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Cancers
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Plasma Proteomics Analysis Predicts Cancer Biomarkers
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Plasma Proteomics Analysis Predicts Cancer Biomarkers

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Methods and Technologies Development".

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 4012

Special Issue Editors

Dr. Seong Beom Ahn

E-Mail Website
Guest Editor
Macquarie Medical School, Macquarie University, Macquarie Park, NSW 2109, Australia
Interests: colorectal cancer; proteomics; mass spectrometry; antibody; plasma biomarker; proteins; cancer patient survival; tumor recurrence/relapse; mold biotoxin; chronic inflammatory response syndrome (CIRS)
Special Issues, Collections and Topics in MDPI journals
Dr. Abidali Mohamedali

E-Mail Website
Guest Editor
Department of Molecular Sciences, School of Life Sciences, Macquarie University, Macquarie, NSW 2109, Australia
Interests: colorectal cancer; proteomics; mass spectrometry; antibody; plasma biomarker; proteins; cancer patient survival; tumor recurrence/relapse; mold biotoxin; chronic inflammatory response syndrome (CIRS)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Cancer continues to pose a significant challenge to global health, and thus its early detection and accurate diagnosis are crucial to providing effective treatment and enhanced patient outcomes. In recent years, plasma proteomics has emerged as a promising approach to identifying cancer biomarkers, which are specific molecular signatures that can indicate the presence, stage, or prognosis of cancer, and are suitable for screening, monitoring, and personalized medicine.

This Special Issue aims to showcase the latest advancements in the field of plasma proteomics and its potential to predict cancer biomarkers. We invite researchers and experts from various disciplines, including proteomics (on both mass spectrometry-based and antibody-based technologies), cancer biology, oncology, bioinformatics, and translational medicine, to contribute their original research articles, reviews, and perspectives on this topic.

We welcome contributions that attend the following areas of interest:

  1. Novel plasma proteomics techniques and technologies for cancer biomarker discovery;
  2. Identification and validation of plasma-based biomarkers for various types of cancers;
  3. Role of plasma proteomics analysis in early cancer detection and diagnosis;
  4. Functional characterization of plasma-derived cancer biomarkers;
  5. Translational applications of plasma proteomics in cancer management, including prognosis, prediction, and therapeutic monitoring;
  6. Integration of plasma proteomics data with other omics data for multi-dimensional cancer biomarker analysis;
  7. Bioinformatics and computational approaches for data analysis and interpretation in plasma proteomics-based cancer biomarker research;
  8. Challenges and opportunities in the field of plasma proteomics analysis for predicting cancer biomarkers;
  9. Clinical implementation and commercialization of plasma proteomics-based cancer biomarkers;
  10. Future directions and perspectives in the field of plasma proteomics analysis for cancer biomarker prediction.

We hope this Special Issue will provide a comprehensive platform for researchers to share their latest findings, insights, and perspectives on the exciting field of plasma proteomics analysis and its potential to predict cancer biomarkers.

Dr. Seong Beom Ahn
Dr. Abidali Mohamedali
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 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. Cancers 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 2900 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

  • plasma proteomics
  • mass spectrometry-based technologies
  • antibody-based technologies
  • cancer biomarkers
  • cancer biology
  • diagnostic makers
  • prognostic makers
  • predictive analysis
  • early detection
  • bioinformatics

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Published Papers (2 papers)

