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Special Issue "Proteomics and Nucleotide Profiling as Tools for Biomarker and Drug Target 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: 15 February 2020.

Special Issue Editors

Prof. Dr. Bent Honoré
E-Mail Website
Guest Editor
1. Department of Biomedicine, Aarhus University, Aarhus, Denmark;
2. Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
Interests: discovery based and targeted proteomics; tandem mass spectrometry; protein biomarkers; lymphoma; eye diseases; cardiovascular diseases
Prof. Dr. Gregory Edward Rice
E-Mail
Guest Editor
Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
Interests: in vitro diagnostics; endogenous nanoparticles; miRNA; biomarker discovery; complications of pregnancy; gynaecological oncology; research quality management systems
Prof. Dr. Henrik Vorum
E-Mail Website
Guest Editor
1. Department of Clinical Medicine, Aalborg University, Aalborg, Denmark;
2. Department of Ophthalmology, Aalborg University Hospital, Aalborg, Denmark
Interests: ocular proteomics; ophthalmology; biomarkers (diagnostic, prognostic, predictive, etc.); proteomics methods (2D-PAGE, LC-MS, protein arrays); discovery based proteomics; drug targets; bioinformatics

Special Issue Information

Dear Colleagues,

Separate developments of a wide variety of techniques including two-dimensional gel electrophoresis (2D-PAGE), mass spectrometry (MS), construction of databases with structural information as well as the development of software applications and computer science formed the basis for the field of proteomics some decades ago. The field has shown tremendous advancement ever since, especially more recently. Proteins originate from protein-coding RNA. More recently, non-coding RNAs have been shown to be important regulators of cell function, biomarkers of pathology and as putative clinical interventions.

This Special Issue addresses the challenges in the application of proteomic analysis and nucleotide profiling to support clinical decisions based on the mapping of disease-associated protein and nucleotide changes that may highlight protein and nucleotide candidates as biomarkers or drug targets. Challenges include the establishment of protocols to reliably prepare proteins or nucleotides from a variety of sample sources including cell preparations, frozen solid tumours or formalin-fixed paraffin-embedded (FFPE) tissue to liquids like plasma or cerebrospinal fluid that may each present heterogeneity or a high dynamic range of protein concentrations, different posttranslational modifications, etc. Descriptions of efforts to address such issues as well as technological developments and advances in software applications are highly welcome.

This Special Issue calls for original research manuscripts, communications and reviews that describe the current knowledge and future perspectives in the development of proteomics and nucleotide-based techniques to reveal candidate biomarkers or drug targets for diseases. Topics include but are not limited to the keywords below.

Prof. Dr. Bent Honoré
Prof. Dr. Gregory Edward Rice
Prof. Dr. Henrik Vorum
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 papers will be 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

  • Sample preparation (frozen tissue, FFPE tissue, cells, plasma, CSF, urine, etc.)
  • Proteomic methods (2D-PAGE, LC-MS, protein arrays)
  • Discovery-based and targeted proteomics
  • SWATH (sequential windowed acquisition of all theoretical mass spectra) MS
  • Biomarkers (diagnostic, prognostic, predictive, etc.)
  • Drug targets
  • Bioinformatics
  • miRNA
  • aptamers
  • nanoparticle methods

Published Papers (1 paper)

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Research

Open AccessArticle
Gel-Based Proteomics of Clinical Samples Identifies Potential Serological Biomarkers for Early Detection of Colorectal Cancer
Int. J. Mol. Sci. 2019, 20(23), 6082; https://doi.org/10.3390/ijms20236082 - 02 Dec 2019
Abstract
The burden of colorectal cancer (CRC) is considerable—approximately 1.8 million people are diagnosed each year with CRC and of these about half will succumb to the disease. In the case of CRC, there is strong evidence that an early diagnosis leads to a [...] Read more.
The burden of colorectal cancer (CRC) is considerable—approximately 1.8 million people are diagnosed each year with CRC and of these about half will succumb to the disease. In the case of CRC, there is strong evidence that an early diagnosis leads to a better prognosis, with metastatic CRC having a 5-year survival that is only slightly greater than 10% compared with up to 90% for stage I CRC. Clearly, biomarkers for the early detection of CRC would have a major clinical impact. We implemented a coherent gel-based proteomics biomarker discovery platform for the identification of clinically useful biomarkers for the early detection of CRC. Potential protein biomarkers were identified by a 2D gel-based analysis of a cohort composed of 128 CRC and site-matched normal tissue biopsies. Potential biomarkers were prioritized and assays to quantitatively measure plasma expression of the candidate biomarkers were developed. Those biomarkers that fulfilled the preset criteria for technical validity were validated in a case-control set of plasma samples, including 70 patients with CRC, adenomas, or non-cancer diseases and healthy individuals in each group. We identified 63 consistently upregulated polypeptides (factor of four-fold or more) in our proteomics analysis. We selected 10 out of these 63 upregulated polypeptides, and established assays to measure the concentration of each one of the ten biomarkers in plasma samples. Biomarker levels were analyzed in plasma samples from healthy individuals, individuals with adenomas, CRC patients, and patients with non-cancer diseases and we identified one protein, tropomyosin 3 (Tpm3) that could discriminate CRC at a significant level (p = 0.0146). Our results suggest that at least one of the identified proteins, Tpm3, could be used as a biomarker in the early detection of CRC, and further studies should provide unequivocal evidence for the real-life clinical validity and usefulness of Tpm3. Full article
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