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1.
Sci Rep ; 14(1): 10199, 2024 05 03.
Article in English | MEDLINE | ID: mdl-38702437

ABSTRACT

In pancreatic ductal adenocarcinoma (PDAC) patients, the importance of peritoneal lavage cytology, which indicates unresectability, remains controversial. This study sought to determine whether positive peritoneal lavage cytology (CY+) precludes pancreatectomy. Furthermore, we propose a novel liquid biopsy using peritoneal lavage fluid to detect viable peritoneal tumor cells (v-PTCs) with TelomeScan F35, a telomerase-specific replication-selective adenovirus engineered to express green fluorescent protein. Resectable cytologically or histologically proven PDAC patients (n = 53) were enrolled. CY was conducted immediately following laparotomy. The resulting fluid was examined by conventional cytology (conv-CY; Papanicolaou staining and MOC-31 immunostaining) and by the novel technique (Telo-CY; using TelomeScan F35). Of them, 5 and 12 were conv-CY+ and Telo-CY+, respectively. All underwent pancreatectomy. The two double-CY+ (conv-CY+ and Telo-CY+) patients showed early peritoneal recurrence (P-rec) postoperatively, despite adjuvant chemotherapy. None of the three conv-CY+ Telo-CY- patients exhibited P-rec. Six of the 10 Telo-CY+ conv-CY- patients (60%) relapsed with P-rec. Of the remaining 38 double-CY- [conv-CY-, Telo-CY-, conv-CY± (Class III)] patients, 3 (8.3%) exhibited P-rec. Although conv-CY+ status predicted poor prognosis and a higher risk of P-rec, Telo-CY was more sensitive for detecting v-PTC. Staging laparoscopy and performing conv-CY and Telo-CY are needed to confirm the indication for pancreatectomy.


Subject(s)
Carcinoma, Pancreatic Ductal , Pancreatectomy , Pancreatic Neoplasms , Peritoneal Lavage , Humans , Pancreatic Neoplasms/pathology , Pancreatic Neoplasms/diagnosis , Pancreatic Neoplasms/surgery , Male , Female , Aged , Middle Aged , Carcinoma, Pancreatic Ductal/pathology , Carcinoma, Pancreatic Ductal/diagnosis , Cytodiagnosis/methods , Aged, 80 and over , Neoplasm Recurrence, Local/pathology , Liquid Biopsy/methods , Peritoneal Neoplasms/pathology , Peritoneal Neoplasms/diagnosis , Adult , Cytology
2.
JAMA Netw Open ; 7(5): e2410171, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38713467

ABSTRACT

This cross-sectional study evaluates the information on a circulating tumor DNA test available to the public on popular internet resources.


Subject(s)
Access to Information , Humans , Liquid Biopsy/methods , Female , Male , Middle Aged
3.
Mol Biomed ; 5(1): 17, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38724687

ABSTRACT

Uveal cancer (UM) offers a complex molecular landscape characterized by substantial heterogeneity, both on the genetic and epigenetic levels. This heterogeneity plays a critical position in shaping the behavior and response to therapy for this uncommon ocular malignancy. Targeted treatments with gene-specific therapeutic molecules may prove useful in overcoming radiation resistance, however, the diverse molecular makeups of UM call for a patient-specific approach in therapy procedures. We need to understand the intricate molecular landscape of UM to develop targeted treatments customized to each patient's specific genetic mutations. One of the promising approaches is using liquid biopsies, such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), for detecting and monitoring the disease at the early stages. These non-invasive methods can help us identify the most effective treatment strategies for each patient. Single-cellular is a brand-new analysis platform that gives treasured insights into diagnosis, prognosis, and remedy. The incorporation of this data with known clinical and genomics information will give a better understanding of the complicated molecular mechanisms that UM diseases exploit. In this review, we focused on the heterogeneity and molecular panorama of UM, and to achieve this goal, the authors conducted an exhaustive literature evaluation spanning 1998 to 2023, using keywords like "uveal melanoma, "heterogeneity". "Targeted therapies"," "CTCs," and "single-cellular analysis".


Subject(s)
Genetic Heterogeneity , Melanoma , Molecular Targeted Therapy , Uveal Neoplasms , Humans , Melanoma/genetics , Melanoma/pathology , Melanoma/therapy , Melanoma/drug therapy , Molecular Targeted Therapy/methods , Uveal Neoplasms/genetics , Uveal Neoplasms/therapy , Uveal Neoplasms/pathology , Neoplastic Cells, Circulating/metabolism , Neoplastic Cells, Circulating/pathology , Biomarkers, Tumor/genetics , Mutation , Circulating Tumor DNA/genetics , Circulating Tumor DNA/blood , Liquid Biopsy/methods
4.
Technol Cancer Res Treat ; 23: 15330338241252706, 2024.
Article in English | MEDLINE | ID: mdl-38766867