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22 pages, 2813 KiB  
Article
A Proteomic Examination of Plasma Extracellular Vesicles Across Colorectal Cancer Stages Uncovers Biological Insights That Potentially Improve Prognosis
by Abidali Mohamedali, Benjamin Heng, Ardeshir Amirkhani, Shivani Krishnamurthy, David Cantor, Peter Jun Myung Lee, Joo-Shik Shin, Michael Solomon, Gilles J. Guillemin, Mark S. Baker and Seong Beom Ahn
Cancers 2024, 16(24), 4259; https://doi.org/10.3390/cancers16244259 - 21 Dec 2024
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Abstract
Background: Recent advancements in understanding plasma extracellular vesicles (EVs) and their role in disease biology have provided additional unique insights into the study of Colorectal Cancer (CRC). Methods: This study aimed to gain biological insights into disease progression from plasma-derived extracellular vesicle proteomic [...] Read more.
Background: Recent advancements in understanding plasma extracellular vesicles (EVs) and their role in disease biology have provided additional unique insights into the study of Colorectal Cancer (CRC). Methods: This study aimed to gain biological insights into disease progression from plasma-derived extracellular vesicle proteomic profiles of 80 patients (20 from each CRC stage I–IV) against 20 healthy age- and sex-matched controls using a high-resolution SWATH-MS proteomics with a reproducible centrifugation method to isolate plasma EVs. Results: We applied the High-Stringency Human Proteome Project (HPP) guidelines for SWATH-MS analysis, which refined our initial EV protein identification from 1362 proteins (10,993 peptides) to a more reliable and confident subset of 853 proteins (6231 peptides). In early-stage CRC, we identified 11 plasma EV proteins with differential expression between patients and healthy controls (three up-regulated and eight down-regulated), many of which are involved in key cancer hallmarks. Additionally, within the same cohort, we analysed EV proteins associated with tumour recurrence to identify potential prognostic indicators for CRC. A subset of up-regulated proteins associated with extracellular vesicle formation (GDI1, NSF, and TMED9) and the down-regulation of TSG101 suggest that micro-metastasis may have occurred earlier than previously anticipated. Discussion: By employing stringent proteomic analysis and a robust SWATH-MS approach, we identified dysregulated EV proteins that potentially indicate early-stage CRC and predict recurrence risk, including proteins involved in metabolism, cytoskeletal remodelling, and immune response. While our findings underline discrepancies with other studies due to differing isolation and stringency parameters, they provide valuable insights into the complexity of the EV proteome, emphasising the need for standardised protocols and larger, well-controlled studies to validate potential biomarkers. Full article
(This article belongs to the Special Issue Plasma Proteomics Analysis Predicts Cancer Biomarkers)
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22 pages, 3044 KiB  
Systematic Review
Deciphering Urogenital Cancers through Proteomic Biomarkers: A Systematic Review and Meta-Analysis
by Aafaque Ahmad Khan, Nahad Al-Mahrouqi, Aida Al-Yahyaee, Hasan Al-Sayegh, Munjid Al-Harthy and Shoaib Al-Zadjali
Cancers 2024, 16(1), 22; https://doi.org/10.3390/cancers16010022 - 20 Dec 2023
Cited by 2 | Viewed by 1884
Abstract
Urogenital cancers, which include prostate, bladder, and kidney malignancies, exert a substantial impact on global cancer-related morbidity and mortality. Proteomic biomarkers, emerging as valuable tools, aim to enhance early detection, prognostic accuracy, and the development of personalized therapeutic strategies. This study undertook a [...] Read more.
Urogenital cancers, which include prostate, bladder, and kidney malignancies, exert a substantial impact on global cancer-related morbidity and mortality. Proteomic biomarkers, emerging as valuable tools, aim to enhance early detection, prognostic accuracy, and the development of personalized therapeutic strategies. This study undertook a comprehensive systematic review and meta-analysis of the existing literature investigating the role and potential of proteomic biomarkers in plasma, tissue, and urine samples in urogenital cancers. Our extensive search across several databases identified 1879 differentially expressed proteins from 37 studies, signifying their potential as unique biomarkers for these cancers. A meta-analysis of the significantly differentially expressed proteins was executed, accentuating the findings through visually intuitive volcano plots. A functional enrichment analysis unveiled their significant involvement in diverse biological processes, including signal transduction, immune response, cell communication, and cell growth. A pathway analysis highlighted the participation of key pathways such as the nectin adhesion pathway, TRAIL signaling pathway, and integrin signaling pathways. These findings not only pave the way for future investigations into early detection and targeted therapeutic approaches but also underscore the fundamental role of proteomics in advancing our understanding of the molecular mechanisms underpinning urogenital cancer pathogenesis. Ultimately, these findings hold remarkable potential to significantly enhance patient care and improve clinical outcomes. Full article
(This article belongs to the Special Issue Plasma Proteomics Analysis Predicts Cancer Biomarkers)
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