Cell-Free DNA as Prognostic and Predictive Biomarker in Solid Cancers (2nd Edition)

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Cancer Biomarkers".

Deadline for manuscript submissions: 31 May 2025 | Viewed by 930

Special Issue Editors


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Department of Experimental and Clinical Medicine, University of Florence, 50121 Florence, Italy
Interests: hormone-sensitive prostate cancer; metastatic castration-resistant prostate cancer; androgen receptor agents; bone health agents; bone metastases; cfDNA; taxanes; biomarkers
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Guest Editor
Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA
Interests: genitourinary malignancies; liquid biopsy; cfDNA; methylated DNA; genetic and epigenetic biomarkers
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Guest Editor
Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
Interests: breast cancer; urogenital cancers; neuropathology; molecular pathology; digital pathology; tumor microenvironment
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Special Issue Information

Dear Colleagues,

This Special Issue is the second edition of the previous one, entitled "Cell-Free DNA as Prognostic and Predictive Biomarker in Solid Cancers" (https://www.mdpi.com/journal/cancers/special_issues/cfDNA_Biomarker).

In recent years, we have witnessed the approval of an increasing number of therapeutic options extending the survival of patients with solid malignancies. However, the selection of the optimal drug, timing, sequencing, and combinations has become increasingly challenging, as the number of genomic, molecular, and clinical biomarkers is still insufficient to effectively personalize treatment. Tailoring patient therapy would allow for maximizing the efficacy of novel agents while avoiding toxicity and the direct and indirect costs of futile treatments. Consequently, there is an urgent need for novel prognostic and predictive biomarkers to guide treatment selection.

In this regard, the analysis of cell-free DNA (cfDNA) derived from body fluids, such as plasma or urine, was recently shown to be a minimally invasive and accurate method of comprehensive tumor genetic and epigenetic profiling, including the profiling of copy number alterations, mutations, and methylation patterns. Furthermore, there is evidence suggesting that both the total quantity of cfDNA in the blood and the estimated tumor-derived fraction of cfDNA could have potential prognostic and predictive value. While tissue biopsies are invasive and impractical to perform on a routine basis, the discovery and validation of genetic or epigenetic biomarkers through cfDNA analysis would allow for advancing precision medicine and facilitating its application in clinical practice.

This Special Issue will highlight the role of cfDNA in the research of novel prognostic and predictive biomarkers for solid malignancies as well as in the monitoring of the courses of these diseases.

Dr. Edoardo Francini
Dr. Pier Vitale Nuzzo
Dr. Giuseppe Fanelli
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

  • cell-free DNA
  • cfDNA
  • solid tumors
  • predictive biomarkers
  • prognostic biomarkers
  • precision medicine
  • treatment personalization

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Published Papers (1 paper)

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Review

20 pages, 1367 KiB  
Review
LINE-1 cfDNA Methylation as an Emerging Biomarker in Solid Cancers
by Ugur Gezer, Emre Özgür, Ebru E. Yörüker, Eleni Polatoglou, Stefan Holdenrieder and Abel Bronkhorst
Cancers 2024, 16(22), 3725; https://doi.org/10.3390/cancers16223725 - 5 Nov 2024
Viewed by 582
Abstract
Epigenetic dysregulation is a hallmark of many human malignancies, with DNA methylation being a primary mechanism influencing gene expression and maintaining genomic stability. Genome-wide hypomethylation, characteristic of many cancers, is partly attributed to the demethylation of repetitive elements, including LINE-1, a prevalent non-LTR [...] Read more.
Epigenetic dysregulation is a hallmark of many human malignancies, with DNA methylation being a primary mechanism influencing gene expression and maintaining genomic stability. Genome-wide hypomethylation, characteristic of many cancers, is partly attributed to the demethylation of repetitive elements, including LINE-1, a prevalent non-LTR retrotransposon. The methylation status of LINE-1 is closely associated with overall genomic methylation levels in tumors. cfDNA comprises extracellular DNA fragments found in bodily fluids such as plasma, serum, and urine, offering a dynamic snapshot of the genetic and epigenetic landscape of tumors. This real-time sampling provides a minimally invasive avenue for cancer diagnostics, prognostics, and monitoring. The methylation status of LINE-1 in cfDNA has emerged as a promising biomarker, with several studies highlighting its potential in diagnosing and predicting outcomes in cancer patients. Recent research also suggests that cfDNA-based LINE-1 methylation analysis could serve as a valuable tool in evaluating the efficacy of cancer therapies, including immunotherapy. The growing clinical significance of cfDNA calls for a closer examination of its components, particularly repetitive elements like LINE-1. Despite their importance, the role of LINE-1 elements in cfDNA has not been thoroughly gauged. We aim to address this gap by reviewing the current literature on LINE-1 cfDNA assays, focusing on their potential applications in diagnostics and disease monitoring. Full article
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