International Journal of Molecular Sciences

Research

Jump to: Review

26 pages, 7778 KiB

Open AccessArticle

Comparison Study of Small Extracellular Vesicle Isolation Methods for Profiling Protein Biomarkers in Breast Cancer Liquid Biopsies

by Yujin Lee, Jie Ni, Valerie C. Wasinger, Peter Graham and Yong Li

Int. J. Mol. Sci. 2023, 24(20), 15462; https://doi.org/10.3390/ijms242015462 - 23 Oct 2023

Cited by 7 | Viewed by 2415

Abstract

Small extracellular vesicles (sEVs) are an important intercellular communicator, participating in all stages of cancer metastasis, immunity, and therapeutic resistance. Therefore, protein cargoes within sEVs are considered as a superior source for breast cancer (BC) biomarker discovery. Our study aimed to optimise the [...] Read more.

Small extracellular vesicles (sEVs) are an important intercellular communicator, participating in all stages of cancer metastasis, immunity, and therapeutic resistance. Therefore, protein cargoes within sEVs are considered as a superior source for breast cancer (BC) biomarker discovery. Our study aimed to optimise the approach for sEV isolation and sEV proteomic analysis to identify potential sEV protein biomarkers for BC diagnosis. sEVs derived from BC cell lines, BC patients’ plasma, and non-cancer controls were isolated using ultracentrifugation (UC), a Total Exosome Isolation kit (TEI), and a combined approach named UCT. In BC cell lines, the UC isolates showed a higher sEV purity and marker expression, as well as a higher number of sEV proteins. In BC plasma samples, the UCT isolates showed the highest proportion of sEV-related proteins and the lowest percentage of lipoprotein-related proteins. Our data suggest that the assessment of both the quantity and quality of sEV isolation methods is important in selecting the optimal approach for the specific sEV research purpose, depending on the sample types and downstream analysis. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Graphical abstract

22 pages, 4972 KiB

Open AccessArticle

The Comparison of Serum Exosome Protein Profile in Diagnosis of NSCLC Patients

by Kamila Baran, Joanna Waśko, Jakub Kryczka, Joanna Boncela, Sławomir Jabłoński, Beata Kolesińska, Ewa Brzeziańska-Lasota and Jacek Kordiak

Int. J. Mol. Sci. 2023, 24(18), 13669; https://doi.org/10.3390/ijms241813669 - 5 Sep 2023

Cited by 11 | Viewed by 2942

Abstract

A thorough study of the exosomal proteomic cargo may enable the identification of proteins that play an important role in cancer development. The aim of this study was to compare the protein profiles of the serum exosomes derived from non-small lung cancer (NSCLC) [...] Read more.

A thorough study of the exosomal proteomic cargo may enable the identification of proteins that play an important role in cancer development. The aim of this study was to compare the protein profiles of the serum exosomes derived from non-small lung cancer (NSCLC) patients and healthy volunteers (control) using the high-performance liquid chromatography coupled to mass spectrometry (HPLC-MS) method to identify potentially new diagnostic and/or prognostic protein biomarkers. Proteins exclusively identified in NSCLC and control groups were analyzed using several bioinformatic tools and platforms (FunRich, Vesiclepedia, STRING, and TIMER2.0) to find key protein hubs involved in NSCLC progression and the acquisition of metastatic potential. This analysis revealed 150 NSCLC proteins, which are significantly involved in osmoregulation, cell–cell adhesion, cell motility, and differentiation. Among them, 3 proteins: Interleukin-34 (IL-34), HLA class II histocompatibility antigen, DM alpha chain (HLA-DMA), and HLA class II histocompatibility antigen, DO beta chain (HLA-DOB) were shown to be significantly involved in the cancer-associated fibroblasts (CAFs) and tumor-associated macrophages (TAMs) infiltration processes. Additionally, detected proteins were analyzed according to the presence of lymph node metastasis, showing that differences in frequency of detection of protein FAM166B, killer cell immunoglobulin-like receptor 2DL1, and olfactory receptor 52R1 correlate with the N feature according to the TNM Classification of Malignant Tumors. These results prove their involvement in NSCLC lymph node spread and metastasis. However, this study requires further investigation. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Figure 1