ABSTRACT

Objectives: In this study, stool samples were evaluated for tumor mutation analysis via a targeted next generation sequencing (NGS) approach in a small patient cohort suffering from localized rectal cancer. Introduction: Colorectal cancer (CRC) causes the second highest cancer-related death rate worldwide. Thus, improvements in disease assessment and monitoring that may facilitate treatment allocation and allow organ-sparing "watch-and-wait" treatment strategies are highly relevant for a significant number of CRC patients. Methods: Stool-based results were compared with mutation profiles derived from liquid biopsies and the gold standard procedure of tumor biopsy from the same patients. A workflow was established that enables the detection of de-novo tumor mutations in stool samples of CRC patients via ultra-sensitive cell-free tumor DNA target enrichment. Results: Notably, only a 19% overall concordance was found in mutational profiles across the compared sample specimens of stool, tumor, and liquid biopsies. Conclusion: Based on these results, the analysis of stool and liquid biopsy samples can provide important additional information on tumor heterogeneity and potentially on the assessment of minimal residual disease and clonal tumor evolution.


Subject(s)
Biomarkers, Tumor , Feces , High-Throughput Nucleotide Sequencing , Mutation , Rectal Neoplasms , Humans , Feces/chemistry , Rectal Neoplasms/genetics , Rectal Neoplasms/pathology , Rectal Neoplasms/blood , Biomarkers, Tumor/genetics , Liquid Biopsy/methods , Female , Male , Circulating Tumor DNA/genetics , Circulating Tumor DNA/blood , Middle Aged , Aged , DNA Mutational Analysis , Genetic Heterogeneity , DNA, Neoplasm/blood , DNA, Neoplasm/genetics
5.
Sci Rep ; 14(1): 11398, 2024 05 18.
Article in English | MEDLINE | ID: mdl-38762534

ABSTRACT

Glioblastoma (GB) is a devastating tumor of the central nervous system characterized by a poor prognosis. One of the best-established predictive biomarker in IDH-wildtype GB is O6-methylguanine-DNA methyltransferase (MGMT) methylation (mMGMT), which is associated with improved treatment response and survival. However, current efforts to monitor GB patients through mMGMT detection have proven unsuccessful. Small extracellular vesicles (sEVs) hold potential as a key element that could revolutionize clinical practice by offering new possibilities for liquid biopsy. This study aimed to determine the utility of sEV-based liquid biopsy as a predictive biomarker and disease monitoring tool in patients with IDH-wildtype GB. Our findings show consistent results with tissue-based analysis, achieving a remarkable sensitivity of 85.7% for detecting mMGMT in liquid biopsy, the highest reported to date. Moreover, we suggested that liquid biopsy assessment of sEV-DNA could be a powerful tool for monitoring disease progression in IDH-wildtype GB patients. This study highlights the critical significance of overcoming molecular underdetection, which can lead to missed treatment opportunities and misdiagnoses, possibly resulting in ineffective therapies. The outcomes of our research significantly contribute to the field of sEV-DNA-based liquid biopsy, providing valuable insights into tumor tissue heterogeneity and establishing it as a promising tool for detecting GB biomarkers. These results have substantial implications for advancing predictive and therapeutic approaches in the context of GB and warrant further exploration and validation in clinical settings.


Subject(s)
Biomarkers, Tumor , Brain Neoplasms , DNA Methylation , DNA Modification Methylases , DNA Repair Enzymes , Extracellular Vesicles , Glioblastoma , Tumor Suppressor Proteins , Humans , Glioblastoma/genetics , Glioblastoma/pathology , Glioblastoma/diagnosis , Extracellular Vesicles/metabolism , Extracellular Vesicles/genetics , Liquid Biopsy/methods , DNA Modification Methylases/genetics , DNA Modification Methylases/metabolism , DNA Repair Enzymes/genetics , DNA Repair Enzymes/metabolism , Male , Female , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Middle Aged , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/metabolism , Brain Neoplasms/genetics , Brain Neoplasms/pathology , Brain Neoplasms/diagnosis , Aged , Adult , Prognosis
6.
Int J Mol Sci ; 25(9)2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38732099

ABSTRACT

Medulloblastoma is the most common malignant brain tumor in childhood. Initial treatment generally includes surgery, irradiation, and chemotherapy. Approximately 20-30% of patients will experience a recurrence, which portends a very poor prognosis. The current standard of care for evaluation for relapse includes radiographic surveillance with magnetic resonance imaging at regular intervals. The presence of circulating tumor DNA in the cerebrospinal fluid has been demonstrated to be a predictor of a higher risk of progression in a research setting for patients with medulloblastoma treated on a prospective single institution clinical trial. We have previously published and clinically validated a liquid-biopsy-based genetic assay utilizing low-pass whole genome sequencing to detect copy number alterations in circulating tumor DNA. Here, we present two teenage patients with posterior fossa medulloblastoma with recurrent disease who have been monitored with serial liquid biopsies showing tumor evolution over time, demonstrating the clinical utility of these approaches.


