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Proteomics and Its Applications in Human Biology
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Proteomics and Its Applications in Human Biology

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Immunology".

Deadline for manuscript submissions: 31 May 2024 | Viewed by 4039

Special Issue Editor

Dr. Paula Díez

E-Mail Website
Guest Editor
Health Research Institute of Asturias (ISPA), Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain
Interests: proteomics; mass spectrometry; mass cytometry; -omics integration; immunology; myeloid cells; cancer

Special Issue Information

Dear Colleagues,

In the era of omics technologies, proteomics is an outstanding platform for high-throughput analysis, even at the single-cell level. The recent advancements in this field, particularly the development of highly sensitive equipment and cutting-edge pipelines, have boosted the in-depth description of protein maps and their relationships. Such networks are crucial in the functioning of complex systems, such as the immune system, or in disease conditions including cancer. Even though other non-proteomics-based strategies have significantly contributed to the characterization of human biology, numerous questions still remain unanswered. Therefore, proteomics techniques, such as those based on the usage of mass spectrometry, flow cytometry, mass cytometry, protein microarrays or other antibody-based systems, will help in the understanding the actual molecular events triggering cellular responses. Ultimately, these responses will determine disease or health status, response vs. non-response to immunotherapies, the effectiveness of treatments or the development of autoimmune disorders.

For this Special Issue, ‘Proteomics and Its Applications in Human Biology’, we welcome submissions of original research and review articles on all molecular aspects of human biology studied under the umbrella of proteomics, including health and disease conditions.

Dr. Paula Díez
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • proteins
  • post-translational modifications
  • immune system
  • inflammasome
  • biomarkers
  • imaging proteomics
  • disease
  • cancer immunology
  • immune cross-talk
  • patient care
  • immunotherapy
  • autoimmune disorder

Published Papers (3 papers)