20 pages, 4309 KiB

Open AccessArticle

Real-World Use of Highly Sensitive Liquid Biopsy Monitoring in Metastatic Breast Cancer Patients Treated with Endocrine Agents after Exposure to Aromatase Inhibitors

by Jesús Fuentes-Antrás, Ana Martínez-Rodríguez, Kissy Guevara-Hoyer, Igor López-Cade, Víctor Lorca, Alejandro Pascual, Alicia de Luna, Carmen Ramírez-Ruda, Jennifer Swindell, Paloma Flores, Ana Lluch, David W. Cescon, Pedro Pérez-Segura, Alberto Ocaña, Frederick Jones, Fernando Moreno, Vanesa García-Barberán and José Ángel García-Sáenz

Int. J. Mol. Sci. 2023, 24(14), 11419; https://doi.org/10.3390/ijms241411419 - 13 Jul 2023

Cited by 8 | Viewed by 3557

Abstract

Endocrine-resistant, hormone receptor-positive, and HER2-negative (HR+/HER2-) metastatic breast cancer (mBC) is largely governed by acquired mutations in the estrogen receptor, which promote ligand-independent activation, and by truncal alterations in the PI3K signaling pathway, with a broader range of gene alterations occurring with less [...] Read more.

Endocrine-resistant, hormone receptor-positive, and HER2-negative (HR+/HER2-) metastatic breast cancer (mBC) is largely governed by acquired mutations in the estrogen receptor, which promote ligand-independent activation, and by truncal alterations in the PI3K signaling pathway, with a broader range of gene alterations occurring with less prevalence. Circulating tumor DNA (ctDNA)-based technologies are progressively permeating the clinical setting. However, their utility for serial monitoring has been hindered by their significant costs, inter-technique variability, and real-world patient heterogeneity. We interrogated a longitudinal collection of 180 plasma samples from 75 HR+/HER2- mBC patients who progressed or relapsed after exposure to aromatase inhibitors and were subsequently treated with endocrine therapy (ET) by means of highly sensitive and affordable digital PCR and SafeSEQ sequencing. Baseline PIK3CA and TP53 mutations were prognostic of a shorter progression-free survival in our population. Mutant PIK3CA was prognostic in the subset of patients receiving fulvestrant monotherapy after progression to a CDK4/6 inhibitor (CDK4/6i)-containing regimen, and its suppression was predictive in a case of long-term benefit with alpelisib. Mutant ESR1 was prognostic in patients who did not receive concurrent CDK4/6i, an impact influenced by the variant allele frequency, and its early suppression was strongly predictive of efficacy and associated with long-term benefit in the whole cohort. Mutations in ESR1, TP53, and KRAS emerged as putative drivers of acquired resistance. These findings collectively contribute to the characterization of longitudinal ctDNA in real-world cases of HR+/HER2- mBC previously exposed to aromatase inhibitors and support ongoing studies either targeting actionable alterations or leveraging the ultra-sensitive tracking of ctDNA. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Figure 1

19 pages, 2663 KiB

Open AccessArticle

Assessment of Different Circulating Tumor Cell Platforms for Uveal Melanoma: Potential Impact for Future Routine Clinical Practice

by Arnaud Martel, Baharia Mograbi, Barnabe Romeo, Lauris Gastaud, Salome Lalvee, Katia Zahaf, Julien Fayada, Sacha Nahon-Esteve, Christelle Bonnetaud, Myriam Salah, Virginie Tanga, Stéphanie Baillif, Corine Bertolotto, Sandra Lassalle and Paul Hofman

Int. J. Mol. Sci. 2023, 24(13), 11075; https://doi.org/10.3390/ijms241311075 - 4 Jul 2023

Cited by 5 | Viewed by 2482

Abstract

Liquid biopsy and circulating tumor cell (CTC) screening has gained interest over the last two decades for detecting almost all solid malignancies. To date, the major limitation in terms of the applicability of CTC screening in daily clinical practice is the lack of [...] Read more.

Liquid biopsy and circulating tumor cell (CTC) screening has gained interest over the last two decades for detecting almost all solid malignancies. To date, the major limitation in terms of the applicability of CTC screening in daily clinical practice is the lack of reproducibility due to the high number of platforms available that use various technologies (e.g., label-dependent versus label-free detection). Only a few studies have compared different CTC platforms. The aim of this study was to compare the efficiency of four commercially available CTC platforms (Vortex (VTX-1), ClearCell FX, ISET, and Cellsearch) for the detection and identification of uveal melanoma cells (OMM 2.3 cell line). Tumor cells were seeded in RPMI medium and venous blood from healthy donors, and then processed similarly using these four platforms. Melan-A immunochemistry was performed to identify tumor cells, except when the Cellsearch device was used (automated identification). The mean overall recovery rates (with mean recovered cells) were 39.2% (19.92), 22.2% (11.31), 8.9% (4.85), and 1.1% (0.20) for the ISET, Vortex (VTX-1), ClearCell FX, and CellSearch platforms, respectively. Although paramount, the recovery rate is not sufficient to assess a CTC platform. Other parameters, such as the purpose for using a platform (diagnosis, genetics, drug sensitivity, or patient-derived xenograft models), reproducibility, purity, user-friendliness, cost-effectiveness, and ergonomics, should also be considered before they can be used in daily clinical practice and are discussed in this article. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Graphical abstract

