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Liquid Biopsies in Oncology II
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Liquid Biopsies in Oncology II

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Oncology".

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 7268

Special Issue Editors

Dr. Sandra V. Fernandez

E-Mail Website
Guest Editor
Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
Interests: breast cancer; circulating tumor cells (CTCs); cell-free DNA (cfDNA); cell-tumor DNA (ctDNA); liquid biopsies; genetic variants
Special Issues, Collections and Topics in MDPI journals
Dr. Carmela Paolillo

E-Mail Website
Guest Editor
Department of Clinical and Experimental Medicine, University of Study of Foggia, 71122 Foggia, Italy
Interests: precision medicine; personalized medicine; cancer genomics; genomics; liquid biopsy; molecular diagnostic; laboratory medicine; clinical molecular biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the era of precision oncology, tumor molecular characterization plays a key role in selecting the right treatment for each patient at the right time. Technological advances, particularly next-generation sequencing (NGS), have paved the way to personalized medicine, reducing the time and costs required to assess the tumor’s genetic profile. Unfortunately, in some cases, tumor biopsies are not feasible, due to insufficient or inaccessible material. The use of liquid biopsies has revolutionized the standard clinical approach by allowing the detection of different circulating molecules in the bloodstream and other body fluids, which may have a key role in diagnosing and monitoring the evolution of the tumor, and evaluating the response or resistance to the treatment. Since their FDA approval in 2016, for a therapy-guiding blood-based test to detect EGFR mutations in lung cancer patients, liquid biopsies are emerging as the standard of care. Liquid biopsies have several advantages, including minimal invasiveness and repeatability, which could guarantee a dynamic picture of the tumor and the chance to monitor pharmacological responses to the biopsy.

We invite scientists to submit original research focused on the application of liquid biopsies as an innovative tool in cancer diagnosis and monitoring, as well as its possible application in clinical practice. Articles may also be focused on understanding how circulating molecules offer new therapeutic strategies in cancer treatment. Review articles that describe the state of the art on this topic are also encouraged. This Special Issue, focusing on liquid biopsies in oncology, includes the use of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), circulating tumor RNAs (ctRNAs) as well as miRNAs, and extracellular vesicles (EVs). The topics of interest for this Special Issue include, but are not limited to, the following:

  • Liquid biopsy for cancer screening, diagnosis, prognosis, follow-up and therapeutic management of tumors;
  • Liquid biopsy for stratification and monitoring of cancer patients;
  • Liquid biopsy for the detection of actionable oncogenic mutations in cancers;
  • Liquid biopsy targeting ctDNA for molecular diagnosis of cancer;
  • Clinical validity and utility of ctDNA and ctRNA for tumor analysis;
  • Extracellular vesicle biomarkers;
  • New techniques to evaluate cell-free molecules;
  • Liquid biopsy on exosome for cancer diagnosis;
  • Liquid biopsies and epigenetics.

Dr. Sandra V. Fernandez
Dr. Carmela Paolillo
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • precision oncology
  • personalized therapy
  • cancer biomarkers
  • liquid biopsy
  • biological fluids
  • circulating molecules
  • circulating tumor cells
  • CTCs
  • ctDNA
  • ctRNA
  • cell-free DNA
  • cfDNA
  • NGS
  • circulating miRNAs
  • exosomes
  • extracellular vesicles

Related Special Issue

Published Papers (5 papers)

