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Cell-Free DNA as Prognostic and Predictive Biomarker in Solid Cancers...
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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: 1 September 2025 | Viewed by 7823

Special Issue Editors

Dr. Edoardo Francini

E-Mail Website
Guest Editor
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
Special Issues, Collections and Topics in MDPI journals
Dr. Pier Vitale Nuzzo

E-Mail Website
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
Special Issues, Collections and Topics in MDPI journals
Dr. Giuseppe Fanelli

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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
Special Issues, Collections and Topics in MDPI journals

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 (6 papers)

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Research

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13 pages, 1141 KiB  
Article
Multi-Cancer Genome Profiling for Neurotrophic Tropomyosin Receptor Kinase (NTRK) Fusion Genes: Analysis of Profiling Database of 88,688 Tumors
by Hinano Nishikubo, Kyoka Kawabata, Saki Kanei, Rika Aoyama, Dongheng Ma, Tomoya Sano, Daiki Imanishi, Takashi Sakuma, Koji Maruo, Canfeng Fan, Yurie Yamamoto and Masakazu Yashiro
Cancers 2025, 17(13), 2250; https://doi.org/10.3390/cancers17132250 - 4 Jul 2025
Viewed by 434
Abstract
Background/Objectives: The neurotrophic tropomyosin receptor kinase (NTRK) genes NTRK1, NTRK2, and NTRK3 encode tyrosine kinase receptors, and their fusion genes are known as the oncogenic driver genes for cancer. This study aimed to compare the diagnostic ability of NTRK fusion [...] Read more.
Background/Objectives: The neurotrophic tropomyosin receptor kinase (NTRK) genes NTRK1, NTRK2, and NTRK3 encode tyrosine kinase receptors, and their fusion genes are known as the oncogenic driver genes for cancer. This study aimed to compare the diagnostic ability of NTRK fusion among five types of multi-cancer genome profiling tests (multi-CGP tests) and determine a useful multi-CGP test for NTRK fusion, recorded in the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) database in Japan. This study aimed to compare the diagnostic results for NTRK fusions among the five different CGP tests. Methods: A total of 88,688 tumor cases were enrolled in the C-CAT profiling database from 2019 to 2024. The detection frequency of NTRK fusion genes was compared to the results for five multi-CGP tests: NCC Oncopanel, FoundationOne CDx (F1), FoundationOne Liquid (F1L), GenMineTOP (GMT), and Guardant360. Results: NTRK fusion genes were detected in 175 (0.20%) of the 88,688 total cases. GMT, which is equipped with RNA sequencing function, frequently detected NTRK fusion genes (20 of 2926 cases; 0.68%) in comparison with the other four multi-CGP tests that do not have RNA sequencing analysis. GMT showed significantly (p < 0.05) higher diagnostic ability for NTRK fusions compared with the other four multi-CGP tests. Especially, NTRK2 fusion was significantly (p < 0.001) more highly determined by GMT than it was by the other four multi-CGP tests. The detection rates for FGFR1 and FGFR3 were significantly higher in GMT than in other multi-CGP tests. In contrast, the detection rates of the ALK and RET fusion genes were significantly higher in F1L. Conclusions: GMT, which is equipped with RNA sequencing analysis, might show a useful diagnostic ability for NTRK fusions, especially for NTRK2 fusion genes. Full article
(This article belongs to the Special Issue Cell-Free DNA as Prognostic and Predictive Biomarker in Solid Cancers (2nd Edition))
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Review

