII, Red Nacional de Laboratorios de Proteomica-ISCIII, Madrid, Spain
| | - Javier De Las Rivas
- Bioinformatics and Functional Genomics Group, Cancer Research Center (IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas & University of Salamanca, Salamanca, Spain
| | - Jose A Lorente
- Department of Critical Care Medicine, Hospital Universitario de Getafe, Madrid, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Investigación Carlos III, Madrid, Spain.,Fundación de Investigación Biomédica del Hospital Universitario de Getafe, Madrid, Spain.,Universidad Europea de Madrid, Madrid, Spain
| | - Ángela-Patricia Hernández
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.,PROTEORED-ISCIII, Red Nacional de Laboratorios de Proteomica-ISCIII, Madrid, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
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5
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Devi SS, Kardam V, Dubey KD, Dwivedi M. Deciphering the immunogenic T-cell epitopes from spike protein of SARS-CoV-2 concerning the diverse population of India. J Biomol Struct Dyn 2022; 41:2713-2732. [PMID: 35132938 DOI: 10.1080/07391102.2022.2037462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Scientists are rigorously looking for an efficient vaccine against the current pandemic due to the SARS-CoV-2 virus. The reverse vaccinology approach may provide us with significant therapeutic leads in this direction and further determination of T-cell/B-cell response to antigen. In the present study, we conducted a population coverage analysis referring to the diverse Indian population. From the Immune epitope database (IEDB), HLA- distribution analysis was performed to find the most promiscuous T-cell epitope out of In silico determined epitope of Spike protein from SARS-CoV-2. Epitopes were selected based on their binding affinity with the maximum number of HLA alleles belonging to the highest population coverage rate values for the chosen geographical area in India. 404 cleavage sites within the 1288 amino acids sequence of spike glycoprotein were determined by NetChop proteasomal cleavage prediction suggesting the presence of adequate sites in the protein sequence for cleaving into appropriate epitopes. For population coverage analysis, 179 selected epitopes present the projected population coverage up to 97.45% with 56.16 average hit and 15.07 pc90. 54 epitopes are found with the highest coverage among the Indian population and highly conserved within the given spike RBD domain sequence. Among all the predicted epitopes, 9-mer TRFASVYAW and RFDNPVLPF along with 12-mer LLAGTITSGWTF and VSQPFLMDLEGK epitopes are observed as the best due to their decent docking score and best binding affinity to corresponding HLA alleles during MD simulations. Outcomes from this study could be critical to design a vaccine against SARS-CoV-2 for a different set of populations within the country.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Vandana Kardam
- Department of Chemistry, Shiv Nadar University, Greater Noida, India
| | | | - Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
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Moore SM. Challenges of Rabies Serology: Defining Context of Interpretation. Viruses 2021; 13:v13081516. [PMID: 34452381 PMCID: PMC8402924 DOI: 10.3390/v13081516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 12/25/2022] Open
Abstract
The case fatality rate of rabies, nearly 100%, is one of the most unique characteristic of this ancient virus infection. The crucial role rabies virus neutralizing antibody plays in protection is both well established and explanation of why rabies serology is important. Various laboratory methods can and have been used but serum neutralization methods have long been the gold standard due to the ability to measure function (neutralization), however these methods can be difficult to perform for several reasons. Assays such as enzyme linked absorbance assays (ELISA), indirect fluorescence antibody (IFA) and more recently lateral flow methods are in use. Interpretation of results can be problematic, not only between methods but also due to modifications of the same method that can lead to misinterpretations. A common assumption in review of laboratory test results is that different methods for the same component produce comparable results under all conditions or circumstances. Assumptions and misinterpretations provide the potential for detrimental decisions, ranging from regulatory to clinically related, and most importantly what ‘level’ is protective. Review of the common challenges in performance and interpretation of rabies serology and specific examples illuminate critical issues to consider when reviewing and applying results of rabies serological testing.
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Affiliation(s)
- Susan M Moore
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
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Hernández ÁP, Juanes-Velasco P, Landeira-Viñuela A, Bareke H, Montalvillo E, Góngora R, Fuentes M. Restoring the Immunity in the Tumor Microenvironment: Insights into Immunogenic Cell Death in Onco-Therapies. Cancers (Basel) 2021; 13:2821. [PMID: 34198850 PMCID: PMC8201010 DOI: 10.3390/cancers13112821] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/31/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
Immunogenic cell death (ICD) elicited by cancer therapy reshapes the tumor immune microenvironment. A long-term adaptative immune response can be initiated by modulating cell death by therapeutic approaches. Here, the major hallmarks of ICD, endoplasmic reticulum (ER) stress, and damage-associated molecular patterns (DAMPs) are correlated with ICD inducers used in clinical practice to enhance antitumoral activity by suppressing tumor immune evasion. Approaches to monitoring the ICD triggered by antitumoral therapeutics in the tumor microenvironment (TME) and novel perspective in this immune system strategy are also reviewed to give an overview of the relevance of ICD in cancer treatment.
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Affiliation(s)
- Ángela-Patricia Hernández
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (Á.-P.H.); (P.J.-V.); (A.L.-V.); (H.B.); (E.M.); (R.G.)
| | - Pablo Juanes-Velasco
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (Á.-P.H.); (P.J.-V.); (A.L.-V.); (H.B.); (E.M.); (R.G.)
| | - Alicia Landeira-Viñuela
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (Á.-P.H.); (P.J.-V.); (A.L.-V.); (H.B.); (E.M.); (R.G.)
| | - Halin Bareke
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (Á.-P.H.); (P.J.-V.); (A.L.-V.); (H.B.); (E.M.); (R.G.)
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Institute of Health Sciences, Marmara University, 34722 Istanbul, Turkey
| | - Enrique Montalvillo
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (Á.-P.H.); (P.J.-V.); (A.L.-V.); (H.B.); (E.M.); (R.G.)
| | - Rafael Góngora
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (Á.-P.H.); (P.J.-V.); (A.L.-V.); (H.B.); (E.M.); (R.G.)
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (Á.-P.H.); (P.J.-V.); (A.L.-V.); (H.B.); (E.M.); (R.G.)
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
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