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Cancers
Special Issues
Liquid Biopsy in Cancer 2.0
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Liquid Biopsy in Cancer 2.0

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

Deadline for manuscript submissions: 10 November 2024 | Viewed by 7573

Special Issue Editors

Prof. Dr. Fabio Puglisi

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Guest Editor
1. Department of Medical Oncology, IRCCS, CRO di Aviano, National Cancer Institute, Aviano, Italy
2. Department of Medicine, University of Udine, 33100 Udine, Italy
Interests: breast cancer; translational research; predictive factors; prognostic factors; liquid biopsy
Special Issues, Collections and Topics in MDPI journals
Dr. Lorenzo Gerratana

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Guest Editor
1. Department of Medical Oncology, IRCCS, CRO di Aviano, National Cancer Institute, Aviano, Italy
2. Department of Medicine, University of Udine, 33100 Udine, Italy
Interests: translational trials; breast cancer; ctDNA; CTC; circulating biomarkers; endocrine resistance; DNA repair; clinical methodology
Special Issues, Collections and Topics in MDPI journals
Dr. Linda Cucciniello

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Guest Editor
1. Department of Medical Oncology, IRCCS, CRO di Aviano, National Cancer Institute, Aviano, Italy
2. Department of Medicine, University of Udine, 33100 Udine, Italy
Interests: breast cancer; translational research; ctDNA; circulating biomarkers

Special Issue Information

Dear Colleagues,

This Issue is the second edition of a previous issue on “Liquid Biopsy in Cancer” (https://www.mdpi.com/journal/cancers/special_issues/liquid_biopsy-cancer).

Precision medicine is becoming the new paradigm in healthcare as it enables treatment optimization, potential side-effect reduction, and better resources allocation. Liquid biopsy is the cornerstone of this revolution since it provides real-time prognostic and predictive information for advanced cancer patients, without the analytical and procedural drawbacks of tissue biopsy.

Several technologies are included under the umbrella-term of “liquid biopsy”, each with its strengths and peculiarities. In particular, circulating tumor DNA (ctDNA), together with circulating tumor cells (CTCs), and microvesicles are gaining momentum as promising markers for early disease characterization and longitudinal monitoring for resistance detection.

Given the high profile of the manuscripts received for the Special Issue “Liquid Biopsy in Cancer” and the rapid pace of this constantly developing field, a second edition is launched, with a special focus on its clinical utility and how its deployment will ultimately lead to a growingly cancer care personalization.

Prof. Dr. Fabio Puglisi
Dr. Lorenzo Gerratana
Dr. Linda Cucciniello
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

  • circulating biomarkers
  • clinical utility
  • circulating tumor DNA
  • circulating tumor cells
  • exosomes
  • circulating RNA
  • precision medicine

Published Papers (6 papers)