Subject(s)
Cerebellar Neoplasms , Medulloblastoma , Neoplasm Recurrence, Local , Humans , Medulloblastoma/cerebrospinal fluid , Medulloblastoma/genetics , Medulloblastoma/diagnosis , Medulloblastoma/pathology , Medulloblastoma/diagnostic imaging , Liquid Biopsy/methods , Neoplasm Recurrence, Local/cerebrospinal fluid , Neoplasm Recurrence, Local/genetics , Adolescent , Cerebellar Neoplasms/cerebrospinal fluid , Cerebellar Neoplasms/diagnosis , Cerebellar Neoplasms/pathology , Cerebellar Neoplasms/genetics , Male , Circulating Tumor DNA/cerebrospinal fluid , Circulating Tumor DNA/genetics , Circulating Tumor DNA/blood , Female , Disease Progression , Magnetic Resonance Imaging
7.
J Neurooncol ; 168(2): 215-224, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38755519

ABSTRACT

PURPOSE: Clinical sequencing of tumor DNA is necessary to render an integrated diagnosis and select therapy for children with primary central nervous system (CNS) tumors, but neurosurgical biopsy is not without risk. In this study, we describe cell-free DNA (cfDNA) in blood and cerebrospinal fluid (CSF) as sources for "liquid biopsy" in pediatric brain tumors. METHODS: CSF samples were collected by lumbar puncture, ventriculostomy, or surgery from pediatric patients with CNS tumors. Following extraction, CSF-derived cfDNA was sequenced using UW-OncoPlex™, a clinically validated next-generation sequencing platform. CSF-derived cfDNA results and paired plasma and tumor samples concordance was also evaluated. RESULTS: Seventeen CSF samples were obtained from 15 pediatric patients with primary CNS tumors. Tumor types included medulloblastoma (n = 7), atypical teratoid/rhabdoid tumor (n = 2), diffuse midline glioma with H3 K27 alteration (n = 4), pilocytic astrocytoma (n = 1), and pleomorphic xanthoastrocytoma (n = 1). CSF-derived cfDNA was detected in 9/17 (53%) of samples, and sufficient for sequencing in 8/10 (80%) of extracted samples. All somatic mutations and copy-number variants were also detected in matched tumor tissue, and tumor-derived cfDNA was absent in plasma samples and controls. Tumor-derived cfDNA alterations were detected in the absence of cytological evidence of malignant cells in as little as 200 µl of CSF. Several clinically relevant alterations, including a KIAA1549::BRAF fusion were detected. CONCLUSIONS: Clinically relevant genomic alterations are detectable using CSF-derived cfDNA across a range of pediatric brain tumors. Next-generation sequencing platforms are capable of producing a high yield of DNA alterations with 100% concordance rate with tissue analysis.


Subject(s)
Biomarkers, Tumor , Brain Neoplasms , Circulating Tumor DNA , High-Throughput Nucleotide Sequencing , Humans , Child , Brain Neoplasms/genetics , Brain Neoplasms/cerebrospinal fluid , Brain Neoplasms/diagnosis , Male , Female , Child, Preschool , Adolescent , Infant , Circulating Tumor DNA/cerebrospinal fluid , Circulating Tumor DNA/genetics , Circulating Tumor DNA/blood , High-Throughput Nucleotide Sequencing/methods , Biomarkers, Tumor/genetics , Biomarkers, Tumor/cerebrospinal fluid , Cell-Free Nucleic Acids/cerebrospinal fluid , Cell-Free Nucleic Acids/genetics , Cell-Free Nucleic Acids/blood , Liquid Biopsy/methods , Mutation
8.
Biosens Bioelectron ; 259: 116382, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-38749284

ABSTRACT

Small extracellular vesicles (sEVs) reflect the genotype and phenotype of original cells and are biomarkers for early diagnosis and treatment monitoring of tumors. Yet, their small size and low density make them difficult to isolate and detect in body fluid samples. This study proposes a novel acDEP-Exo chip filled with transparent micro-beads, which formed a non-uniform electrical field, and finally achieved rapid, sensitive, and tunable sEVs capture and detection. The method requires only 20-50 µL of sample, achieved a limit of detection (LOD) of 161 particles/µL, and can detect biomarkers within 13 min. We applied the chip to analyze the two markers of sEV's EpCAM and MUC1 in clinical plasma samples from breast cancer (BC) patients and healthy volunteers and found that the combined evaluation of sEV's biomarkers has extremely high sensitivity, specificity and accuracy. The present study introduces an alternative approach to sEVs isolation and detection, has a great potential in real-time sEVs-based liquid biopsy.


