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Proteomics and Personalized Medicine
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Proteomics and Personalized Medicine

A special issue of Journal of Personalized Medicine (ISSN 2075-4426). This special issue belongs to the section "Omics/Informatics".

Deadline for manuscript submissions: closed (5 November 2020) | Viewed by 18584

Special Issue Editor

Prof. Dr. Kurt Boonen

E-Mail Website
Guest Editor
Centre for Proteomics, UAntwerp, Antwerp, Belgium. Unit Environmental Risk & Health, VITO, Mol, Belgium
Interests: clinical proteomics; immunopeptidomics; data analysis

Special Issue Information

Dear Colleagues,

The first successful applications in personalized medicine were made possible largely in part by the advent of next-generation sequencing techniques. The use of proteomics for personalized medicine was hampered by technical limitations, such as high-throughput measurements. However, the field of proteomics is evolving at a fast pace now, and recent breakthroughs will make proteomics a valuable asset in the arsenal of techniques used in personalized medicine.

In this Special Issue, we want to present some of the latest technical developments in proteomics that will enable its use in personalized medicine and also pioneering applications. Therefore, we are looking for interesting cutting-edge contributions to our journal that use proteomics, from hardware to data analysis, for personalized medicine or that facilitate the implantation therein.

Prof. Dr. Kurt Boonen
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. Journal of Personalized Medicine 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 2600 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
  • Proteogenomics
  • Biomarker
  • Prevention
  • Personalized medicine
  • Data integration

Published Papers (5 papers)

