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Biology
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Proteomics in Immunology and Cell Signaling
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Proteomics in Immunology and Cell Signaling

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Immunology".

Deadline for manuscript submissions: 31 July 2024 | Viewed by 7255

Special Issue Editor

Dr. Tuula Nyman

E-Mail Website
Guest Editor
Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
Interests: proteomics; biological mass spectrometry; innate immunity; cell signaling; extracellular vesicles

Special Issue Information

Dear Colleagues,

The immune system is our defense mechanism against microbial infections and tissue injury. A detailed understanding of this highly complex and multifacted system is essential for developing drugs to combat different diseases. The immune system encompasses multiple defense mechanisms including innate and adaptive cell-mediated immune responses, both of which need to be carefully controlled to activate an appropriate immune response.

Proteomics can provide in-depth spatiotemporal information about proteins on a global scale. In particular, mass spectrometry (MS)-based proteomics has developed immensely since the turn of the century, and recent developments in proteomics sample preparation, new high-resolution MS instruments, as well as advances in data analysis tools have enabled unprecedented speed and sensitivity in characterizing proteomes. Using the current methods and instruments available, we have started to acheive single-cell sensitivity through mass spectrometry. In immunology, it is critically important to have a detailed understanding of cellular signaling mechanisms related to immune system activation, and, here, proteomics tools can provide us with unique novel information.

For this Special Issue, ‘Proteomics in Immunology and Cell Signaling’, I invite authors to submit original articles and reviews that focus on the contiribution of proteomics to new knowledge in the field of immune system function and regulation, with a focus on cellular signaling events during immune system activation. Studies using human and model organisms are welcome, as well as proteomic studies applied to clinical immunology research.

Topics of special interest include the following:

  • Detailed understanding of the cell-signaling mechanisms of immune system activation, including quantitative proteome analysis as well as the global mapping of post-translational modicifcations like phosphoproteomics;
  • Proteomics to characterise the role of extracellular vesicles in the immune response and intracellular signaling cascades;
  • Immunopeptidomics;
  • How proteomics can contribute to clinical research.

I look forward to receiving your contributions.

Dr. Tuula Nyman
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biology is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • proteomics
  • biological mass spectrometry
  • cell signaling
  • innate immunity
  • T and B cell immune response
  • extracellular vesicles
  • immunopeptidomics
  • clinical proteomics

Published Papers (3 papers)