Subject(s)
Biomarkers, Tumor , Biosensing Techniques , Breast Neoplasms , Epithelial Cell Adhesion Molecule , Extracellular Vesicles , Lab-On-A-Chip Devices , Mucin-1 , Humans , Breast Neoplasms/diagnosis , Breast Neoplasms/blood , Extracellular Vesicles/chemistry , Female , Biosensing Techniques/instrumentation , Biosensing Techniques/methods , Mucin-1/blood , Mucin-1/analysis , Biomarkers, Tumor/blood , Biomarkers, Tumor/isolation & purification , Limit of Detection , Equipment Design , Electrophoresis/instrumentation , Microfluidic Analytical Techniques/instrumentation , Liquid Biopsy/methods , Liquid Biopsy/instrumentation
9.
Biosens Bioelectron ; 259: 116411, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-38781696

ABSTRACT

The carbohydrate antigen 19-9 (CA19-9) is commonly used as a representative biomarker for pancreatic cancer (PC); however, it lacks sensitivity and specificity for early-stage PC diagnosis. Furthermore, some patients with PC are negative for CA19-9 (<37 U/mL), which introduces additional limitations to their accurate diagnosis and treatment. Hence, improved methods to accurately detect PC stages in CA19-9-negative patients are warranted. In this study, tumor-proximal liquid biopsy and inertial microfluidics were coupled to enable high-throughput enrichment of portal venous circulating tumor cells (CTCs) and support the effective diagnosis of patients with early-stage PC. The proposed inertial microfluidic system was shown to provide size-based enrichment of CTCs using inertial focusing and Dean flow effects in slanted spiral channels. Notably, portal venous blood samples were found to have twice the yield of CTCs (21.4 cells per 5 mL) compared with peripheral blood (10.9 CTCs per 5 mL). A combination of peripheral and portal CTC data along with CA19-9 results showed to greatly improve the average accuracy of CA19-9-negative PC patients from 47.1% with regular CA19-9 tests up to 87.1%. Hence, portal venous CTC-based microfluidic biopsy can be used with high sensitivity and specificity for the diagnosis of early-stage PC, particularly in CA19-9-negative patients.


Subject(s)
Biosensing Techniques , CA-19-9 Antigen , Neoplastic Cells, Circulating , Pancreatic Neoplasms , Portal Vein , Humans , Pancreatic Neoplasms/blood , Pancreatic Neoplasms/diagnosis , Pancreatic Neoplasms/pathology , Neoplastic Cells, Circulating/pathology , CA-19-9 Antigen/blood , Biosensing Techniques/instrumentation , Biomarkers, Tumor/blood , Male , Female , Middle Aged , Microfluidic Analytical Techniques/instrumentation , Microfluidics/methods , Liquid Biopsy/methods
10.
Int J Mol Sci ; 25(10)2024 May 07.
Article in English | MEDLINE | ID: mdl-38791138

ABSTRACT

An early diagnosis of cancer is fundamental not only in regard to reducing its mortality rate but also in terms of counteracting the progression of the tumor in the initial stages. Breast cancer (BC) is the most common tumor pathology in women and the second deathliest cancer worldwide, although its survival rate is increasing thanks to improvements in screening programs. However, the most common techniques to detect a breast tumor tend to be time-consuming, unspecific or invasive. Herein, the use of untargeted hydrophilic interaction liquid chromatography-mass spectrometry analysis appears as an analytical technique with potential use for the early detection of biomarkers in liquid biopsies from BC patients. In this research, plasma samples from 134 BC patients were compared with 136 from healthy controls (HC), and multivariate statistical analyses showed a clear separation between four BC phenotypes (LA, LB, HER2, and TN) and the HC group. As a result, we identified two candidate biomarkers that discriminated between the groups under study with a VIP > 1 and an AUC of 0.958. Thus, targeting the specific aberrant metabolic pathways in future studies may allow for better molecular stratification or early detection of the disease.


Subject(s)
Biomarkers, Tumor , Breast Neoplasms , Hydrophobic and Hydrophilic Interactions , Metabolomics , Humans , Breast Neoplasms/blood , Breast Neoplasms/diagnosis , Breast Neoplasms/metabolism , Breast Neoplasms/pathology , Female , Biomarkers, Tumor/blood , Liquid Biopsy/methods , Metabolomics/methods , Middle Aged , Chromatography, Liquid/methods , Aged , Adult , Mass Spectrometry/methods , Liquid Chromatography-Mass Spectrometry
11.
Anal Chim Acta ; 1308: 342578, 2024 Jun 15.
Article in English | MEDLINE | ID: mdl-38740462