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28 pages, 845 KiB  
Review
Circulating Tumor DNA in Prostate Cancer: A Dual Perspective on Early Detection and Advanced Disease Management
by Stepan A. Kopytov, Guzel R. Sagitova, Dmitry Y. Guschin, Vera S. Egorova, Andrei V. Zvyagin and Alexey S. Rzhevskiy
Cancers 2025, 17(15), 2589; https://doi.org/10.3390/cancers17152589 - 6 Aug 2025
Viewed by 662
Abstract
Prostate cancer (PC) remains a leading cause of malignancy in men worldwide, with current diagnostic methods such as prostate-specific antigen (PSA) testing and tissue biopsies facing limitations in specificity, invasiveness, and ability to capture tumor heterogeneity. Liquid biopsy, especially analysis of circulating tumor [...] Read more.
Prostate cancer (PC) remains a leading cause of malignancy in men worldwide, with current diagnostic methods such as prostate-specific antigen (PSA) testing and tissue biopsies facing limitations in specificity, invasiveness, and ability to capture tumor heterogeneity. Liquid biopsy, especially analysis of circulating tumor DNA (ctDNA), has emerged as a transformative tool for non-invasive detection, real-time monitoring, and treatment selection for PC. This review examines the role of ctDNA in both localized and metastatic PCs, focusing on its utility in early detection, risk stratification, therapy selection, and post-treatment monitoring. In localized PC, ctDNA-based biomarkers, including ctDNA fraction, methylation patterns, fragmentation profiles, and mutations, demonstrate promise in improving diagnostic accuracy and predicting disease recurrence. For metastatic PC, ctDNA analysis provides insights into tumor burden, genomic alterations, and resistance mechanisms, enabling immediate assessment of treatment response and guiding therapeutic decisions. Despite challenges such as the low ctDNA abundance in early-stage disease and the need for standardized protocols, advances in sequencing technologies and multimodal approaches enhance the clinical applicability of ctDNA. Integrating ctDNA with imaging and traditional biomarkers offers a pathway to precision oncology, ultimately improving outcomes. This review underscores the potential of ctDNA to redefine PC management while addressing current limitations and future directions for research and clinical implementation. Full article
(This article belongs to the Special Issue Cell-Free DNA as Prognostic and Predictive Biomarker in Solid Cancers (2nd Edition))
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21 pages, 2238 KiB  
Review
Cell-Free DNA as a Prognostic Biomarker in Oral Carcinogenesis and Oral Squamous Cell Carcinoma: A Translational Perspective
by Pietro Rigotti, Alessandro Polizzi, Vincenzo Quinzi, Andrea Blasi, Teresa Lombardi, Eleonora Lo Muzio and Gaetano Isola
Cancers 2025, 17(14), 2366; https://doi.org/10.3390/cancers17142366 - 16 Jul 2025
Viewed by 607
Abstract
Oral squamous cell carcinoma (OSCC) remains one of the most common malignancies in the head and neck region, often preceded by a spectrum of oral potentially malignant disorders (OPMDs). Despite advances in diagnostic methods, reliable and non-invasive biomarkers for early detection and prognostic [...] Read more.
Oral squamous cell carcinoma (OSCC) remains one of the most common malignancies in the head and neck region, often preceded by a spectrum of oral potentially malignant disorders (OPMDs). Despite advances in diagnostic methods, reliable and non-invasive biomarkers for early detection and prognostic stratification are still lacking. In recent years, circulating cell-free DNA (cfDNA) has emerged as a promising liquid biopsy tool in several solid tumors, offering insights into tumor burden, heterogeneity, and molecular dynamics. However, its application in oral oncology remains underexplored. This study aims to review and discuss the current evidence on cfDNA quantification and mutation analysis (including TP53, NOTCH1, and EGFR) in patients with OPMDs and OSCC. Particular attention is given to cfDNA fragmentation patterns, methylation signatures, and tumor-specific mutations as prognostic and predictive biomarkers. Moreover, we highlight the challenges in standardizing pre-analytical and analytical workflows in oral cancer patients and explore the potential role of cfDNA in monitoring oral carcinogenesis. Understanding cfDNA dynamics in the oral cavity might offer a novel, minimally invasive strategy to improve early diagnosis, risk assessment, and treatment decision-making in oral oncology. Full article
(This article belongs to the Special Issue Cell-Free DNA as Prognostic and Predictive Biomarker in Solid Cancers (2nd Edition))
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23 pages, 524 KiB  
Review
