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Proteomics Analysis in Biomarker Discovery
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Proteomics Analysis in Biomarker Discovery

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (10 February 2021) | Viewed by 17543

Special Issue Editors

Dr. Maria Rosa Mazzoni

E-Mail Website
Guest Editor
Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
Interests: proteome; secretome; biomarkers; molecular mechanisms of diseases; GPCRs
Special Issues, Collections and Topics in MDPI journals
Dr. Laura Giusti

E-Mail Website
Co-Guest Editor
School of Pharmacy, University of Camerino, 62032 Camerino, Italy
Interests: proteomics and biomarkers; endocrine diseases; cancer; proteomics and nutraceuticals
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

Early and accurate diagnosis is pivotal to achieving successful treatment of complex and often fatal diseases such as cancer and autoimmune, cardiovascular, and neurodegenerative diseases. In clinical practice, the prediction outcomes, and responses to treatment, is also considered of great importance. For a long time, some blood biomarkers have been used as tools for diagnosis and follow-up purposes. Nevertheless, currently available biomarkers, which are far from being comprehensive, often lack specificity, and thus in the last decade omics-based technologies have been extensively used for biomarker discovery. Proteomics analysis of various body fluids such as plasma, serum, and saliva, and tissue specimens, has largely contributed to the detection of new potential biomarkers for various diseases. The constant advance of mass spectrometry techniques has been essential to this ongoing process. In recent years, proteomics analysis of cell culture secretome, cell, and body fluid exomes has also been implemented, leading to new discoveries that have shed light on cell communications in pathological conditions such as cancer. Particularly, exosome protein cargos appear to reflect the pathological state of the originated cells and thus can represent enriched sources of pivotal biomarkers.

Scientists working in the field of proteomics analysis applied to biomarkers discovery for human diseases are encouraged to consider this Special Issue for submitting recent research and review articles. While research dealing with innovative approaches is particularly welcome, proteomics investigations that highlight the molecular mechanisms of diseases are also of interest.

Dr. Maria Rosa Mazzoni
Dr. Laura Giusti
Guest Editors

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

  • biomarkers
  • diseases
  • proteome
  • secretome
  • exomes
  • mass spectrometry

Published Papers (4 papers)

