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Cancers
Special Issues
Decoding Cancer Signals Using Liquid Biopsy
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Decoding Cancer Signals Using Liquid Biopsy

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Cancer Causes, Screening and Diagnosis".

Deadline for manuscript submissions: 5 August 2024 | Viewed by 4991

Special Issue Editors

Dr. Fatima Shadma

E-Mail Website
Guest Editor
1. Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia
2. School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2031, Australia
3. School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
Interests: glioblastoma; liquid biopsy, gene sequencing, cancer biology, cell signaling; stem cells
Dr. Fatemeh Vafaee

E-Mail Website
Guest Editor
1. School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2031, Australia
2. UNSW Data Science Hub, University of New South Wales, Sydney, NSW 2031, Australia
Interests: artificial intelligence; machine learning; biomarker discovery

Special Issue Information

Dear Colleagues,

Liquid biopsy is revolutionizing oncology practice as a minimally invasive and easily repeatable way to detect cancer-associated changes in the genome, transcriptome, epigenome, and proteome. These advancements provide tools to understand cancer biology, inform clinical decisions and monitor treatment responses.

We welcome authors to contribute articles for this Special Issue that highlight the recent and upcoming advancements in the uses of liquid biopsies in oncology treatments and cancer care. Articles may address any single circulating analyte or multi-analyte approach using any biological fluid, such as plasma, serum, urine, and cerebrospinal fluid (CSF), among others. We will accept both original research papers outlining breakthrough discoveries and review papers outlining current developments in liquid biopsies.

Dr. Fatima Shadma
Dr. Fatemeh Vafaee
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. 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

  • cancer signals
  • liquid biopsy
  • minimally invasive
  • cancer biology
  • clinical decisions

Published Papers (2 papers)

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Research

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38 pages, 17541 KiB  
Article
Small and Large Extracellular Vesicles Derived from Pleural Mesothelioma Cell Lines Offer Biomarker Potential
by Tamkin Ahmadzada, Abhishek Vijayan, Fatemeh Vafaee, Ali Azimi, Glen Reid, Stephen Clarke, Steven Kao, Georges E. Grau and Elham Hosseini-Beheshti
Cancers 2023, 15(8), 2364; https://doi.org/10.3390/cancers15082364 - 18 Apr 2023
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Abstract
Pleural mesothelioma, previously known as malignant pleural mesothelioma, is an aggressive and fatal cancer of the pleura, with one of the poorest survival rates. Pleural mesothelioma is in urgent clinical need for biomarkers to aid early diagnosis, improve prognostication, and stratify patients for [...] Read more.
Pleural mesothelioma, previously known as malignant pleural mesothelioma, is an aggressive and fatal cancer of the pleura, with one of the poorest survival rates. Pleural mesothelioma is in urgent clinical need for biomarkers to aid early diagnosis, improve prognostication, and stratify patients for treatment. Extracellular vesicles (EVs) have great potential as biomarkers; however, there are limited studies to date on their role in pleural mesothelioma. We conducted a comprehensive proteomic analysis on different EV populations derived from five pleural mesothelioma cell lines and an immortalized control cell line. We characterized three subtypes of EVs (10 K, 18 K, and 100 K), and identified a total of 4054 unique proteins. Major differences were found in the cargo between the three EV subtypes. We show that 10 K EVs were enriched in mitochondrial components and metabolic processes, while 18 K and 100 K EVs were enriched in endoplasmic reticulum stress. We found 46 new cancer-associated proteins for pleural mesothelioma, and the presence of mesothelin and PD-L1/PD-L2 enriched in 100 K and 10 K EV, respectively. We demonstrate that different EV populations derived from pleural mesothelioma cells have unique cancer-specific proteomes and carry oncogenic cargo, which could offer a novel means to extract biomarkers of interest for pleural mesothelioma from liquid biopsies. Full article
(This article belongs to the Special Issue Decoding Cancer Signals Using Liquid Biopsy)
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Review

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24 pages, 1237 KiB  
Review
Biomarker Reproducibility Challenge: A Review of Non-Nucleotide Biomarker Discovery Protocols from Body Fluids in Breast Cancer Diagnosis
by Fatemeh Safari, Cheka Kehelpannala, Azadeh Safarchi, Amani M. Batarseh and Fatemeh Vafaee
Cancers 2023, 15(10), 2780; https://doi.org/10.3390/cancers15102780 - 16 May 2023
Cited by 1 | Viewed by 2541
Abstract
Breast cancer has now become the most commonly diagnosed cancer, accounting for one in eight cancer diagnoses worldwide. Non-invasive diagnostic biomarkers and associated tests are superlative candidates to complement or improve current approaches for screening, early diagnosis, or prognosis of breast cancer. Biomarkers [...] Read more.
Breast cancer has now become the most commonly diagnosed cancer, accounting for one in eight cancer diagnoses worldwide. Non-invasive diagnostic biomarkers and associated tests are superlative candidates to complement or improve current approaches for screening, early diagnosis, or prognosis of breast cancer. Biomarkers detected from body fluids such as blood (serum/plasma), urine, saliva, nipple aspiration fluid, and tears can detect breast cancer at its early stages in a minimally invasive way. The advancements in high-throughput molecular profiling (omics) technologies have opened an unprecedented opportunity for unbiased biomarker detection. However, the irreproducibility of biomarkers and discrepancies of reported markers have remained a major roadblock to clinical implementation, demanding the investigation of contributing factors and the development of standardised biomarker discovery pipelines. A typical biomarker discovery workflow includes pre-analytical, analytical, and post-analytical phases, from sample collection to model development. Variations introduced during these steps impact the data quality and the reproducibility of the findings. Here, we present a comprehensive review of methodological variations in biomarker discovery studies in breast cancer, with a focus on non-nucleotide biomarkers (i.e., proteins, lipids, and metabolites), highlighting the pre-analytical to post-analytical variables, which may affect the accurate identification of biomarkers from body fluids. Full article
(This article belongs to the Special Issue Decoding Cancer Signals Using Liquid Biopsy)
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