16 pages, 4561 KiB

Open AccessArticle

Transcriptome Profiling of Circulating Tumor Cells to Predict Clinical Outcomes in Metastatic Castration-Resistant Prostate Cancer

by Levi Groen, Iris Kloots, David Englert, Kelly Seto, Lana Estafanos, Paul Smith, Gerald W. Verhaegh, Niven Mehra and Jack A. Schalken

Int. J. Mol. Sci. 2023, 24(10), 9002; https://doi.org/10.3390/ijms24109002 - 19 May 2023

Cited by 8 | Viewed by 3008

Abstract

The clinical utility of circulating tumor cells (CTC) as a non-invasive multipurpose biomarker is broadly recognized. The earliest methods for enriching CTCs from whole blood rely on antibody-based positive selection. The prognostic utility of CTC enumeration using positive selection with the FDA-approved CellSearch [...] Read more.

The clinical utility of circulating tumor cells (CTC) as a non-invasive multipurpose biomarker is broadly recognized. The earliest methods for enriching CTCs from whole blood rely on antibody-based positive selection. The prognostic utility of CTC enumeration using positive selection with the FDA-approved CellSearch^TM system has been demonstrated in numerous studies. The capture of cells with specific protein phenotypes does not fully represent cancer heterogeneity and therefore does not realize the prognostic potential of CTC liquid biopsies. To avoid this selection bias, CTC enrichment based on size and deformability may provide better fidelity, i.e., facilitate the characterization of CTCs with any phenotype. In this study, the recently FDA-approved Parsortix^® technology was used to enrich CTCs from prostate cancer (PCa) patients for transcriptome analysis using HyCEAD^TM technology. A tailored PCa gene panel allowed us to stratify metastatic castration-resistant prostate cancer (mCRPC) patients with clinical outcomes. In addition, our findings suggest that targeted CTC transcriptome profiling may be predictive of therapy response. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Graphical abstract

21 pages, 3558 KiB

Open AccessArticle

Clinical Validation of a Size-Based Microfluidic Device for Circulating Tumor Cell Isolation and Analysis in Renal Cell Carcinoma

by Tito Palmela Leitão, Patrícia Corredeira, Sandra Kucharczak, Margarida Rodrigues, Paulina Piairo, Carolina Rodrigues, Patrícia Alves, Ana Martins Cavaco, Miguel Miranda, Marília Antunes, João Ferreira, José Palma Reis, Tomé Lopes, Lorena Diéguez and Luís Costa

Int. J. Mol. Sci. 2023, 24(9), 8404; https://doi.org/10.3390/ijms24098404 - 7 May 2023

Cited by 7 | Viewed by 3428

Abstract

Renal cell carcinoma (RCC) presents as metastatic disease in one third of cases. Research on circulating tumor cells (CTCs) and liquid biopsies is improving the understanding of RCC biology and metastases formation. However, a standardized, sensitive, specific, and cost-effective CTC detection technique is [...] Read more.

Renal cell carcinoma (RCC) presents as metastatic disease in one third of cases. Research on circulating tumor cells (CTCs) and liquid biopsies is improving the understanding of RCC biology and metastases formation. However, a standardized, sensitive, specific, and cost-effective CTC detection technique is lacking. The use of platforms solely relying on epithelial markers is inappropriate in RCC due to the frequent epithelial-mesenchymal transition that CTCs undergo. This study aimed to test and clinically validate RUBYchip™, a microfluidic label-free CTC detection platform, in RCC patients. The average CTC capture efficiency of the device was 74.9% in spiking experiments using three different RCC cell lines. Clinical validation was performed in a cohort of 18 patients, eight non-metastatic (M0), five metastatic treatment-naïve (M1TN), and five metastatic progressing-under-treatment (M1TP). An average CTC detection rate of 77.8% was found and the average (range) total CTC count was 6.4 (0–27), 101.8 (0–255), and 3.2 (0–10), and the average mesenchymal CTC count (both single and clustered cells) was zero, 97.6 (0–255), and 0.2 (0–1) for M0, M1TN, and M1TP, respectively. CTC clusters were detected in 25% and 60% of M0 and M1TN patients, respectively. These results show that RUBYchip™ is an effective CTC detection platform in RCC. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Figure 1