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Research

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25 pages, 6962 KiB  
Article
Expanding the MAPPs Assay to Accommodate MHC-II Pan Receptors for Improved Predictability of Potential T Cell Epitopes
by Katharina Hartman, Guido Steiner, Michel Siegel, Cary M. Looney, Timothy P. Hickling, Katharine Bray-French, Sebastian Springer, Céline Marban-Doran and Axel Ducret
Biology 2023, 12(9), 1265; https://doi.org/10.3390/biology12091265 - 21 Sep 2023
Cited by 1 | Viewed by 1595
Abstract
A critical step in the immunogenicity cascade is attributed to human leukocyte antigen (HLA) II presentation triggering T cell immune responses. The liquid chromatography–tandem mass spectrometry (LC-MS/MS)-based major histocompatibility complex (MHC) II-associated peptide proteomics (MAPPs) assay is implemented during preclinical risk assessments to [...] Read more.
A critical step in the immunogenicity cascade is attributed to human leukocyte antigen (HLA) II presentation triggering T cell immune responses. The liquid chromatography–tandem mass spectrometry (LC-MS/MS)-based major histocompatibility complex (MHC) II-associated peptide proteomics (MAPPs) assay is implemented during preclinical risk assessments to identify biotherapeutic-derived T cell epitopes. Although studies indicate that HLA-DP and HLA-DQ alleles are linked to immunogenicity, most MAPPs studies are restricted to using HLA-DR as the dominant HLA II genotype due to the lack of well-characterized immunoprecipitating antibodies. Here, we address this issue by testing various commercially available clones of MHC-II pan (CR3/43, WR18, and Tü39), HLA-DP (B7/21), and HLA-DQ (SPV-L3 and 1a3) antibodies in the MAPPs assay, and characterizing identified peptides according to binding specificity. Our results reveal that HLA II receptor-precipitating reagents with similar reported specificities differ based on clonality and that MHC-II pan antibodies do not entirely exhibit pan-specific tendencies. Since no individual antibody clone is able to recover the complete HLA II peptide repertoire, we recommend a mixed strategy of clones L243, WR18, and SPV-L3 in a single immunoprecipitation step for more robust compound-specific peptide detection. Ultimately, our optimized MAPPs strategy improves the predictability and additional identification of T cell epitopes in immunogenicity risk assessments. Full article
(This article belongs to the Special Issue Proteomics in Immunology and Cell Signaling)
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17 pages, 3228 KiB  
Article
Regulation of Expression of Extracellular Matrix Proteins by Differential Target Multiplexed Spinal Cord Stimulation (SCS) and Traditional Low-Rate SCS in a Rat Nerve Injury Model
by Dana M. Tilley, Ricardo Vallejo, Francesco Vetri, David C. Platt and David L. Cedeño
Biology 2023, 12(4), 537; https://doi.org/10.3390/biology12040537 - 31 Mar 2023
Viewed by 1183
Abstract
There is limited research on the association between the extracellular matrix (ECM) and chronic neuropathic pain. The objective of this study was twofold. Firstly, we aimed to assess changes in expression levels and the phosphorylation of ECM-related proteins due to the spared nerve [...] Read more.
There is limited research on the association between the extracellular matrix (ECM) and chronic neuropathic pain. The objective of this study was twofold. Firstly, we aimed to assess changes in expression levels and the phosphorylation of ECM-related proteins due to the spared nerve injury (SNI) model of neuropathic pain. Secondly, two modalities of spinal cord stimulation (SCS) were compared for their ability to reverse the changes induced by the pain model back toward normal, non-injury levels. We identified 186 proteins as ECM-related and as having significant changes in protein expression among at least one of the four experimental groups. Of the two SCS treatments, the differential target multiplexed programming (DTMP) approach reversed expression levels of 83% of proteins affected by the pain model back to levels seen in uninjured animals, whereas a low-rate (LR-SCS) approach reversed 67%. There were 93 ECM-related proteins identified in the phosphoproteomic dataset, having a combined 883 phosphorylated isoforms. DTMP back-regulated 76% of phosphoproteins affected by the pain model back toward levels found in uninjured animals, whereas LR-SCS back-regulated 58%. This study expands our knowledge of ECM-related proteins responding to a neuropathic pain model as well as providing a better perspective on the mechanism of action of SCS therapy. Full article
(This article belongs to the Special Issue Proteomics in Immunology and Cell Signaling)
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11 pages, 675 KiB  
Perspective
Immunopeptidomics in the Era of Single-Cell Proteomics
by Rupert L. Mayer and Karl Mechtler
Biology 2023, 12(12), 1514; https://doi.org/10.3390/biology12121514 - 12 Dec 2023
Viewed by 3119
Abstract
Immunopeptidomics, as the analysis of antigen peptides being presented to the immune system via major histocompatibility complexes (MHC), is being seen as an imperative tool for identifying epitopes for vaccine development to treat cancer and viral and bacterial infections as well as parasites. [...] Read more.
Immunopeptidomics, as the analysis of antigen peptides being presented to the immune system via major histocompatibility complexes (MHC), is being seen as an imperative tool for identifying epitopes for vaccine development to treat cancer and viral and bacterial infections as well as parasites. The field has made tremendous strides over the last 25 years but currently still faces challenges in sensitivity and throughput for widespread applications in personalized medicine and large vaccine development studies. Cutting-edge technological advancements in sample preparation, liquid chromatography as well as mass spectrometry, and data analysis, however, are currently transforming the field. This perspective showcases how the advent of single-cell proteomics has accelerated this transformation of immunopeptidomics in recent years and will pave the way for even more sensitive and higher-throughput immunopeptidomics analyses. Full article
(This article belongs to the Special Issue Proteomics in Immunology and Cell Signaling)
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