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Research

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14 pages, 2204 KiB  
Article
TP53 and/or BRCA1 Mutations Based on CtDNA Analysis as Prognostic Biomarkers for Primary Triple-Negative Breast Cancer
by Akiko Arimura, Kazuko Sakai, Kazuhisa Kaneshiro, Takafumi Morisaki, Saori Hayashi, Kimihisa Mizoguchi, Mai Yamada, Masaya Kai, Mayumi Ono, Kazuto Nishio, Masafumi Nakamura and Makoto Kubo
Cancers 2024, 16(6), 1184; https://doi.org/10.3390/cancers16061184 - 18 Mar 2024
Viewed by 747
Abstract
Precise biomarkers for predicting the therapeutic efficacy of molecularly targeted drugs are limited at the protein level; thus, it has been important to broadly scrutinize individual cancer driver gene mutations for effective cancer treatments. Multiplex cancer genome profiling can comprehensively identify gene mutations [...] Read more.
Precise biomarkers for predicting the therapeutic efficacy of molecularly targeted drugs are limited at the protein level; thus, it has been important to broadly scrutinize individual cancer driver gene mutations for effective cancer treatments. Multiplex cancer genome profiling can comprehensively identify gene mutations that are therapeutic targets using next-generation sequencing (NGS). In addition, circulating tumor DNA (ctDNA) is a DNA fragment released into the blood by tumor cell-derived cell death or apoptosis. Liquid biopsy with ctDNA is a novel clinical test for identifying genetic mutations in an entire population noninvasively, in real-time, and heterogeneously. Although there are several reports on ctDNA, fewer have evaluated ctDNA with NGS before an initial treatment for breast cancer patients. Therefore, we examined whether analyzing tumor-associated gene mutations in primary breast cancer based on ctDNA could serve as a biomarker for prognosis and optimal treatment selection. Ninety-five primary breast cancer patients treated at our department from January 2017 to October 2020 were included. Pretreatment plasma samples were subjected to NGS analysis of ctDNA, and correlations with patients’ clinicopathological characteristics were evaluated. Fifty-nine (62.1%) patients were positive for ctDNA. ctDNA tended to be positive in hormone receptor-negative, and TP53 (34%), BRCA1 (20%), and BRCA2 (17%) gene mutations were more frequent. Regarding recurrence-free survival, the prognosis was poor in the TP53 and/or BRCA1 mutation-positive groups, especially in triple-negative breast cancer (TNBC) patients. In conclusion, the results of this study indicate that ctDNA with liquid biopsy could identify the poor prognosis group before treatment among TNBC patients and for those for whom optimal treatment selection is desirable; additionally, optimal treatment could be selected according to the ctDNA analysis results. Full article
(This article belongs to the Special Issue Liquid Biopsy in Cancer 2.0)
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16 pages, 3207 KiB  
Article
Cell-Free DNA Genomic Profiling and Its Clinical Implementation in Advanced Prostate Cancer
by Ivana Bratic Hench, Luca Roma, Floriana Conticelli, Lenard Bubendorf, Byron Calgua, Clémentine Le Magnen, Salvatore Piscuoglio, Mark A. Rubin, Alin Chirindel, Guillaume P. Nicolas, Tatjana Vlajnic, Tobias Zellweger, Arnoud J. Templeton, Frank Stenner, Christian Ruiz, Cyrill Rentsch and Lukas Bubendorf
Cancers 2024, 16(1), 45; https://doi.org/10.3390/cancers16010045 - 21 Dec 2023
Viewed by 1026
Abstract
Most men with prostate cancer (PCa), despite potentially curable localized disease at initial diagnosis, progress to metastatic disease. Despite numerous treatment options, choosing the optimal treatment for individual patients remains challenging. Biomarkers guiding treatment sequences in an advanced setting are lacking. To estimate [...] Read more.
Most men with prostate cancer (PCa), despite potentially curable localized disease at initial diagnosis, progress to metastatic disease. Despite numerous treatment options, choosing the optimal treatment for individual patients remains challenging. Biomarkers guiding treatment sequences in an advanced setting are lacking. To estimate the diagnostic potential of liquid biopsies in guiding personalized treatment of PCa, we evaluated the utility of a custom-targeted next-generation sequencing (NGS) panel based on the AmpliSeq HD Technology. Ultra-deep sequencing on plasma circulating free DNA (cfDNA) samples of 40 metastatic castration-resistant PCa (mCRPC) and 28 metastatic hormone-naive PCa (mCSPC) was performed. CfDNA somatic mutations were detected in 48/68 (71%) patients. Of those 68 patients, 42 had matched tumor and cfDNA samples. In 21/42 (50%) patients, mutations from the primary tumor tissue were detected in the plasma cfDNA. In 7/42 (17%) patients, mutations found in the primary tumor were not detected in the cfDNA. Mutations from primary tumors were detected in all tested mCRPC patients (17/17), but only in 4/11 with mCSPC. AR amplifications were detected in 12/39 (31%) mCRPC patients. These results indicate that our targeted NGS approach has high sensitivity and specificity for detecting clinically relevant mutations in PCa. Full article
(This article belongs to the Special Issue Liquid Biopsy in Cancer 2.0)
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11 pages, 1351 KiB  
Article
Plasma Assay of Cell-Free Methylated DNA Markers of Colorectal Cancer: A Tumor-Agnostic Approach to Monitor Recurrence and Response to Anticancer Therapies
by Mojun Zhu, William R. Taylor, Douglas W. Mahoney, Sara S. Then, Calise K. Berger, Kelli N. Burger, Anna M. Gonser, Karen A. Doering, Hao Xie, Patrick H. Foote, Michael W. Kaiser, Hatim T. Allawi, Joleen M. Hubbard and John B. Kisiel
Cancers 2023, 15(24), 5778; https://doi.org/10.3390/cancers15245778 - 09 Dec 2023
Viewed by 880
Abstract
Background: Radiographic surveillance of colorectal cancer (CRC) after curative-intent therapy is costly and unreliable. Methylated DNA markers (MDMs) detected primary CRC and metastatic recurrence with high sensitivity and specificity in cross-sectional studies. This study evaluated using serial MDMs to detect recurrence and monitor [...] Read more.