13 pages, 816 KiB

Open AccessArticle

The Potential of Liquid Biopsy in Detection of Endometrial Cancer Biomarkers: A Pilot Study

by Dominik Kodada, Michaela Hyblova, Patrik Krumpolec, Nikola Janostiakova, Peter Barath, Marian Grendar, Gabriela Blandova, Oliver Petrovic, Pavol Janega, Vanda Repiska and Gabriel Minarik

Int. J. Mol. Sci. 2023, 24(9), 7811; https://doi.org/10.3390/ijms24097811 - 25 Apr 2023

Cited by 4 | Viewed by 2535

Abstract

Endometrial cancer belongs to the most common gynecologic cancer types globally, with increasing incidence. There are numerous ways of classifying different cases. The most recent decade has brought advances in molecular classification, which show more accurate prognostic factors and the possibility of personalised [...] Read more.

Endometrial cancer belongs to the most common gynecologic cancer types globally, with increasing incidence. There are numerous ways of classifying different cases. The most recent decade has brought advances in molecular classification, which show more accurate prognostic factors and the possibility of personalised adjuvant treatment. In addition, diagnostic approaches lag behind these advances, with methods causing patients discomfort while lacking the reproducibility of tissue sampling for biopsy. Minimally invasive liquid biopsies could therefore represent an alternative screening and diagnostic approach in patients with endometrial cancer. The method could potentially detect molecular changes in this cancer type and identify patients at early stages. In this pilot study, we tested such a detection method based on circulating tumour DNA isolated from the peripheral blood plasma of 21 Slovak endometrial cancer patients. We successfully detected oncomutations in the circulating DNA of every single patient, although the prognostic value of the detected mutations failed to offer certainty. Furthermore, we detected changes associated with clonal hematopoiesis, including DNMT3A mutations, which were present in the majority of circulating tumour DNA samples. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Figure 1

16 pages, 1555 KiB

Open AccessArticle

Uveal Melanoma Patients Have a Distinct Metabolic Phenotype in Peripheral Blood

by Daniël P. de Bruyn, Michiel Bongaerts, Ramon Bonte, Jolanda Vaarwater, Magda A. Meester-Smoor, Robert M. Verdijk, Dion Paridaens, Nicole C. Naus, Annelies de Klein, George J. G. Ruijter, Emine Kiliç and Erwin Brosens

Int. J. Mol. Sci. 2023, 24(6), 5077; https://doi.org/10.3390/ijms24065077 - 7 Mar 2023

Cited by 2 | Viewed by 2431

Abstract

Uveal melanomas (UM) are detected earlier. Consequently, tumors are smaller, allowing for novel eye-preserving treatments. This reduces tumor tissue available for genomic profiling. Additionally, these small tumors can be hard to differentiate from nevi, creating the need for minimally invasive detection and prognostication. [...] Read more.

Uveal melanomas (UM) are detected earlier. Consequently, tumors are smaller, allowing for novel eye-preserving treatments. This reduces tumor tissue available for genomic profiling. Additionally, these small tumors can be hard to differentiate from nevi, creating the need for minimally invasive detection and prognostication. Metabolites show promise as minimally invasive detection by resembling the biological phenotype. In this pilot study, we determined metabolite patterns in the peripheral blood of UM patients (n = 113) and controls (n = 46) using untargeted metabolomics. Using a random forest classifier (RFC) and leave-one-out cross-validation, we confirmed discriminatory metabolite patterns in UM patients compared to controls with an area under the curve of the receiver operating characteristic of 0.99 in both positive and negative ion modes. The RFC and leave-one-out cross-validation did not reveal discriminatory metabolite patterns in high-risk versus low-risk of metastasizing in UM patients. Ten-time repeated analyses of the RFC and LOOCV using 50% randomly distributed samples showed similar results for UM patients versus controls and prognostic groups. Pathway analysis using annotated metabolites indicated dysregulation of several processes associated with malignancies. Consequently, minimally invasive metabolomics could potentially allow for screening as it distinguishes metabolite patterns that are putatively associated with oncogenic processes in the peripheral blood plasma of UM patients from controls at the time of diagnosis. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Figure 1