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15 pages, 3137 KiB  
Article
Integration of Cell-Free DNA End Motifs and Fragment Lengths Can Identify Active Genes in Liquid Biopsies
by Christoffer Trier Maansson, Louise Skov Thomsen, Peter Meldgaard, Anders Lade Nielsen and Boe Sandahl Sorensen
Int. J. Mol. Sci. 2024, 25(2), 1243; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms25021243 - 19 Jan 2024
Viewed by 1504
Abstract
Multiple studies have shown that cell-free DNA (cfDNA) from cancer patients differ in both fragment length and fragment end motif (FEM) from healthy individuals, yet there is a lack of understanding of how the two factors combined are associated with cancer and gene [...] Read more.
Multiple studies have shown that cell-free DNA (cfDNA) from cancer patients differ in both fragment length and fragment end motif (FEM) from healthy individuals, yet there is a lack of understanding of how the two factors combined are associated with cancer and gene transcription. In this study, we conducted cfDNA fragmentomics evaluations using plasma from lung cancer patients (n = 12) and healthy individuals (n = 7). A personal gene expression profile was established from plasma using H3K36me3 cell-free chromatin immunoprecipitation sequencing (cfChIP-seq). The genes with the highest expression displayed an enrichment of short cfDNA fragments (median = 19.99%, IQR: 16.94–27.13%, p < 0.0001) compared to the genes with low expression. Furthermore, distinct GC-rich FEMs were enriched after cfChIP. Combining the frequency of short cfDNA fragments with the presence of distinct FEMs resulted in an even further enrichment of the most expressed genes (median = 37.85%, IQR: 30.10–39.49%, p < 0.0001). An in vitro size selection of <150 bp cfDNA could isolate cfDNA representing active genes and the size-selection enrichment correlated with the cfChIP-seq enrichment (Spearman r range: 0.499–0.882, p < 0.0001). This study expands the knowledge regarding cfDNA fragmentomics and sheds new light on how gene activity is associated with both cfDNA fragment lengths and distinct FEMs. Full article
(This article belongs to the Special Issue Liquid Biopsies in Oncology II)
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18 pages, 898 KiB  
Article
Validation of a Molecular Diagnostic Test for Circulating Tumor DNA by Next-Gen Sequencing
by Sandra V. Fernandez, Yin Fei Tan, Shilpa Rao, Patricia Fittipaldi, Fathima Sheriff, Hossein Borghaei, Efrat Dotan, Jennifer S. Winn, Martin J. Edelman, Joseph Treat, Julia Judd, R. Katherine Alpaugh, Y. Lynn Wang, Jian Q. Yu, Mariusz Wasik and Don A. Baldwin
Int. J. Mol. Sci. 2023, 24(21), 15779; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms242115779 - 30 Oct 2023
Viewed by 1288
Abstract
A modified version of the PGDx elioTM Plasma Resolve assay was validated as a laboratory-developed test (LDT) for clinical use in the Molecular Diagnostics Laboratory at Fox Chase Cancer Center. The test detects single nucleotide variants (SNVs) and small insertions and deletions [...] Read more.
A modified version of the PGDx elioTM Plasma Resolve assay was validated as a laboratory-developed test (LDT) for clinical use in the Molecular Diagnostics Laboratory at Fox Chase Cancer Center. The test detects single nucleotide variants (SNVs) and small insertions and deletions (indels) in 33 target genes using fragmented genomic DNA extracted from plasma. The analytical performance of this assay was assessed with reference standard DNA and 29 samples from cancer patients and detected 66 SNVs and 23 indels. Using 50 ng of input DNA, the sensitivity was 95.5% to detect SNVs at 0.5% allele frequency, and the specificity was 92.3%. The sensitivity to detect indels at 1% allele frequency was 70.4%. A cutoff of 0.25% variant allele frequency (VAF) was set up for diagnostic reporting. An inter-laboratory study of concordance with an orthologous test resulted in a positive percent agreement (PPA) of 91.7%. Full article
(This article belongs to the Special Issue Liquid Biopsies in Oncology II)
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17 pages, 2430 KiB  
Article
OncoUroMiR: Circulating miRNAs for Detection and Discrimination of the Main Urological Cancers Using a ddPCR-Based Approach
by José Pedro Sequeira, Daniela Barros-Silva, Patrícia Ferreira-Torre, Sofia Salta, Isaac Braga, João Carvalho, Rui Freitas, Rui Henrique and Carmen Jerónimo
Int. J. Mol. Sci. 2023, 24(18), 13890; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241813890 - 09 Sep 2023
Cited by 1 | Viewed by 1977
Abstract
The three most common genitourinary malignancies (prostate/kidney/bladder cancers) constitute a substantial proportion of all cancer cases, mainly in the elderly population. Early detection is key to maximizing the patients’ survival, but the lack of highly accurate biomarkers that might be used through non-/minimally [...] Read more.