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Research

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15 pages, 1281 KiB  
Article
From Proteomics to Personalized Medicine: The Importance of Isoflavone Dose and Estrogen Receptor Status in Breast Cancer Cells
by Maria Ilieș, Alina Uifălean, Sergiu Pașca, Vishnu Mukund Dhople, Michael Lalk, Cristina Adela Iuga and Elke Hammer
J. Pers. Med. 2020, 10(4), 292; https://doi.org/10.3390/jpm10040292 - 19 Dec 2020
Cited by 7 | Viewed by 3057
Abstract
Continuing efforts are directed towards finding alternative breast cancer chemotherapeutics, with improved safety and efficacy profiles. Soy isoflavones represent promising agents but, despite extensive research, limited information exists regarding their impact on the breast cancer cell proteome. The purpose of this study was [...] Read more.
Continuing efforts are directed towards finding alternative breast cancer chemotherapeutics, with improved safety and efficacy profiles. Soy isoflavones represent promising agents but, despite extensive research, limited information exists regarding their impact on the breast cancer cell proteome. The purpose of this study was to compare the proteomic profiles of MCF-7 (estrogen responsive) and MDA-MB-231 (estrogen non-responsive) breast cancer cells exposed to different concentrations of genistein, daidzein, and a soy seed extract, using a high throughput LC–UDMSE protein profiling approach. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay confirmed the dual activity of soy isoflavones on MCF-7 cells and the inhibitory effect on MDA-MB-231 cells. Proteome profiling of paramagnetic beads prepared peptides by nano-LC UDMSE and pathway enrichment analysis revealed that isoflavones affected distinct molecular pathways in MCF-7 and MDA-MB-231 cells, such as tyrosine kinases signaling pathway, cytoskeleton organization, lipid and phospholipid catabolism, extracellular matrix degradation and mRNA splicing. Also, in MCF-7 cells, low and high isoflavone doses induced different changes of the proteome, including cell cycle alterations. Therefore, the expression of estrogen receptors and the isoflavone dose are determinant factors for the molecular impact of isoflavones and must be taken into account when considering adjuvant breast cancer therapy towards personalized medicine. Full article
(This article belongs to the Special Issue Proteomics and Personalized Medicine)
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19 pages, 2533 KiB  
Article
Effects of Growth Hormone Treatment and Rehabilitation in Incomplete Chronic Traumatic Spinal Cord Injury: Insight from Proteome Analysis
by Tatiana Martin-Rojas, Tamara Sastre-Oliva, Ana Esclarín-Ruz, Felix Gil-Dones, Laura Mourino-Alvarez, Nerea Corbacho-Alonso, Rafael Moreno-Luna, German Hernandez-Fernandez, Juan Antonio Lopez, Antonio Oliviero and María G. Barderas
J. Pers. Med. 2020, 10(4), 183; https://doi.org/10.3390/jpm10040183 - 21 Oct 2020
Cited by 2 | Viewed by 2423
Abstract
Despite promising advances in the medical management of spinal cord injury (SCI), there is still no available effective therapy to repair the neurological damage in patients who experience this life-transforming condition. Recently, we performed a phase II/III placebo-controlled randomized trial of safety and [...] Read more.
Despite promising advances in the medical management of spinal cord injury (SCI), there is still no available effective therapy to repair the neurological damage in patients who experience this life-transforming condition. Recently, we performed a phase II/III placebo-controlled randomized trial of safety and efficacy of growth hormone (GH) treatment in incomplete chronic traumatic spinal cord injury. The main findings were that the combined treatment of GH plus rehabilitation treatment is feasible and safe, and that GH but not placebo slightly improves the SCI individual motor score. Moreover, we found that an intensive and long-lasting rehabilitation program per se increases the functional outcome of SCI individuals. To understand the possible mechanisms of the improvement due to GH treatment (motor score) and due to rehabilitation (functional outcome), we used a proteomic approach. Here, we used a multiple proteomic strategy to search for recovery biomarkers in blood plasma with the potential to predict response to somatropin treatment and to delayed intensive rehabilitation. Forty-six patients were recruited and followed for a minimum period of 1 year. Patients were classified into two groups based on their treatment: recombinant somatropin (0.4 mg) or placebo. Both groups received rehabilitation treatment. Our strategy allowed us to perform one of the deepest plasma proteomic analyses thus far, which revealed two proteomic signatures with predictive value: (i) response to recombinant somatropin treatment and (ii) response to rehabilitation. The proteins implicated in these signatures are related to homeostasis, inflammation, and coagulation functions. These findings open novel possibilities to assess and therapeutically manage patients with SCI, which could have a positive impact on their clinical response. Full article
(This article belongs to the Special Issue Proteomics and Personalized Medicine)
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19 pages, 3075 KiB  
Article
Protein Expression Analysis of an In Vitro Murine Model of Prostate Cancer Progression: Towards Identification of High-Potential Therapeutic Targets
by Hisham F. Bahmad, Wenjing Peng, Rui Zhu, Farah Ballout, Alissar Monzer, Mohamad K. Elajami, Firas Kobeissy, Wassim Abou-Kheir and Yehia Mechref
J. Pers. Med. 2020, 10(3), 83; https://doi.org/10.3390/jpm10030083 - 10 Aug 2020
Cited by 7 | Viewed by 3843
Abstract
Background: Prostate cancer (PC) is the most frequently diagnosed cancer among men worldwide. The poor prognosis of PC is largely due to late diagnosis of the disease when it has progressed to advanced stages marked by androgen-independence. We interrogated proteomic signatures that embody [...] Read more.
Background: Prostate cancer (PC) is the most frequently diagnosed cancer among men worldwide. The poor prognosis of PC is largely due to late diagnosis of the disease when it has progressed to advanced stages marked by androgen-independence. We interrogated proteomic signatures that embody the transition of PC from an androgen-dependent (AD) to an androgen-independent (AI) state. Methods: We have previously established AD and AI murine PC cell lines, PLum-AD and PLum-AI, respectively, which recapitulate primary and progressive PC at phenotypic and subcellular levels. We statistically surveyed global protein expression profiles in these cell lines. Differential profiles were functionally interrogated by pathways and protein–protein interaction network analyses. Results: Protein expression pattern analysis revealed a total of 683 proteins, among which 99 were significantly differentially altered in PLum-AI cells as compared to PLum-AD cells (45 increased and 54 decreased). Principal component analysis (PCA) revealed that the two different cell lines clearly separated apart, indicating a significant proteome expression difference between them. Four of the proteins (vimentin, catalase, EpCAM, and caspase 3) that were differentially expressed in PLum-AI cells compared to PLum-AD cells were subjected to biochemical validation by Western blotting. Biological process gene ontology (GO) analysis of the differentially expressed proteins demonstrated enrichment of biological functions and pathways in PLum-AI cells that are central to PI3 kinase and androgen receptor pathways. Besides, other relevant biological processes that are enriched in PLum-AI cells included cell adhesion and cell migration processes, cell and DNA damage, apoptosis, and cell cycle regulation. Conclusions: Our protein expression analysis of a murine in vitro model of PC progression identified differential protein spots that denote this progression and that comprise high-potential targets for early treatment of PC with a personalized patient-specific approach. Efforts are underway to functionally assess the potential roles of these proteins as therapeutic targets for PC progression. Full article
(This article belongs to the Special Issue Proteomics and Personalized Medicine)
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Review