ABSTRACT

Cancer is one of the serious threats to public life and health. Early diagnosis, real-time monitoring, and individualized treatment are the keys to improve the survival rate and prolong the survival time of cancer patients. Liquid biopsy is a potential technique for cancer early diagnosis due to its non-invasive and continuous monitoring properties. However, most current liquid biopsy techniques lack the ability to detect cancers at the early stage. Therefore, effective detection of a variety of cancers is expected through the combination of various techniques. Recently, DNA frameworks with tailorable functionality and precise addressability have attracted wide spread attention in biomedical applications, especially in detecting cancer biomarkers such as circulating tumor cells (CTCs), exosomes and circulating tumor nucleic acid (ctNA). Encouragingly, DNA frameworks perform outstanding in detecting these cancer markers, but also face some challenges and opportunities. In this review, we first briefly introduced the development of DNA frameworks and its typical structural characteristics and advantages. Then, we mainly focus on the recent progress of DNA frameworks in detecting commonly used cancer markers in liquid-biopsy. We summarize the advantages and applications of DNA frameworks for detecting CTCs, exosomes and ctNA. Furthermore, we provide an outlook on the possible opportunities and challenges for exploiting the structural advantages of DNA frameworks in the field of cancer diagnosis. Finally, we envision the marriage of DNA frameworks with other emerging materials and technologies to develop the next generation of disease diagnostic biosensors.


Subject(s)
DNA , Neoplasms , Liquid Biopsy/methods , Humans , DNA/chemistry , Neoplasms/diagnosis , Neoplasms/pathology , Biomarkers, Tumor/analysis , Neoplastic Cells, Circulating/pathology , Circulating Tumor DNA/blood , Circulating Tumor DNA/analysis , Exosomes/chemistry
12.
Cancer Control ; 31: 10732748241255548, 2024.
Article in English | MEDLINE | ID: mdl-38764160

ABSTRACT

Background: Ovarian cancer stands as the deadliest malignant tumor within the female reproductive tract. As a result of the absence of effective diagnostic and monitoring markers, 75% of ovarian cancer cases are diagnosed at a late stage, leading to a mere 50% survival rate within five years. The advancement of molecular biology is essential for accurate diagnosis and treatment of ovarian cancer. Methods: A review of several randomized clinical trials, focusing on the ovarian cancer, was undertaken. The advancement of molecular biology and diagnostic methods related to accurate diagnosis and treatment of ovarian cancer were examined. Results: Liquid biopsy is an innovative method of detecting malignant tumors that has gained increasing attention over the past few years. Cell-free DNA assay-based liquid biopsies show potential in delineating tumor status heterogeneity and tracking tumor recurrence. DNA methylation influences a multitude of biological functions and diseases, especially during the initial phases of cancer. The cell-free DNA methylation profiling system has emerged as a sensitive and non-invasive technique for identifying and detecting the biological origins of cancer. It holds promise as a biomarker, enabling early screening, recurrence monitoring, and prognostic evaluation of cancer. Conclusions: This review evaluates recent advancements and challenges associated with cell-free DNA methylation analysis for the diagnosis, prognosis monitoring, and assessment of therapeutic responses in the management of ovarian cancers, aiming to offer guidance for precise diagnosis and treatment of this disease.


Ovarian cancer stands as the deadliest malignant tumor within the female reproductive tract. As a result of the absence of effective diagnostic and monitoring markers, 75% of ovarian cancer cases are diagnosed at a late stage, leading to a mere 50% survival rate within five years. Nearly 80% of advanced stages have a poor prognosis or recurrence within five years. Ovarian cancer is linked to a grim long-term prognosis attributable to its elevated mortality and recurrence rates. The advancement of molecular biology and diagnostic methods is essential for accurate diagnosis and treatment of ovarian cancer. Liquid biopsy is an innovative method of detecting malignant tumors that has gained increasing attention over the past few years. Cell-free DNA assay-based liquid biopsies show potential in delineating tumor status heterogeneity and tracking tumor recurrence. DNA methylation represents a prevalent epigenetic modification. DNA methylation influences a multitude of biological functions and diseases, especially during the initial phases of cancer. The cell-free DNA methylation profiling system has emerged as a sensitive and non-invasive technique for identifying and detecting the biological origins of cancer. This review assesses recent progress and obstacles linked to cell-free DNA methylation analysis for diagnosing, prognostic monitoring, and evaluating therapeutic responses in managing ovarian cancers.