The three most common genitourinary malignancies (prostate/kidney/bladder cancers) constitute a substantial proportion of all cancer cases, mainly in the elderly population. Early detection is key to maximizing the patients’ survival, but the lack of highly accurate biomarkers that might be used through non-/minimally invasive methods has impaired progress in this domain. Herein, we sought to develop a minimally invasive test to detect and discriminate among those urological cancers based on miRNAs assessment through ddPCR. Plasma samples from 268 patients with renal cell (RCC; n = 119), bladder (BlCa; n = 73), and prostate (PCa; n = 76) carcinomas (UroCancer group), and 74 healthy donors were selected. Hsa-miR-126-3p, hsa-miR-141-3p, hsa-miR-153-5p, hsa-miR-155-5p, hsa-miR-182-5p, hsa-miR-205-5p, and hsa-miR-375-3p levels were assessed. UroCancer cases displayed significantly different circulating hsa-miR-182-5p/hsa-miR-375-3p levels compared to healthy donors. Importantly, the hsa-miR-155-5p/hsa-miR-375-3p panel detected RCC with a high specificity (80.54%) and accuracy (66.04%). Furthermore, the hsa-miR-126-3p/hsa-miR-375-3p panel identified BlCa with a 94.87% specificity and 76.45% NPV whereas higher hsa-miR-126-3p levels were found in PCa patients. We concluded that plasma-derived miRNAs can identify and discriminate among the main genitourinary cancers, with high analytical performance. Although validation in a larger cohort is mandatory, these findings demonstrate that circulating miRNA assessment by ddPCR might provide a new approach for early detection and risk stratification of the most common urological cancers. Full article
(This article belongs to the Special Issue Liquid Biopsies in Oncology II)
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16 pages, 2359 KiB  
Article
miR-124 as a Liquid Biopsy Prognostic Biomarker in Small Extracellular Vesicles from NSCLC Patients
by Darío Sanchez-Cabrero, Álvaro Garcia-Guede, Miranda Burdiel, Olga Pernía, Julián Colmenarejo-Fernandez, Laura Gutierrez, Oliver Higuera, Isabel Esteban Rodriguez, Rocío Rosas-Alonso, Carlos Rodriguez-Antolín, Itsaso Losantos-García, Olga Vera, Javier De Castro-Carpeño and Inmaculada Ibanez de Caceres
Int. J. Mol. Sci. 2023, 24(14), 11464; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241411464 - 14 Jul 2023
Viewed by 1324
Abstract
Despite advances in non-small cell lung cancer (NSCLC) research, this is still the most common cancer type that has been diagnosed up to date. microRNAs have emerged as useful clinical biomarkers in both tissue and liquid biopsy. However, there are no reliable predictive [...] Read more.
Despite advances in non-small cell lung cancer (NSCLC) research, this is still the most common cancer type that has been diagnosed up to date. microRNAs have emerged as useful clinical biomarkers in both tissue and liquid biopsy. However, there are no reliable predictive biomarkers for clinical use. We evaluated the preclinical use of seven candidate miRNAs previously identified by our group. We collected a total of 120 prospective samples from 88 NSCLC patients. miRNA levels were analyzed via qRT-PCR from tissue and blood samples. miR-124 gene target prediction was performed using RNA sequencing data from our group and interrogating data from 2952 NSCLC patients from two public databases. We found higher levels of all seven miRNAs in tissue compared to plasma samples, except for miR-124. Our findings indicate that levels of miR-124, both free-circulating and within exosomes, are increased throughout the progression of the disease, suggesting its potential as a marker of disease progression in both advanced and early stages. Our bioinformatics approach identified KPNA4 and SPOCK1 as potential miR-124 targets in NSCLC. miR-124 levels can be used to identify early-stage NSCLC patients at higher risk of relapse. Full article
(This article belongs to the Special Issue Liquid Biopsies in Oncology II)
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12 pages, 3694 KiB  
Case Report
Treatment Monitoring of a Patient with Synchronous Metastatic Angiosarcoma and Breast Cancer Using ctDNA
by Christoffer Vannas, Mandy Escobar, Tobias Österlund, Daniel Andersson, Pia Mouhanna, Amanda Soomägi, Claes Molin, David Wennergren, Henrik Fagman and Anders Ståhlberg
Int. J. Mol. Sci. 2024, 25(7), 4023; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms25074023 - 04 Apr 2024
Viewed by 480
Abstract
Angiosarcoma is a rare and aggressive type of soft-tissue sarcoma with high propensity to metastasize. For patients with metastatic angiosarcoma, prognosis is dismal and treatment options are limited. To improve the outcomes, identifying patients with poor treatment response at an earlier stage is [...] Read more.
Angiosarcoma is a rare and aggressive type of soft-tissue sarcoma with high propensity to metastasize. For patients with metastatic angiosarcoma, prognosis is dismal and treatment options are limited. To improve the outcomes, identifying patients with poor treatment response at an earlier stage is imperative, enabling alternative therapy. Consequently, there is a need for improved methods and biomarkers for treatment monitoring. Quantification of circulating tumor-DNA (ctDNA) is a promising approach for patient-specific monitoring of treatment response. In this case report, we demonstrate that quantification of ctDNA using SiMSen-Seq was successfully utilized to monitor a patient with metastatic angiosarcoma. By quantifying ctDNA levels using 25 patient-specific mutations in blood plasma throughout surgery and palliative chemotherapy, we predicted the outcome and monitored the clinical response to treatment. This was accomplished despite the additional complexity of the patient having a synchronous breast cancer. The levels of ctDNA showed a superior correlation to the clinical outcome compared with the radiological evaluations. Our data propose a promising approach for personalized biomarker analysis to monitor treatment in angiosarcomas, with potential applicability to other cancers and for patients with synchronous malignancies. Full article
(This article belongs to the Special Issue Liquid Biopsies in Oncology II)
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