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Proteomics Progress in Cancer Research
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Proteomics Progress in Cancer Research

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (1 March 2022) | Viewed by 7457

Special Issue Editors

Dr. Francesca Raimondo

E-Mail Website
Guest Editor
School of Medicine and Surgery, University Milan Bicocca, 20900 Monza, Italy
Interests: extracellular vesicles; exosomes; urine; biological fluids; membrane proteins; renal cell carcinoma; renal diseases; proteomics; lipidomics; glycoproteomics
Prof. Dr. Marina Pitto

E-Mail Website
Guest Editor
School of Medicine and Surgery, University Milan Bicocca, 20900 Monza, Italy
Interests: extracellular vesicles; exosomes; biological fluids; cancer; diabetes; renal diseases; proteomics; membrane lipids; membrane proteins; plasma membrane domains

Special Issue Information

Dear Colleagues,

Proteomics has shown to be a promising approach for understanding the etiopathogenesis of cancers, and for identifying potential biomarkers and therapeutic targets. Proteomic approaches allow an all-round study of proteins considering not only their quantitative expression but also the complex post-translational modifications (glycosylation, phosphorylation, etc.) and the protein–protein interactions, fundamental for functional understandings. Proteomics provides a variety of technologies that can be applied to different type of samples, from patient tissues to biological fluids and from cultured cells to animal models, through to extracellular vesicles and the tumor microenvironment. The combined study of different samples may allow the improvement of the knowledge of the dynamic biology of a specific cancer system. Moreover, the integration of proteomics into multi-omics studies could open the way for the rapid translation of laboratory discoveries to the bedside, having a positive impact on the clinical management and outcomes of cancer patients.

The present Special Issue on “Proteomics Progress in Cancer Research” welcomes articles reporting original discoveries, technical improvements and reviews in the field of cancer proteomics research, with an emphasis on the use of different sample types and data integration.

Dr. Francesca Raimondo
Prof. Marina Pitto
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. Molecules is an international peer-reviewed open access semimonthly 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

  • biological fluids
  • cancer
  • cultured cells
  • extracellular vesicles
  • multi-omics
  • post-translational modifications
  • proteomics
  • tissues
  • tumor microenvironment

Published Papers (2 papers)

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Research

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24 pages, 2936 KiB  
Article
Transcriptomic and Proteomic Analysis of Clear Cell Foci (CCF) in the Human Non-Cirrhotic Liver Identifies Several Differentially Expressed Genes and Proteins with Functions in Cancer Cell Biology and Glycogen Metabolism
by Christoph Metzendorf, Katharina Wineberger, Jenny Rausch, Antonio Cigliano, Kristin Peters, Baodong Sun, Daniela Mennerich, Thomas Kietzmann, Diego F. Calvisi, Frank Dombrowski and Silvia Ribback
Molecules 2020, 25(18), 4141; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25184141 - 10 Sep 2020
Cited by 3 | Viewed by 2875
Abstract
Clear cell foci (CCF) of the liver are considered to be pre-neoplastic lesions of hepatocellular adenomas and carcinomas. They are hallmarked by glycogen overload and activation of AKT (v-akt murine thymoma viral oncogene homolog)/mTOR (mammalian target of rapamycin)-signaling. Here, we report the transcriptome [...] Read more.
Clear cell foci (CCF) of the liver are considered to be pre-neoplastic lesions of hepatocellular adenomas and carcinomas. They are hallmarked by glycogen overload and activation of AKT (v-akt murine thymoma viral oncogene homolog)/mTOR (mammalian target of rapamycin)-signaling. Here, we report the transcriptome and proteome of CCF extracted from human liver biopsies by laser capture microdissection. We found 14 genes and 22 proteins differentially expressed in CCF and the majority of these were expressed at lower levels in CCF. Using immunohistochemistry, the reduced expressions of STBD1 (starch-binding domain-containing protein 1), USP28 (ubiquitin-specific peptidase 28), monad/WDR92 (WD repeat domain 92), CYB5B (Cytochrome b5 type B), and HSPE1 (10 kDa heat shock protein, mitochondrial) were validated in CCF in independent specimens. Knockout of Stbd1, the gene coding for Starch-binding domain-containing protein 1, in mice did not have a significant effect on liver glycogen levels, indicating that additional factors are required for glycogen overload in CCF. Usp28 knockout mice did not show changes in glycogen storage in diethylnitrosamine-induced liver carcinoma, demonstrating that CCF are distinct from this type of cancer model, despite the decreased USP28 expression. Moreover, our data indicates that decreased USP28 expression is a novel factor contributing to the pre-neoplastic character of CCF. In summary, our work identifies several novel and unexpected candidates that are differentially expressed in CCF and that have functions in glycogen metabolism and tumorigenesis. Full article
(This article belongs to the Special Issue Proteomics Progress in Cancer Research)
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Review

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23 pages, 826 KiB  
Review
Quantitative Mass Spectrometry-Based Proteomics for Biomarker Development in Ovarian Cancer
by Joohyun Ryu and Stefani N. Thomas
Molecules 2021, 26(9), 2674; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26092674 - 03 May 2021
Cited by 15 | Viewed by 4125
Abstract
Ovarian cancer is the most lethal gynecologic malignancy among women. Approximately 70–80% of patients with advanced ovarian cancer experience relapse within five years and develop platinum-resistance. The short life expectancy of patients with platinum-resistant or platinum-refractory disease underscores the need to develop new [...] Read more.
Ovarian cancer is the most lethal gynecologic malignancy among women. Approximately 70–80% of patients with advanced ovarian cancer experience relapse within five years and develop platinum-resistance. The short life expectancy of patients with platinum-resistant or platinum-refractory disease underscores the need to develop new and more effective treatment strategies. Early detection is a critical step in mitigating the risk of disease progression from early to an advanced stage disease, and protein biomarkers have an integral role in this process. The best biological diagnostic tool for ovarian cancer will likely be a combination of biomarkers. Targeted proteomics methods, including mass spectrometry-based approaches, have emerged as robust methods that can address the chasm between initial biomarker discovery and the successful verification and validation of these biomarkers enabling their clinical translation due to the robust sensitivity, specificity, and reproducibility of these versatile methods. In this review, we provide background information on the fundamental principles of biomarkers and the need for improved treatment strategies in ovarian cancer. We also provide insight into the ways in which mass spectrometry-based targeted proteomics approaches can provide greatly needed solutions to many of the challenges related to ovarian cancer biomarker development. Full article
(This article belongs to the Special Issue Proteomics Progress in Cancer Research)
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