Subject(s)
Biomarkers, Tumor , DNA Methylation , Ovarian Neoplasms , Humans , Female , Ovarian Neoplasms/genetics , Ovarian Neoplasms/diagnosis , Ovarian Neoplasms/pathology , Prognosis , Biomarkers, Tumor/genetics , Cell-Free Nucleic Acids/genetics , Liquid Biopsy/methods
13.
PLoS One ; 19(5): e0302129, 2024.
Article in English | MEDLINE | ID: mdl-38753705

ABSTRACT

Emerging technologies focused on the detection and quantification of circulating tumor DNA (ctDNA) in blood show extensive potential for managing patient treatment decisions, informing risk of recurrence, and predicting response to therapy. Currently available tissue-informed approaches are often limited by the need for additional sequencing of normal tissue or peripheral mononuclear cells to identify non-tumor-derived alterations while tissue-naïve approaches are often limited in sensitivity. Here we present the analytical validation for a novel ctDNA monitoring assay, FoundationOne®Tracker. The assay utilizes somatic alterations from comprehensive genomic profiling (CGP) of tumor tissue. A novel algorithm identifies monitorable alterations with a high probability of being somatic and computationally filters non-tumor-derived alterations such as germline or clonal hematopoiesis variants without the need for sequencing of additional samples. Monitorable alterations identified from tissue CGP are then quantified in blood using a multiplex polymerase chain reaction assay based on the validated SignateraTM assay. The analytical specificity of the plasma workflow is shown to be 99.6% at the sample level. Analytical sensitivity is shown to be >97.3% at ≥5 mean tumor molecules per mL of plasma (MTM/mL) when tested with the most conservative configuration using only two monitorable alterations. The assay also demonstrates high analytical accuracy when compared to liquid biopsy-based CGP as well as high qualitative (measured 100% PPA) and quantitative precision (<11.2% coefficient of variation).


Subject(s)
Circulating Tumor DNA , Neoplasms , Humans , Circulating Tumor DNA/blood , Circulating Tumor DNA/genetics , Neoplasms/genetics , Neoplasms/blood , Neoplasms/diagnosis , Genomics/methods , Biomarkers, Tumor/blood , Biomarkers, Tumor/genetics , Sensitivity and Specificity , Algorithms , Multiplex Polymerase Chain Reaction/methods , Liquid Biopsy/methods
14.
Int J Mol Sci ; 25(10)2024 May 10.
Article in English | MEDLINE | ID: mdl-38791247

ABSTRACT

Over the last decades, the survival of multiple myeloma (MM) patients has considerably improved. However, despite the availability of new treatments, most patients still relapse and become therapy-resistant at some point in the disease evolution. The mutation profile has an impact on MM patients' outcome, while typically evolving over time. Because of the patchy bone marrow (BM) infiltration pattern, the analysis of a single bone marrow sample can lead to an underestimation of the known genetic heterogeneity in MM. As a result, interest is shifting towards blood-derived liquid biopsies, which allow for a more comprehensive and non-invasive genetic interrogation without the discomfort of repeated BM aspirations. In this review, we compare the application potential for mutation profiling in MM of circulating-tumor-cell-derived DNA, cell-free DNA and extracellular-vesicle-derived DNA, while also addressing the challenges associated with their use.


Subject(s)
Multiple Myeloma , Mutation , Multiple Myeloma/genetics , Multiple Myeloma/pathology , Multiple Myeloma/diagnosis , Humans , Liquid Biopsy/methods , Circulating Tumor DNA/genetics , Cell-Free Nucleic Acids/genetics , Biomarkers, Tumor/genetics , DNA Mutational Analysis/methods , Neoplastic Cells, Circulating/metabolism , Neoplastic Cells, Circulating/pathology , Extracellular Vesicles/genetics , Extracellular Vesicles/metabolism
15.
Anal Chim Acta ; 1302: 342473, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38580402

ABSTRACT

In the medical field, extracellular vesicles (EVs) are gaining importance as they act as cells mediators. These are phospholipid bilayer vesicles and contain crucial biochemical information about their mother cells being carrier of different biomolecules such as small molecules, proteins, lipids, and nucleic acids. After release into the extracellular matrix, they enter the systemic circulation and can be found in all human biofluids. Since EVs reflect the state of the cell of origin, there is exponential attention as potential source of new circulating biomarkers for liquid biopsy. The use of EVs in clinical practice faces several challenges that need to be addressed: these include the standardization of lysis protocols, the availability of low-cost reagents and the development of analytical tools capable of detecting biomarkers. The process of lysis is a crucial step that can impact all subsequent analyses, towards the development of novel analytical strategies. To aid researchers to support the evolution of measurement science technology, this tutorial review evaluates and discuss the most commonly protocols used to characterize the contents of EVs, including their advantages and disadvantages in terms of experimental procedures, time and equipment. The purpose of this tutorial review is to offer practical guide to researchers which are intended to develop novel analytical approaches. Some of the most significant applications are considered, highlighting their main characteristics divided per mechanism of action. Finally, comprehensive tables which provide an overview at a glance are provided to readers.