Background: Radiographic surveillance of colorectal cancer (CRC) after curative-intent therapy is costly and unreliable. Methylated DNA markers (MDMs) detected primary CRC and metastatic recurrence with high sensitivity and specificity in cross-sectional studies. This study evaluated using serial MDMs to detect recurrence and monitor the treatment response to anti-cancer therapies. Methods: A nested case-control study was drawn from a prospective cohort of patients with CRC who completed curative-intent therapy for CRC of all stages. Plasma MDMs were assayed vis target enrichment long-probe quantitative-amplified signal assays, normalized to B3GALT6, and analyzed in combination with serum carcinoembryonic antigen to yield an MDM score. Clinical information, including treatment and radiographic measurements of the tumor burden, were longitudinally collected. Results: Of the 35 patients, 18 had recurrence and 17 had no evidence of disease during the study period. The MDM score was positive in 16 out of 18 patients who recurred and only 2 of the 17 patients without recurrence. The MDM score detected recurrence in 12 patients preceding clinical or radiographic detection of recurrent CRC by a median of 106 days (range 90–232 days). Conclusions: Plasma MDMs can detect recurrent CRC prior to radiographic detection; this tumor-agnostic liquid biopsy approach may assist cancer surveillance and monitoring. Full article
(This article belongs to the Special Issue Liquid Biopsy in Cancer 2.0)
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13 pages, 1821 KiB  
Article
A Luminex Approach to Develop an Anti-Tumor-Associated Antigen Autoantibody Panel for the Detection of Prostate Cancer in Racially/Ethnically Diverse Populations
by Cuipeng Qiu, Xiao Wang, Serina A. Batson, Bofei Wang, Carlos A. Casiano, Giulio Francia and Jian-Ying Zhang
Cancers 2023, 15(16), 4064; https://doi.org/10.3390/cancers15164064 - 11 Aug 2023
Viewed by 1038
Abstract
(1) Background: Autoantibodies to tumor-associated antigens (TAAs) have emerged as promising cancer biomarkers. Luminex technology offers a powerful approach for the simultaneous detection of multiple anti-TAA autoantibodies. (2) Methods: We aimed to utilize Luminex technology to evaluate and optimize a panel of anti-TAAs [...] Read more.
(1) Background: Autoantibodies to tumor-associated antigens (TAAs) have emerged as promising cancer biomarkers. Luminex technology offers a powerful approach for the simultaneous detection of multiple anti-TAA autoantibodies. (2) Methods: We aimed to utilize Luminex technology to evaluate and optimize a panel of anti-TAAs autoantibodies for detecting prostate cancer (PCa), which included autoantibodies to fourteen TAAs. A total of 163 serum samples (91 PCa, 72 normal controls) were screened to determine the levels of the autoantibodies using the Luminex assay. (3) Results: Twelve autoantibodies exhibited significantly high frequencies ranging from 19.8% to 51.6% in the PCa group. Receiver operating characteristic (ROC) curve analysis revealed area under the curve (AUC) values ranging from 0.609 to 0.868 for the twelve autoantibodies individually. We further confirmed the performance of the HSP60 autoantibody by using an enzyme-linked immunosorbent assay (ELISA) in a larger sample comprising 200 PCa sera, 20 benign prostatic hyperplasia (BPH) sera, and 137 normal control sera. The results obtained from the Luminex assay were consistent with the ELISA findings. We developed a panel consisting of three autoantibodies (p16, IMP2, and HSP60) which achieved an impressive AUC of 0.910 with a sensitivity of 71.4% and a specificity of 95.8%. The panel was also evaluated in PCa patients from different races/ethnicities with the best performance observed in distinguishing the Hispanic American patients with PCa from normal controls. (4) Conclusions: We developed an anti-TAA autoantibody panel for the detection of PCa that exhibits promising performance. This panel holds significant potential as a high-throughput tool to facilitate PCa detection. Full article
(This article belongs to the Special Issue Liquid Biopsy in Cancer 2.0)
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18 pages, 3262 KiB  
Article
Feasibility of Leukemia-Derived Exosome Enrichment and Co-isolated dsDNA Sequencing in Acute Myeloid Leukemia Patients: A Proof of Concept for New Leukemia Biomarkers Detection
by Simona Bernardi, Mirko Farina, Katia Bosio, Anna Di Lucanardo, Alessandro Leoni, Federica Re, Nicola Polverelli, Alessandro Turra, Enrico Morello, Eugenia Accorsi Buttini, Tatiana Zollner, Cristian Bonvicini, Michele Malagola and Domenico Russo
Cancers 2022, 14(18), 4504; https://doi.org/10.3390/cancers14184504 - 16 Sep 2022
Cited by 3 | Viewed by 1532
Abstract
Exosomes are extracellular vesicles playing a pivotal role in the intercellular communication. They shuttle different cargoes, including nucleic acids from their cell of origin. For this reason, they have been studied as carriers of tumor markers in different liquid biopsy approaches, in particular [...] Read more.
Exosomes are extracellular vesicles playing a pivotal role in the intercellular communication. They shuttle different cargoes, including nucleic acids from their cell of origin. For this reason, they have been studied as carriers of tumor markers in different liquid biopsy approaches, in particular for solid tumors. Few data are available concerning exosomes as markers of myeloid neoplasia. To better understand their real potential and the best approach to investigate leukemic exosomes, we present the results of a pilot feasibility study evaluating the application of next-generation sequencing analysis of dsDNA derived from exosomes isolated in 14 adult patients affected by acute myeloid leukemias. In particular, leukemia-derived exosome fractions have been analyzed. The concentration of dsDNA co-extracted with exosomes and the number and types of mutations detected were considered and compared with ones identified in the Bone Marrow (BM) and Peripheral Blood (PB) cells. Exosomal DNA concentration, both considering the cargo and the DNA surrounding the lipid membrane resulted in a linear correlation with leukemic burden. Moreover, exosomal DNA mutation status presented 86.5% of homology with BM and 75% with PB. The results of this pilot study confirmed the feasibility of a leukemia-derived exosome enrichment approach followed by exosomal dsDNA NGS analysis for AML biomarker detection. These data point to the use of liquid biopsy in myeloid neoplasia for the detection of active leukemic cells resident in the BM via a painless procedure. Full article
(This article belongs to the Special Issue Liquid Biopsy in Cancer 2.0)
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Review