A Narrative Review of the Role of Non-Viral Circulating Tumor DNA Profiling in Predicting the Treatment Response and Recurrence in Head and Neck Squamous Cell Carcinoma
by Ugur Gezer, Rasim Meral, Emre Özgür, Ebru. E. Yörüker, Abel Bronkhorst and Stefan Holdenrieder
Cancers 2025, 17(14), 2279; https://doi.org/10.3390/cancers17142279 - 9 Jul 2025
Viewed by 764
Abstract
Head and neck squamous cell carcinomas (HNSCCs) that develop from the mucosal epithelium in the oral cavity, pharynx, and larynx are a heterogeneous group of malignant tumors. A lack of appropriate screening and diagnostic methods leads to late diagnoses, with the majority of [...] Read more.
Head and neck squamous cell carcinomas (HNSCCs) that develop from the mucosal epithelium in the oral cavity, pharynx, and larynx are a heterogeneous group of malignant tumors. A lack of appropriate screening and diagnostic methods leads to late diagnoses, with the majority of patients having locally advanced disease, which is associated with a high risk of local recurrence and a poor prognosis and is usually treated with combination therapies. Biomarkers for predicting the therapy response and risk of recurrence in HNSCC patients are urgently needed. Liquid biopsy, e.g., the profiling of circulating biomarkers in bodily fluids, is a promising approach with increasing utility in the early detection and diagnosis of cancer, monitoring cancer progression, patient stratification and treatment selection, detecting minimal residual disease (MRD), and predicting recurrence across different cancer types, including HNSCC. Among liquid biomarkers, circulating tumor DNA (ctDNA), which is based on detecting tumor-specific mutations, insertions/deletions, copy number alterations, and methylation, is the most promising transformative tool in cancer management and personalized cancer treatment. In this review, we provide an update of recent data on the role of non-viral ctDNA in the management of HNSCC patients. Accumulating data suggests the enormous potential of ctDNA profiling by serial sampling during and after definitive therapy in detecting MRD and predicting recurrence in HNSSC patients treated with a single treatment modality (surgery or radiotherapy) or with combination therapies, including immune-checkpoint-inhibitor-based immunotherapy. By incorporating the latest immunotherapy trials and organizing the data by the treatment modality, this review offers a novel perspective not found in previous surveys. Full article
(This article belongs to the Special Issue Cell-Free DNA as Prognostic and Predictive Biomarker in Solid Cancers (2nd Edition))
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19 pages, 806 KiB  
Review
Unlocking the Potential of ctDNA in Sarcomas: A Review of Recent Advances
by Sahana Aiyer, Tae-Hee Kim, Katharine Collier, Raphael Pollock, Claire Verschraegen, Daniel G. Stover and Gabriel Tinoco
Cancers 2025, 17(6), 1040; https://doi.org/10.3390/cancers17061040 - 20 Mar 2025
Cited by 2 | Viewed by 1420
Abstract
Soft tissue sarcomas (STSs) constitute a group of tumors with heterogeneous alterations and different biological behavior. Genetic profiling techniques have immense potential to revolutionize sarcoma classification, detection, and treatment. Cell-free DNA (cfDNA) analysis offers a minimally invasive approach to profiling tumor alterations, including [...] Read more.
Soft tissue sarcomas (STSs) constitute a group of tumors with heterogeneous alterations and different biological behavior. Genetic profiling techniques have immense potential to revolutionize sarcoma classification, detection, and treatment. Cell-free DNA (cfDNA) analysis offers a minimally invasive approach to profiling tumor alterations, including tracking specific mutations or targeted panels of cancer-related genes via DNA sequencing methods. Circulating tumor DNA (ctDNA) platforms have gained popularity as a noninvasive alternative to tissue biopsies, offering a less invasive approach to tumor profiling. Nonetheless, ctDNA profiling in concordance with standard solid tumor comprehensive genomic profiling (CGP) is poorly characterized for STSs. Ultra-low-pass whole-genome sequencing and whole exome sequencing of cfDNA have yet to be fully leveraged in patients with sarcomas. This comprehensive review provides an overview of the application of ctDNA in STSs. Full article
(This article belongs to the Special Issue Cell-Free DNA as Prognostic and Predictive Biomarker in Solid Cancers (2nd Edition))
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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
Cited by 2 | Viewed by 3083
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
(This article belongs to the Special Issue Cell-Free DNA as Prognostic and Predictive Biomarker in Solid Cancers (2nd Edition))
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