Subject(s)
Extracellular Vesicles , Nucleic Acids , Humans , Extracellular Vesicles/chemistry , Liquid Biopsy/methods , Biomarkers/analysis , Nucleic Acids/analysis , Cell Death
16.
Int J Mol Sci ; 25(8)2024 Apr 20.
Article in English | MEDLINE | ID: mdl-38674117

ABSTRACT

Up to 80% of patients under immune checkpoint inhibitors (ICI) face resistance. In this context, stereotactic ablative radiotherapy (SABR) can induce an immune or abscopal response. However, its molecular determinants remain unknown. We present early results of a translational study assessing biomarkers of response to combined ICI and SABR (I-SABR) in liquid biopsy from oligoprogressive patients in a prospective observational multicenter study. Cohort A includes metastatic patients in oligoprogression to ICI maintaining the same ICI due to clinical benefit and who receive concomitant SABR. B is a comparative group of oligometastatic patients receiving only SABR. Blood samples are extracted at baseline (T1), after the first (T2) and last (T3) fraction, two months post-SABR (T4) and at further progression (TP). Response is evaluated by iRECIST and defined by the objective response rate (ORR)-complete and partial responses. We assess peripheral blood mononuclear cells (PBMCs), circulating cell-free DNA (cfDNA) and small RNA from extracellular vesicles. Twenty-seven patients could be analyzed (cohort A: n = 19; B: n = 8). Most were males with non-small cell lung cancer and one progressing lesion. With a median follow-up of 6 months, the last ORR was 63% (26% complete and 37% partial response). A decrease in cfDNA from T2 to T3 correlated with a good response. At T2, CD8+PD1+ and CD8+PDL1+ cells were increased in non-responders and responders, respectively. At T2, 27 microRNAs were differentially expressed. These are potential biomarkers of response to I-SABR in oligoprogressive disease.


Subject(s)
Biomarkers, Tumor , Immune Checkpoint Inhibitors , Lung Neoplasms , Radiosurgery , Humans , Male , Lung Neoplasms/therapy , Lung Neoplasms/pathology , Lung Neoplasms/blood , Lung Neoplasms/radiotherapy , Radiosurgery/methods , Female , Aged , Biomarkers, Tumor/blood , Middle Aged , Immune Checkpoint Inhibitors/therapeutic use , Immunotherapy/methods , Cell-Free Nucleic Acids/blood , Prospective Studies , Carcinoma, Non-Small-Cell Lung/blood , Carcinoma, Non-Small-Cell Lung/therapy , Carcinoma, Non-Small-Cell Lung/radiotherapy , Carcinoma, Non-Small-Cell Lung/pathology , Aged, 80 and over , Neoplasm Metastasis , Disease Progression , Liquid Biopsy/methods , Leukocytes, Mononuclear/metabolism , Treatment Outcome
17.
Curr Treat Options Oncol ; 25(5): 659-678, 2024 May.
Article in English | MEDLINE | ID: mdl-38656685

ABSTRACT

OPINION STATEMENT: Diffuse large B-cell lymphoma (DLBCL) is a curable disease with variable outcomes due to underlying heterogeneous clinical and molecular features-features that are insufficiently characterized with our current tools. Due to these limitations, treatment largely remains a "one-size-fits-all" approach. Circulating tumor DNA (ctDNA) is a novel biomarker in cancers that is increasingly utilized for risk stratification and response assessment. ctDNA is readily detectable from the plasma of patients with DLBCL but has not yet been incorporated into clinical care to guide treatment. Here, we describe how ctDNA sequencing represents a promising technology in development to personalize the care of patients with DLBCL. We will review the different types of ctDNA assays being studied and the rapidly growing body of evidence supporting the utility of ctDNA in different treatment settings in DLBCL. Risk stratification by estimation of tumor burden and liquid genotyping, molecular response assessment during treatment, and monitoring for measurable residual disease (MRD) to identify therapy resistance and predict clinical relapse are all potential applications of ctDNA. It is time for clinical trials in DLBCL to utilize ctDNA as an integral biomarker for patient selection, response-adapted designs, and surrogate endpoints. As more ctDNA assays become commercially available for routine use, clinicians should consider liquid biopsy when treatment response is equivocal on imaging. Incorporating MRD may also guide decision-making if patients experience severe treatment toxicities. Though important barriers remain, we believe that ctDNA will soon be ready to transition from bench to bedside to individualize treatment for our patients with DLBCL.


Subject(s)
Biomarkers, Tumor , Circulating Tumor DNA , Lymphoma, Large B-Cell, Diffuse , Lymphoma, Large B-Cell, Diffuse/therapy , Lymphoma, Large B-Cell, Diffuse/diagnosis , Lymphoma, Large B-Cell, Diffuse/blood , Lymphoma, Large B-Cell, Diffuse/genetics , Humans , Circulating Tumor DNA/blood , Biomarkers, Tumor/blood , Liquid Biopsy/methods , Disease Management , Translational Research, Biomedical , Precision Medicine/methods , Prognosis , Clinical Decision-Making , Disease Susceptibility
18.
Prostate ; 84(9): 850-865, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38571290