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20 pages, 335 KiB  
Review
Extracellular Vesicle-DNA: The Next Liquid Biopsy Biomarker for Early Cancer Diagnosis?
by Irène Tatischeff
Cancers 2023, 15(5), 1456; https://doi.org/10.3390/cancers15051456 - 24 Feb 2023
Cited by 1 | Viewed by 1526
Abstract
After a short introduction about the history of liquid biopsy, aimed to noninvasively replace the common tissue biopsy as a help for cancer diagnosis, this review is focused on extracellular vesicles (EVs), as the main third component, which is now coming into the [...] Read more.
After a short introduction about the history of liquid biopsy, aimed to noninvasively replace the common tissue biopsy as a help for cancer diagnosis, this review is focused on extracellular vesicles (EVs), as the main third component, which is now coming into the light of liquid biopsy. Cell-derived EV release is a recently discovered general cellular property, and EVs harbor many cellular components reflecting their cell of origin. This is also the case for tumoral cells, and their cargoes might therefore be a “treasure chest” for cancer biomarkers. This has been extensively explored for a decade, but the EV-DNA content escaped this worldwide query until recently. The aim of this review is to gather the pilot studies focused on the DNA content of circulating cell-derived EVs, and the following five years of studies about the circulating tumor EV-DNA. The recent preclinical studies about the circulating tEV-derived gDNA as a potential cancer biomarker developed into a puzzling controversy about the presence of DNA into exosomes, coupled with an increased unexpected non vesicular complexity of the extracellular environment. This is discussed in the present review, together with the challenges that need to be solved before any efficient clinical transfer of EV-DNA as a quite promising cancer diagnosis biomarker. Full article
(This article belongs to the Special Issue Liquid Biopsy in Cancer 2.0)
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