15 pages, 1141 KiB

Open AccessArticle

Development of a Novel NGS Methodology for Ultrasensitive Circulating Tumor DNA Detection as a Tool for Early-Stage Breast Cancer Diagnosis

by Begoña Jiménez-Rodríguez, Alfonso Alba-Bernal, Esperanza López-López, María Elena Quirós-Ortega, Guillermo Carbajosa, Alicia Garrido-Aranda, Martina Álvarez, Ana Godoy-Ortiz, María Isabel Queipo-Ortuño, Luis Vicioso, Gema Díaz-Córdoba, María Dunia Roldán-Díaz, Jesús Velasco-Suelto, Cristina Hernando, Begoña Bermejo, Ana Julve-Parreño, Ana Lluch, Javier Pascual, Iñaki Comino-Méndez and Emilio Alba

Int. J. Mol. Sci. 2023, 24(1), 146; https://doi.org/10.3390/ijms24010146 - 21 Dec 2022

Cited by 7 | Viewed by 3826

Abstract

Breast cancer (BC) is the most prevalent cancer in women. While usually detected when localized, invasive procedures are still required for diagnosis. Herein, we developed a novel ultrasensitive pipeline to detect circulating tumor DNA (ctDNA) in a series of 75 plasma samples from [...] Read more.

Breast cancer (BC) is the most prevalent cancer in women. While usually detected when localized, invasive procedures are still required for diagnosis. Herein, we developed a novel ultrasensitive pipeline to detect circulating tumor DNA (ctDNA) in a series of 75 plasma samples from localized BC patients prior to any medical intervention. We first performed a tumor-informed analysis to correlate the mutations found in tumor tissue and plasma. Disregarding the tumor data next, we developed an approach to detect tumor mutations in plasma. We observed a mutation concordance between the tumor and plasma of 29.50% with a sensitivity down to 0.03% in mutant variant allele frequency (VAF). We detected mutations in 33.78% of the samples, identifying eight patients with plasma-only mutations. Altogether, we determined a specificity of 86.36% and a positive predictive value of 88.46% for BC detection. We demonstrated an association between higher ctDNA median VAF and higher tumor grade, multiple plasma mutations with a likelihood of relapse and more frequent TP53 plasma mutations in hormone receptor-negative tumors. Overall, we have developed a unique ultra-sensitive sequencing workflow with a technology not previously employed in early BC, paving the way for its application in BC screening. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Figure 1

Review

Jump to: Research

26 pages, 1602 KiB

Open AccessReview

Clinical Significance of Extracellular Vesicles in Prostate and Renal Cancer

by Tzu-Yi Chen, Meredith Mihalopoulos, Laura Zuluaga, Jordan Rich, Teja Ganta, Reza Mehrazin, Che-Kai Tsao, Ash Tewari, Edgar Gonzalez-Kozlova, Ketan Badani, Navneet Dogra and Natasha Kyprianou

Int. J. Mol. Sci. 2023, 24(19), 14713; https://doi.org/10.3390/ijms241914713 - 28 Sep 2023

Cited by 5 | Viewed by 3103

Abstract

Extracellular vesicles (EVs)—including apoptotic bodies, microvesicles, and exosomes—are released by almost all cell types and contain molecular footprints from their cell of origin, including lipids, proteins, metabolites, RNA, and DNA. They have been successfully isolated from blood, urine, semen, and other body fluids. [...] Read more.

Extracellular vesicles (EVs)—including apoptotic bodies, microvesicles, and exosomes—are released by almost all cell types and contain molecular footprints from their cell of origin, including lipids, proteins, metabolites, RNA, and DNA. They have been successfully isolated from blood, urine, semen, and other body fluids. In this review, we discuss the current understanding of the predictive value of EVs in prostate and renal cancer. We also describe the findings supporting the use of EVs from liquid biopsies in stratifying high-risk prostate/kidney cancer and advanced disease, such as castration-resistant (CRPC) and neuroendocrine prostate cancer (NEPC) as well as metastatic renal cell carcinoma (RCC). Assays based on EVs isolated from urine and blood have the potential to serve as highly sensitive diagnostic studies as well as predictive measures of tumor recurrence in patients with prostate and renal cancers. Overall, we discuss the biogenesis, isolation, liquid-biopsy, and therapeutic applications of EVs in CRPC, NEPC, and RCC. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Figure 1

25 pages, 1845 KiB

Open AccessReview

CTC, ctDNA, and Exosome in Thyroid Cancers: A Review

by Wenwen Wang, Zhiyao Zheng and Jianyong Lei

Int. J. Mol. Sci. 2023, 24(18), 13767; https://doi.org/10.3390/ijms241813767 - 6 Sep 2023

Cited by 11 | Viewed by 3448

Abstract

Thyroid cancer has become more common in recent years all around the world. Many issues still need to be urgently addressed in the diagnosis, treatment, and prognosis of thyroid cancer. Liquid biopsy (mainly circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and circulating [...] Read more.