ABSTRACT

INTRODUCTION: We describe the development of a molecular assay from publicly available tumor tissue mRNA databases using machine learning and present preliminary evidence of functionality as a diagnostic and monitoring tool for prostate cancer (PCa) in whole blood. MATERIALS AND METHODS: We assessed 1055 PCas (public microarray data sets) to identify putative mRNA biomarkers. Specificity was confirmed against 32 different solid and hematological cancers from The Cancer Genome Atlas (n = 10,990). This defined a 27-gene panel which was validated by qPCR in 50 histologically confirmed PCa surgical specimens and matched blood. An ensemble classifier (Random Forest, Support Vector Machines, XGBoost) was trained in age-matched PCas (n = 294), and in 72 controls and 64 BPH. Classifier performance was validated in two independent sets (n = 263 PCas; n = 99 controls). We assessed the panel as a postoperative disease monitor in a radical prostatectomy cohort (RPC: n = 47). RESULTS: A PCa-specific 27-gene panel was identified. Matched blood and tumor gene expression levels were concordant (r = 0.72, p < 0.0001). The ensemble classifier ("PROSTest") was scaled 0%-100% and the industry-standard operating point of ≥50% used to define a PCa. Using this, the PROSTest exhibited an 85% sensitivity and 95% specificity for PCa versus controls. In two independent sets, the metrics were 92%-95% sensitivity and 100% specificity. In the RPCs (n = 47), PROSTest scores decreased from 72% ± 7% to 33% ± 16% (p < 0.0001, Mann-Whitney test). PROSTest was 26% ± 8% in 37 with normal postoperative PSA levels (<0.1 ng/mL). In 10 with elevated postoperative PSA, PROSTest was 60% ± 4%. CONCLUSION: A 27-gene whole blood signature for PCa is concordant with tissue mRNA levels. Measuring blood expression provides a minimally invasive genomic tool that may facilitate prostate cancer management.


Subject(s)
Biomarkers, Tumor , Prostatic Neoplasms , Humans , Male , Prostatic Neoplasms/genetics , Prostatic Neoplasms/blood , Prostatic Neoplasms/diagnosis , Prostatic Neoplasms/pathology , Prostatic Neoplasms/surgery , Liquid Biopsy/methods , Biomarkers, Tumor/blood , Biomarkers, Tumor/genetics , Aged , Middle Aged , Machine Learning , RNA, Messenger/blood , RNA, Messenger/genetics , Prostatectomy , Sensitivity and Specificity
19.
Int J Mol Sci ; 25(8)2024 Apr 10.
Article in English | MEDLINE | ID: mdl-38673779

ABSTRACT

Meningiomas are tumors of the central nervous system that vary in their presentation, ranging from benign and slow-growing to highly aggressive. The standard method for diagnosing and classifying meningiomas involves invasive surgery and can fail to provide accurate prognostic information. Liquid biopsy methods, which exploit circulating tumor biomarkers such as DNA, extracellular vesicles, micro-RNA, proteins, and more, offer a non-invasive and dynamic approach for tumor classification, prognostication, and evaluating treatment response. Currently, a clinically approved liquid biopsy test for meningiomas does not exist. This review provides a discussion of current research and the challenges of implementing liquid biopsy techniques for advancing meningioma patient care.


Subject(s)
Biomarkers, Tumor , Meningeal Neoplasms , Meningioma , Humans , Meningioma/diagnosis , Meningioma/pathology , Liquid Biopsy/methods , Meningeal Neoplasms/diagnosis , Meningeal Neoplasms/pathology , Extracellular Vesicles/metabolism , Prognosis
20.
Indian J Med Res ; 159(2): 163-180, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38577857

ABSTRACT

ABSTRACT: From an initial thought of being used as a cellular garbage bin to a promising target for liquid biopsies, the role of exosomes has drastically evolved in just a few years of their discovery in 1983. Exosomes are naturally secreted nano-sized vesicles, abundant in all types of body fluids and can be isolated intact even from the stored biological samples. Being stable carriers of genetic material (cellular DNA, mRNA and miRNA) and having specific cargo (signature content of originating cells), exosomes play a crucial role in pathogenesis and have been identified as a novel source of biomarkers in a variety of disease conditions. Recently exosomes have emerged as a promising 'liquid biopsy tool'and have shown great potential in the field of non-invasive disease diagnostics, prognostics and treatment response monitoring in both communicable as well as non-communicable diseases. However, there are certain limitations to overcome which restrict the use of exosome-based liquid biopsy as a gold standard testing procedure in routine clinical practices. The present review summarizes the current knowledge on the role of exosomes as the liquid biopsy tool in diagnosis, prognosis and treatment response monitoring in communicable and non-communicable diseases and highlights the major limitations, technical advancements and future prospects of the utilization of exosome-based liquid biopsy in clinical interventions.


Subject(s)
Exosomes , Noncommunicable Diseases , Humans , Exosomes/genetics , Exosomes/pathology , Liquid Biopsy/methods , Prognosis , Biomarkers
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