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Research

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13 pages, 6107 KiB  
Article
A Low-Cost Modular Imaging System for Rapid, Multiplexed Immunofluorescence Detection in Clinical Tissues
by Joshua Gu, Hannah Jian, Christine Wei, Jessica Shiu, Anand Ganesan, Weian Zhao and Per Niklas Hedde
Int. J. Mol. Sci. 2023, 24(8), 7008; https://doi.org/10.3390/ijms24087008 - 10 Apr 2023
Viewed by 1940
Abstract
To image 4-plex immunofluorescence-stained tissue samples at a low cost with cellular level resolution and sensitivity and dynamic range required to detect lowly and highly abundant targets, here we describe a robust, inexpensive (<$9000), 3D printable portable imaging device (Tissue Imager). The Tissue [...] Read more.
To image 4-plex immunofluorescence-stained tissue samples at a low cost with cellular level resolution and sensitivity and dynamic range required to detect lowly and highly abundant targets, here we describe a robust, inexpensive (<$9000), 3D printable portable imaging device (Tissue Imager). The Tissue Imager can immediately be deployed on benchtops for in situ protein detection in tissue samples. Applications for this device are broad, ranging from answering basic biological questions to clinical pathology, where immunofluorescence can detect a larger number of markers than the standard H&E or chromogenic immunohistochemistry (CIH) staining, while the low cost also allows usage in classrooms. After characterizing our platform’s specificity and sensitivity, we demonstrate imaging of a 4-plex immunology panel in human cutaneous T-cell lymphoma (CTCL) formalin-fixed paraffin-embedded (FFPE) tissue samples. From those images, positive cells were detected using CellProfiler, a popular open-source software package, for tumor marker profiling. We achieved a performance on par with commercial epifluorescence microscopes that are >10 times more expensive than our Tissue Imager. This device enables rapid immunofluorescence detection in tissue sections at a low cost for scientists and clinicians and can provide students with a hands-on experience to understand engineering and instrumentation. We note that for using the Tissue Imager as a medical device in clinical settings, a comprehensive review and approval processes would be required. Full article
(This article belongs to the Special Issue Proteomics and Its Applications in Human Biology)
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10 pages, 961 KiB  
Article
Increased Immunoglobulin Gamma-3 Chain C in the Serum, Saliva, and Urine of Patients with Systemic Lupus Erythematosus
by Ju-Yang Jung, Ji-Won Kim, Sang-Won Lee, Wook-Young Baek, Hyoun-Ah Kim and Chang-Hee Suh
Int. J. Mol. Sci. 2023, 24(8), 6927; https://doi.org/10.3390/ijms24086927 - 08 Apr 2023
Viewed by 1173
Abstract
Immunoglobulin gamma-3 chain C (IGHG3) levels have been detected in the blood and tissue of patients with systemic lupus erythematosus (SLE). This study aims to assess its clinical value by measuring and comparing levels of IGHG3 in different body fluids in patients with [...] Read more.
Immunoglobulin gamma-3 chain C (IGHG3) levels have been detected in the blood and tissue of patients with systemic lupus erythematosus (SLE). This study aims to assess its clinical value by measuring and comparing levels of IGHG3 in different body fluids in patients with SLE. The levels of IGHG3 in saliva, serum, and urine from 181 patients with SLE and 99 healthy controls were measured and analyzed. In patients with SLE and healthy controls, salivary IGHG3 levels were 3078.9 ± 2473.8 and 1413.6 ± 1075.3 ng/mL, serum IGHG3 levels were 478.1 ± 160.9 and 364.4 ± 97.9 μg/mL, and urine IGHG3 levels were 64.0 ± 74.5 and 27.1 ± 16.2 ng/mL, respectively (all p < 0.001). Salivary IGHG3 was correlated with ESR (correlation coefficient [r], 0.173; p = 0.024). Serum IGHG3 was correlated with leukocyte count (r, −0.219; p = 0.003), lymphocyte count (r, 0.22; p = 0.03), anti-dsDNA antibody positivity (r, 0.22; p = 0.003), and C3 levels (r, −0.23; p = 0.002). Urinary IGHG3 was correlated with hemoglobin level (r, −0.183; p = 0.021), ESR (r, 0.204; p = 0.01), anti-dsDNA antibody positivity (r, 0.262; p = 0.001), C3 levels (r, −0.202; p = 0.011), and SLE disease activity index (r, 0.332; p = 0.01). Urinary IGHG3 was higher in patients with nephritis than in those without (119.5 ± 110.0 vs. 49.8 ± 54.4 ng/mL; p < 0.01). IGHG3 was increased in the saliva, serum, and urine of patients with SLE. While salivary IGHG3 was not identified to be specific to SLE disease activity, serum IGHG3 showed correlations with clinical characteristics. Urinary IGHG3 levels were associated with disease activity and renal involvement in SLE. Full article
(This article belongs to the Special Issue Proteomics and Its Applications in Human Biology)
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Review

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31 pages, 1725 KiB  
Review
Characterization of Human B Cell Hematological Malignancies Using Protein-Based Approaches
by Cristina Jiménez, Alba Garrote-de-Barros, Carlos López-Portugués, María Hernández-Sánchez and Paula Díez
Int. J. Mol. Sci. 2024, 25(9), 4644; https://doi.org/10.3390/ijms25094644 - 24 Apr 2024
Viewed by 212
Abstract
The maturation of B cells is a complex, multi-step process. During B cell differentiation, errors can occur, leading to the emergence of aberrant versions of B cells that, finally, constitute a malignant tumor. These B cell malignancies are classified into three main groups: [...] Read more.
The maturation of B cells is a complex, multi-step process. During B cell differentiation, errors can occur, leading to the emergence of aberrant versions of B cells that, finally, constitute a malignant tumor. These B cell malignancies are classified into three main groups: leukemias, myelomas, and lymphomas, the latter being the most heterogeneous type. Since their discovery, multiple biological studies have been performed to characterize these diseases, aiming to define their specific features and determine potential biomarkers for diagnosis, stratification, and prognosis. The rise of advanced -omics approaches has significantly contributed to this end. Notably, proteomics strategies appear as promising tools to comprehensively profile the final molecular effector of these cells. In this narrative review, we first introduce the main B cell malignancies together with the most relevant proteomics approaches. Then, we describe the core studies conducted in the field and their main findings and, finally, we evaluate the advantages and drawbacks of flow cytometry, mass cytometry, and mass spectrometry for the profiling of human B cell disorders. Full article
(This article belongs to the Special Issue Proteomics and Its Applications in Human Biology)
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