Thyroid cancer has become more common in recent years all around the world. Many issues still need to be urgently addressed in the diagnosis, treatment, and prognosis of thyroid cancer. Liquid biopsy (mainly circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and circulating exosomes) may provide a novel and ideal approach to solve these issues, allows us to assess the features of diseases more comprehensively, and has a function in a variety of malignancies. Recently, liquid biopsy has been shown to be critical in thyroid cancer diagnosis, treatment, and prognosis in numerous previous studies. In this review, by testing CTCs, ctDNA, and exosomes, we focus on the possible clinical role of liquid biopsy in thyroid cancer, including diagnostic and prognostic biomarkers and response to therapy. We briefly review how liquid biopsy components have progressed in thyroid cancer by consulting the existing public information. We also discuss the clinical potential of liquid biopsy in thyroid cancer and provide a reference for liquid biopsy research. Liquid biopsy has the potential to be a useful tool in the early detection, monitoring, or prediction of response to therapies and prognosis in thyroid cancer, with promising clinical applications. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Figure 1

28 pages, 827 KiB

Open AccessReview

Using cfDNA and ctDNA as Oncologic Markers: A Path to Clinical Validation

by Jonathan Dao, Patrick J. Conway, Baskaran Subramani, Devi Meyyappan, Sammy Russell and Daruka Mahadevan

Int. J. Mol. Sci. 2023, 24(17), 13219; https://doi.org/10.3390/ijms241713219 - 25 Aug 2023

Cited by 40 | Viewed by 8293

Abstract

The detection of circulating tumor DNA (ctDNA) in liquid biopsy samples as an oncological marker is being used in clinical trials at every step of clinical management. As ctDNA-based liquid biopsy kits are developed and used in clinics, companies work towards increased convenience, [...] Read more.

The detection of circulating tumor DNA (ctDNA) in liquid biopsy samples as an oncological marker is being used in clinical trials at every step of clinical management. As ctDNA-based liquid biopsy kits are developed and used in clinics, companies work towards increased convenience, accuracy, and cost over solid biopsies and other oncological markers. The technology used to differentiate ctDNA and cell-free DNA (cfDNA) continues to improve with new tests and methodologies being able to detect down to mutant allele frequencies of 0.001% or 1/100,000 copies. Recognizing this development in technology, the FDA has recently given pre-market approval and breakthrough device designations to multiple companies. The purpose of this review is to look at the utility of measuring total cfDNA, techniques used to differentiate ctDNA from cfDNA, and the utility of different ctDNA-based liquid biopsy kits using relevant articles from PubMed, clinicaltrials.gov, FDA approvals, and company newsletters. Measuring total cfDNA could be a cost-effective, viable prognostic marker, but various factors do not favor it as a monitoring tool during chemotherapy. While there may be a place in the clinic for measuring total cfDNA in the future, the lack of standardization means that it is difficult to move forward with large-scale clinical validation studies currently. While the detection of ctDNA has promising standardized liquid biopsy kits from various companies with large clinical trials ongoing, their applications in screening and minimal residual disease can suffer from lower sensitivity. However, researchers are working towards solutions to these issues with innovations in technology, multi-omics, and sampling. With great promise, further research is needed before liquid biopsies can be recommended for everyday clinical management. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Figure 1

14 pages, 1347 KiB

Open AccessReview

Circulating Tumor DNA as a Minimal Residual Disease Assessment and Recurrence Risk in Patients Undergoing Curative-Intent Resection with or without Adjuvant Chemotherapy in Colorectal Cancer: A Systematic Review and Meta-Analysis

by Anusha Chidharla, Eliot Rapoport, Kriti Agarwal, Samragnyi Madala, Brenda Linares, Weijing Sun, Sakti Chakrabarti and Anup Kasi

Int. J. Mol. Sci. 2023, 24(12), 10230; https://doi.org/10.3390/ijms241210230 - 16 Jun 2023

Cited by 22 | Viewed by 4919

Abstract

Emerging data have suggested that circulating tumor DNA (ctDNA) can be a reliable biomarker for minimal residual disease (MRD) in CRC patients. Recent studies have shown that the ability to detect MRD using ctDNA assay after curative-intent surgery will change how to assess [...] Read more.