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15 pages, 1036 KiB  
Review
Contribution of Multiplex Immunoassays to Rheumatoid Arthritis Management: From Biomarker Discovery to Personalized Medicine
by Carlos M. Laborde, Patricia Castro-Santos and Roberto Díaz-Peña
J. Pers. Med. 2020, 10(4), 202; https://doi.org/10.3390/jpm10040202 - 30 Oct 2020
Cited by 10 | Viewed by 3626
Abstract
Rheumatoid arthritis (RA) is a multifactorial, inflammatory and progressive autoimmune disease that affects approximately 1% of the population worldwide. RA primarily involves the joints and causes local inflammation and cartilage destruction. Immediate and effective therapies are crucial to control inflammation and prevent deterioration, [...] Read more.
Rheumatoid arthritis (RA) is a multifactorial, inflammatory and progressive autoimmune disease that affects approximately 1% of the population worldwide. RA primarily involves the joints and causes local inflammation and cartilage destruction. Immediate and effective therapies are crucial to control inflammation and prevent deterioration, functional disability and unfavourable progression in RA patients. Thus, early diagnosis is critical to prevent joint damage and physical disability, increasing the chance of achieving remission. A large number of biomarkers have been investigated in RA, although only a few have made it through the discovery and validation phases and reached the clinic. The single biomarker approach mostly used in clinical laboratories is not sufficiently accurate due to its low sensitivity and specificity. Multiplex immunoassays could provide a more complete picture of the disease and the pathways involved. In this review, we discuss the latest proposed protein biomarkers and the advantages of using protein panels for the clinical management of RA. Simultaneous analysis of multiple proteins could yield biomarker signatures of RA subtypes to enable patients to benefit from personalized medicine. Full article
(This article belongs to the Special Issue Proteomics and Personalized Medicine)
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12 pages, 1384 KiB  
Review
Implementation of MALDI Mass Spectrometry Imaging in Cancer Proteomics Research: Applications and Challenges
by Eline Berghmans, Kurt Boonen, Evelyne Maes, Inge Mertens, Patrick Pauwels and Geert Baggerman
J. Pers. Med. 2020, 10(2), 54; https://doi.org/10.3390/jpm10020054 - 22 Jun 2020
Cited by 17 | Viewed by 5063
Abstract
Studying the proteome–the entire set of proteins in cells, tissues, organs and body fluids—is of great relevance in cancer research, as differential forms of proteins are expressed in response to specific intrinsic and extrinsic signals. Discovering protein signatures/pathways responsible for cancer transformation may [...] Read more.
Studying the proteome–the entire set of proteins in cells, tissues, organs and body fluids—is of great relevance in cancer research, as differential forms of proteins are expressed in response to specific intrinsic and extrinsic signals. Discovering protein signatures/pathways responsible for cancer transformation may lead to a better understanding of tumor biology and to a more effective diagnosis, prognosis, recurrence and response to therapy. Moreover, proteins can act as a biomarker or potential drug targets. Hence, it is of major importance to implement proteomic, particularly mass spectrometric, approaches in cancer research, to provide new crucial insights into tumor biology. Recently, mass spectrometry imaging (MSI) approaches were implemented in cancer research, to provide individual molecular characteristics of each individual tumor while retaining molecular spatial distribution, essential in the context of personalized disease management and medicine. Full article
(This article belongs to the Special Issue Proteomics and Personalized Medicine)
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