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Research

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14 pages, 3213 KiB  
Article
Multiplexed MRM-Based Proteomics Identified Multiple Biomarkers of Disease Severity in Human Heart Failure
by Maura Brioschi, Erica Gianazza, Piergiuseppe Agostoni, Beatrice Zoanni, Alice Mallia and Cristina Banfi
Int. J. Mol. Sci. 2021, 22(2), 838; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22020838 - 15 Jan 2021
Cited by 9 | Viewed by 2810
Abstract
Heart failure (HF) is a complex disease due to the intricate interplay of several mechanisms, which therefore implies the need for a multimarker strategy to better personalize the care of patients with HF. In this study, we developed a targeted mass spectrometry approach [...] Read more.
Heart failure (HF) is a complex disease due to the intricate interplay of several mechanisms, which therefore implies the need for a multimarker strategy to better personalize the care of patients with HF. In this study, we developed a targeted mass spectrometry approach based on multiple reaction monitoring (MRM) to measure multiple circulating protein biomarkers, involved in cardiovascular disease, to address their relevance in the human HF, intending to assess the feasibility of the workflow in the disease monitoring and risk stratification. In this study, we analyzed a total of 60 plasma proteins in 30 plasma samples from eight control subjects and 22 age- and gender- matched HF patients. We identified a panel of four plasma proteins, namely Neuropilin-2, Beta 2 microglobulin, alpha-1-antichymotrypsin, and complement component C9, that were more abundant in HF patients in relation to disease severity and pulmonary dysfunction. Moreover, we showed the ability of the combination of these candidate proteins to discriminate, with sufficient accuracy, HF patients from healthy subjects. In conclusion, we demonstrated the feasibility and potential of a proteomic workflow based on MRM mass spectrometry for the evaluation of multiple proteins in human plasma and the identification of a panel of biomarkers of HF severity. Full article
(This article belongs to the Special Issue Proteomics Analysis in Biomarker Discovery)
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23 pages, 2828 KiB  
Article
Intracellular and Extracellular Markers of Lethality in Osteogenesis Imperfecta: A Quantitative Proteomic Approach
by Luca Bini, Domitille Schvartz, Chiara Carnemolla, Roberta Besio, Nadia Garibaldi, Jean-Charles Sanchez, Antonella Forlino and Laura Bianchi
Int. J. Mol. Sci. 2021, 22(1), 429; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22010429 - 04 Jan 2021
Cited by 12 | Viewed by 3859
Abstract
Osteogenesis imperfecta (OI) is a heritable disorder that mainly affects the skeleton. The inheritance is mostly autosomal dominant and associated to mutations in one of the two genes, COL1A1 and COL1A2, encoding for the type I collagen α chains. According to more [...] Read more.
Osteogenesis imperfecta (OI) is a heritable disorder that mainly affects the skeleton. The inheritance is mostly autosomal dominant and associated to mutations in one of the two genes, COL1A1 and COL1A2, encoding for the type I collagen α chains. According to more than 1500 described mutation sites and to outcome spanning from very mild cases to perinatal-lethality, OI is characterized by a wide genotype/phenotype heterogeneity. In order to identify common affected molecular-pathways and disease biomarkers in OI probands with different mutations and lethal or surviving phenotypes, primary fibroblasts from dominant OI patients, carrying COL1A1 or COL1A2 defects, were investigated by applying a Tandem Mass Tag labeling-Liquid Chromatography-Tandem Mass Spectrometry (TMT LC-MS/MS) proteomics approach and bioinformatic tools for comparative protein-abundance profiling. While no difference in α1 or α2 abundance was detected among lethal (type II) and not-lethal (type III) OI patients, 17 proteins, with key effects on matrix structure and organization, cell signaling, and cell and tissue development and differentiation, were significantly different between type II and type III OI patients. Among them, some non–collagenous extracellular matrix (ECM) proteins (e.g., decorin and fibrillin-1) and proteins modulating cytoskeleton (e.g., nestin and palladin) directly correlate to the severity of the disease. Their defective presence may define proband-failure in balancing aberrances related to mutant collagen. Full article
(This article belongs to the Special Issue Proteomics Analysis in Biomarker Discovery)
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13 pages, 3850 KiB  
Article
Proteomic Profiling of Archived Tissue of Primary Melanoma Identifies Proteins Associated with Metastasis
by Andrew Shapanis, Chester Lai, Mathew Sommerlad, Erika Parkinson, Eugene Healy and Paul Skipp
Int. J. Mol. Sci. 2020, 21(21), 8160; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21218160 - 31 Oct 2020
Cited by 2 | Viewed by 2187
Abstract
Formalin-fixed paraffin embedded (FFPE) clinical tissues represent an abundant and unique resource for translational proteomic studies. In the US, melanoma is the 5th and 6th most common cancer in men and women, respectively, affecting over 230,000 people annually and metastasising in 5–15% of [...] Read more.
Formalin-fixed paraffin embedded (FFPE) clinical tissues represent an abundant and unique resource for translational proteomic studies. In the US, melanoma is the 5th and 6th most common cancer in men and women, respectively, affecting over 230,000 people annually and metastasising in 5–15% of cases. Median survival time for distant metastatic melanoma is 6–9 months with a 5-year-survival of < 15%. In this study, 24 primary FFPE tumours which have metastasised (P-M) and 24 primary FFPE tumours which did not metastasise (P-NM) were subjected to proteomic profiling. In total, 2750 proteins were identified, of which 16 were significantly differentially expressed. Analysis of TCGA data demonstrated that expression of the genes encoding for 6 of these 16 proteins had a significant effect on survival in cutaneous melanoma. Pathway analysis of the proteomics data revealed mechanisms likely involved in the process of melanoma metastasis, including cytoskeleton rearrangement, extracellular changes and immune system alterations. A machine learning prediction model scoring an AUC of 0.922, based on these 16 differentially expressed proteins was able to accurately classify samples into P-M and P-NM. This study has identified potential biomarkers and key processes relating to melanoma metastasis using archived clinical samples, providing a basis for future studies in larger cohorts. Full article
(This article belongs to the Special Issue Proteomics Analysis in Biomarker Discovery)
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Review

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44 pages, 2128 KiB  
Review
Platelets in Healthy and Disease States: From Biomarkers Discovery to Drug Targets Identification by Proteomics
by Erica Gianazza, Maura Brioschi, Roberta Baetta, Alice Mallia, Cristina Banfi and Elena Tremoli
Int. J. Mol. Sci. 2020, 21(12), 4541; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21124541 - 25 Jun 2020
Cited by 33 | Viewed by 7658
Abstract
Platelets are a heterogeneous small anucleate blood cell population with a central role both in physiological haemostasis and in pathological states, spanning from thrombosis to inflammation, and cancer. Recent advances in proteomic studies provided additional important information concerning the platelet biology and the [...] Read more.
Platelets are a heterogeneous small anucleate blood cell population with a central role both in physiological haemostasis and in pathological states, spanning from thrombosis to inflammation, and cancer. Recent advances in proteomic studies provided additional important information concerning the platelet biology and the response of platelets to several pathophysiological pathways. Platelets circulate systemically and can be easily isolated from human samples, making proteomic application very interesting for characterizing the complexity of platelet functions in health and disease as well as for identifying and quantifying potential platelet proteins as biomarkers and novel antiplatelet therapeutic targets. To date, the highly dynamic protein content of platelets has been studied in resting and activated platelets, and several subproteomes have been characterized including platelet-derived microparticles, platelet granules, platelet releasates, platelet membrane proteins, and specific platelet post-translational modifications. In this review, a critical overview is provided on principal platelet proteomic studies focused on platelet biology from signaling to granules content, platelet proteome changes in several diseases, and the impact of drugs on platelet functions. Moreover, recent advances in quantitative platelet proteomics are discussed, emphasizing the importance of targeted quantification methods for more precise, robust and accurate quantification of selected proteins, which might be used as biomarkers for disease diagnosis, prognosis and therapy, and their strong clinical impact in the near future. Full article
(This article belongs to the Special Issue Proteomics Analysis in Biomarker Discovery)
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