Emerging data have suggested that circulating tumor DNA (ctDNA) can be a reliable biomarker for minimal residual disease (MRD) in CRC patients. Recent studies have shown that the ability to detect MRD using ctDNA assay after curative-intent surgery will change how to assess the recurrence risk and patient selection for adjuvant chemotherapy. We performed a meta-analysis of post-operative ctDNA in stage I–IV (oligometastatic) CRC patients after curative-intent resection. We included 23 studies representing 3568 patients with evaluable ctDNA in CRC patient post-curative-intent surgery. Data were extracted from each study to perform a meta-analysis using RevMan 5.4. software. Subsequent subgroup analysis was performed for stages I–III and oligometastatic stage IV CRC patients. Results showed that the pooled hazard ratio (HR) for recurrence-free survival (RFS) in post-surgical ctDNA-positive versus -negative patients in all stages was 7.27 (95% CI 5.49–9.62), p < 0.00001. Subgroup analysis revealed pooled HRs of 8.14 (95% CI 5.60–11.82) and 4.83 (95% CI 3.64–6.39) for stages I–III and IV CRC, respectively. The pooled HR for RFS in post-adjuvant chemotherapy ctDNA-positive versus -negative patients in all stages was 10.59 (95% CI 5.59–20.06), p < 0.00001. Circulating tumor DNA (ctDNA) analysis has revolutionized non-invasive cancer diagnostics and monitoring, with two primary forms of analysis emerging: tumor-informed techniques and tumor-agnostic or tumor-naive techniques. Tumor-informed methods involve the initial identification of somatic mutations in tumor tissue, followed by the targeted sequencing of plasma DNA using a personalized assay. In contrast, the tumor-agnostic approach performs ctDNA analysis without prior knowledge of the patient’s tumor tissue molecular profile. This review highlights the distinctive features and implications of each approach. Tumor-informed techniques enable the precise monitoring of known tumor-specific mutations, leveraging the sensitivity and specificity of ctDNA detection. Conversely, the tumor-agnostic approach allows for a broader genetic and epigenetic analysis, potentially revealing novel alterations and enhancing our understanding of tumor heterogeneity. Both approaches have significant implications for personalized medicine and improved patient outcomes in the field of oncology. The subgroup analysis based on the ctDNA method showed pooled HRs of 8.66 (95% CI 6.38–11.75) and 3.76 (95% CI 2.58–5.48) for tumor-informed and tumor-agnostic, respectively. Our analysis emphasizes that post-operative ctDNA is a strong prognostic marker of RFS. Based on our results, ctDNA can be a significant and independent predictor of RFS. This real-time assessment of treatment benefits using ctDNA can be used as a surrogate endpoint for the development of novel drugs in the adjuvant setting. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Figure 1

12 pages, 660 KiB

Open AccessReview

Is There a Role for Machine Learning in Liquid Biopsy for Brain Tumors? A Systematic Review

by Grazia Menna, Giacomo Piaser Guerrato, Lal Bilgin, Giovanni Maria Ceccarelli, Alessandro Olivi and Giuseppe Maria Della Pepa

Int. J. Mol. Sci. 2023, 24(11), 9723; https://doi.org/10.3390/ijms24119723 - 3 Jun 2023

Cited by 10 | Viewed by 2635

Abstract

The paucity of studies available in the literature on brain tumors demonstrates that liquid biopsy (LB) is not currently applied for central nervous system (CNS) cancers. The purpose of this systematic review focused on the application of machine learning (ML) to LB for [...] Read more.

The paucity of studies available in the literature on brain tumors demonstrates that liquid biopsy (LB) is not currently applied for central nervous system (CNS) cancers. The purpose of this systematic review focused on the application of machine learning (ML) to LB for brain tumors to provide practical guidance for neurosurgeons to understand the state-of-the-art practices and open challenges. The herein presented study was conducted in accordance with the PRISMA-P (preferred reporting items for systematic review and meta-analysis protocols) guidelines. An online literature search was launched on PubMed/Medline, Scopus, and Web of Science databases using the following query: “((Liquid biopsy) AND (Glioblastoma OR Brain tumor) AND (Machine learning OR Artificial Intelligence))”. The last database search was conducted in April 2023. Upon the full-text review, 14 articles were included in the study. These were then divided into two subgroups: those dealing with applications of machine learning to liquid biopsy in the field of brain tumors, which is the main aim of this review (n = 8); and those dealing with applications of machine learning to liquid biopsy in the diagnosis of other tumors (n = 6). Although studies on the application of ML to LB in the field of brain tumors are still in their infancy, the rapid development of new techniques, as evidenced by the increase in publications on the subject in the past two years, may in the future allow for rapid, accurate, and noninvasive analysis of tumor data. Thus making it possible to identify key features in the LB samples that are associated with the presence of a brain tumor. These features could then be used by doctors for disease monitoring and treatment planning. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Figure 1

15 pages, 703 KiB

Open AccessReview

Circulating Tumor DNA in Gastric Adenocarcinoma: Future Clinical Applications and Perspectives

by Giulia Grizzi, Massimiliano Salati, Maria Bonomi, Margherita Ratti, Lauren Holladay, Maria Caterina De Grandis, Daniele Spada, Gian Luca Baiocchi and Michele Ghidini

Int. J. Mol. Sci. 2023, 24(11), 9421; https://doi.org/10.3390/ijms24119421 - 29 May 2023

Cited by 13 | Viewed by 3117

Abstract

Gastric cancer (GC) is still one of the most aggressive cancers with a few targetable alterations and a dismal prognosis. A liquid biopsy allows for identifying and analyzing the DNA released from tumor cells into the bloodstream. Compared to tissue-based biopsy, liquid biopsy [...] Read more.

Gastric cancer (GC) is still one of the most aggressive cancers with a few targetable alterations and a dismal prognosis. A liquid biopsy allows for identifying and analyzing the DNA released from tumor cells into the bloodstream. Compared to tissue-based biopsy, liquid biopsy is less invasive, requires fewer samples, and can be repeated over time in order to longitudinally monitor tumor burden and molecular changes. Circulating tumor DNA (ctDNA) has been recognized to have a prognostic role in all the disease stages of GC. The aim of this article is to review the current and future applications of ctDNA in gastric adenocarcinoma, in particular, with respect to early diagnosis, the detection of minimal residual disease (MRD) following curative surgery, and in the advanced disease setting for treatment decision choice and therapeutic monitoring. Although liquid biopsies have shown potentiality, pre-analytical and analytical steps must be standardized and validated to ensure the reproducibility and standardization of the procedures and data analysis methods. Further research is needed to allow the use of liquid biopsy in everyday clinical practice. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Figure 1

26 pages, 893 KiB

Open AccessReview

Liquid Biopsy in Lung Cancer: Biomarkers for the Management of Recurrence and Metastasis

by Vanessa G. P. Souza, Aisling Forder, Liam J. Brockley, Michelle E. Pewarchuk, Nikita Telkar, Rachel Paes de Araújo, Jessica Trejo, Katya Benard, Ana Laura Seneda, Iael W. Minutentag, Melis Erkan, Greg L. Stewart, Erica N. Hasimoto, Cathie Garnis, Wan L. Lam, Victor D. Martinez and Patricia P. Reis

Int. J. Mol. Sci. 2023, 24(10), 8894; https://doi.org/10.3390/ijms24108894 - 17 May 2023

Cited by 18 | Viewed by 7597

Abstract

Liquid biopsies have emerged as a promising tool for the detection of metastases as well as local and regional recurrence in lung cancer. Liquid biopsy tests involve analyzing a patient’s blood, urine, or other body fluids for the detection of biomarkers, including circulating [...] Read more.

Liquid biopsies have emerged as a promising tool for the detection of metastases as well as local and regional recurrence in lung cancer. Liquid biopsy tests involve analyzing a patient’s blood, urine, or other body fluids for the detection of biomarkers, including circulating tumor cells or tumor-derived DNA/RNA that have been shed into the bloodstream. Studies have shown that liquid biopsies can detect lung cancer metastases with high accuracy and sensitivity, even before they are visible on imaging scans. Such tests are valuable for early intervention and personalized treatment, aiming to improve patient outcomes. Liquid biopsies are also minimally invasive compared to traditional tissue biopsies, which require the removal of a sample of the tumor for further analysis. This makes liquid biopsies a more convenient and less risky option for patients, particularly those who are not good candidates for invasive procedures due to other medical conditions. While liquid biopsies for lung cancer metastases and relapse are still being developed and validated, they hold great promise for improving the detection and treatment of this deadly disease. Herein, we summarize available and novel approaches to liquid biopsy tests for lung cancer metastases and recurrence detection and describe their applications in clinical practice. Full article

(This article belongs to the Special Issue Liquid Biopsy in Cancers)

► Show Figures

Graphical abstract

Journal Menu

Journal Browser

Liquid Biopsy in Cancers

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (16 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI