Integrating liquid biopsies into the management of cancer. Nat Rev Clin Oncol. 2017;14:531-548. [PMID: 28252003 DOI: 10.1038/nrclinonc.2017.14]

Electrochemical detection of circulating-free DNA methylation: A new indicator for early cancer screening

This study introduces a novel electrochemical approach for detecting circulating-free DNA (cfDNA) by leveraging distinct methylation patterns characteristic of cfDNA from healthy controls and cancer patients. Our findings reveal that cfDNA from cancer patients exhibits a unique affinity for gold surfaces due to abnormal methylation, which enables its electrochemical differentiation. By using square wave voltammetry (SWV) with optimized parameters, we achieved high sensitivity (0.89) and specificity (0.73) in distinguishing cfDNA from healthy controls and cancer patients. Clinical trials demonstrated the effectiveness of this method, surpassing conventional tumor markers in early cancer screening. SEPTIN9 (SEPT9) methylation is used as an example to demonstrate the generalizability of our method for analyzing DNA methylation changes, which can subsequently be applied to identify the presence of cancer.This approach offers notable advantages, including simplicity, rapid response, and cost-effectiveness. While the current methodology is primarily suited for detecting the presence of cancer, its potential for prognostic and diagnostic applications warrants further investigation.

Emerging prodrug and nano-drug delivery strategies for the detection and elimination of senescent tumor cells

Tumor cellular senescence, characterized by reversible cell cycle arrest following anti-cancer therapies, presents a complex paradigm in oncology. Given that senescent tumor cells may promote angiogenesis, tumorigenesis, and metastasis, selective killing senescent cells (SCs)-a strategy termed senotherapy-has emerged as a promising approach to improve cancer treatment. However, the clinical implementation of senotherapy faces significant hurdles, including lack of precise methods for SCs identification and the potential for adverse effects associated with highly cytotoxic senolytic agents. In this account, we elucidate recent advancement in developing novel approaches for the detection and selective elimination of SCs, encompassing prodrugs, nanoparticles, and other cutting-edge drug delivery systems such as PROTAC technology and CAR T cell therapy. Furthermore, we explore the paradoxical nature of SCs, which can induce growth arrest in adjacent neoplastic cells and recruit immunomodulatory cells that contribute to tumor suppression. Therefore, we utilize SCs membrane as vehicles to elicit antitumor immunity and potentially augment existing anti-cancer therapies. Finally, the opportunities and challenges are put forward to facilitate the development and clinical transformation of SCs detection, elimination or utilization.

Cell competition as an emerging mechanism and therapeutic target in cancer

Cell competition, as an internal quality control mechanism that constantly monitor cell fitness and eliminate unfit cells, maintains proper embryogenesis and tissue integrity during early development and adult homeostasis. Recent studies have revealed that cell competition functions as a tumor-suppressive mechanism to defend against cancer by removing neoplastic cell, which however, is hijacked by tumor cells and drive cell competition in favor of mutant cells, thereby promoting cancer initiation and progression. In this review, with a special focus on mammalian systems, we discuss the latest insights into the mechanisms regulating cell competition and its dual role in tumor development. We also provide current strategies to modulate the direction of cell competition for the prevention and treatment of cancers.

Expression characteristics and biological functions of CGB5 gene in gastric cancer

OBJECTIVE

The chorionic gonadotropin (CG) subunit beta 5 (CGB5) gene is a member of the glycoprotein hormone β chain family, encoding the β5 subunit of CG, which has been shown to promote tumorigenesis and induce proliferation in various types of cancer including gastric cancer (GC). However, the mechanistic role of CGB5 in GC has not been fully elucidated. Therefore, this study investigated relevant genes that regulate GC through bioinformatics analysis.

METHODS

Immunohistochemistry, immunofluorescence, and western blot (WB) detection methods were appropriately used to evaluate the expression pattern and clinical significance of CGB5 in 100 Chinese GC patients that were recruited from the Gaochun People's Hospital. The effect of small interfering ribonucleic acid (siRNA) on apoptosis, migration, and invasion of GC cells was investigated in vitro. Three-dimensional tumor spheres of these two types of GC cells (NCI-N87 cells and MKN45 cells) were constructed before investigation of the Calcein acetoxymethyl ester (AM)/ Propidium iodide (PI) staining, flow cytometric apoptosis, and apoptotic-related protein content of the tumor spheres after siRNA inhibition of CGB5 expression.

RESULTS

It was observed that compared with adjacent normal gastric tissue, expression of CGB5 was significantly upregulated in GC tissue. The siRNA inhibited CGB5 expression in two GC cell lines (NCI-N87 cells and MKN45 cells). Also, it was discovered that CGB5 highly correlated with microsatellite instability (MSI) and immune cell activity in GC, thus revealing the greater research value of CGB5 gene. More importantly, CGB5 siRNA could inhibit invasion and migration of tumor cells, induce apoptosis of GC cells and GC tumor spheres, as well as the mechanism relating to regulation of apoptosis associated gene expression. Overall, the findings suggest that CGB5 may play a crucial role in the development of GC carcinogenesis. Thus, this research may contribute to design of potential drug targets for treatment of GC.

Specific Cell Adhesion at Nano-Biointerfaces: Synergistic Effect of Topographical Matching and Molecular Recognition

Specific cell adhesion is essential for functional biointerfaces, especially in cancer diagnosis. However, the role of surface nanotopography in this process remains unclear. Herein, we reveal the critical role of surface nanotopography by measuring adhesion forces utilizing fluidic force microscopy (FluidFM). The antibody-coated nanospiky surface exhibits cell adhesion force 1 to 2 orders of magnitude higher than those of the flat, nanospiky, and antibody-coated flat surfaces. This amplified effect is related to a time-dependent reversal, with adhesion force on nanospiky surfaces initially weaker than that on flat surfaces but eventually surpassing it. Mathematical simulations further demonstrate that micro-nanostructured surfaces maximize contact points, enabling multiscale, multipoint cell-substrate interactions, consistent with experimental results. From thermodynamic and kinetic perspectives, we propose a multiscale, multipoint recognition model based on the synergistic effect of topographical matching and molecular recognition. Our findings provide valuable clues for biointerface design in cancer diagnosis, drug screening, and tissue engineering.

A large-scale retrospective study in metastatic breast cancer patients using circulating tumour DNA and machine learning to predict treatment outcome and progression-free survival

Monitoring levels of circulating tumour-derived DNA (ctDNA) provides both a noninvasive snapshot of tumour burden and also potentially clonal evolution. Here, we describe how applying a novel statistical model to serial ctDNA measurements from shallow whole genome sequencing (sWGS) in metastatic breast cancer patients produces a rapid and inexpensive predictive assessment of treatment response and progression-free survival. A cohort of 149 patients had DNA extracted from serial plasma samples (total 1013, mean samples per patient = 6.80). Plasma DNA was assessed using sWGS and the tumour fraction in total cell-free DNA estimated using ichorCNA. This approach was compared with ctDNA targeted sequencing and serial CA15-3 measurements. We identified a transition point of 7% estimated tumour fraction to stratify patients into different categories of progression risk using ichorCNA estimates and a time-dependent Cox Proportional Hazards model and validated it across different breast cancer subtypes and treatments, outperforming the alternative methods. We used the longitudinal ichorCNA values to develop a Bayesian learning model to predict subsequent treatment response with a sensitivity of 0.75 and a specificity of 0.66. In patients with metastatic breast cancer, a strategy of sWGS of ctDNA with longitudinal tracking of tumour fraction provides real-time information on treatment response. These results encourage a prospective large-scale clinical trial to evaluate the clinical benefit of early treatment changes based on ctDNA levels.

Circulating tumour DNA and circulating tumour cells in bladder cancer - from discovery to clinical implementation

Liquid biopsies, indicating the sampling of body fluids rather than solid-tissue biopsies, have the potential to revolutionize cancer care through personalized, noninvasive disease detection and monitoring. Circulating tumour DNA (ctDNA) and circulating tumour cells (CTCs) are promising blood-based biomarkers in bladder cancer. Results from several studies have shown the clinical potential of ctDNA and CTCs in bladder cancer for prognostication, treatment-response monitoring, and early detection of minimal residual disease and disease recurrence. Following successful clinical trial evaluation, assessment of ctDNA and CTCs holds the potential to transform the therapeutic pathway for patients with bladder cancer - potentially in combination with the analysis of urinary tumour DNA - through tailored treatment guidance and optimized disease surveillance.

Ultrasensitive Detection and Monitoring of Circulating Tumor DNA Using Structural Variants in Early-Stage Breast Cancer

PURPOSE

The detection of circulating tumor DNA (ctDNA) after curative-intent therapy in early-stage breast cancer is highly prognostic of disease recurrence. Current ctDNA assays, mainly targeting single-nucleotide variants, vary in sensitivity and specificity. Although increasing the number of single-nucleotide variants in tumor-informed assays improves sensitivity, structural variants (SV) may achieve similar or better sensitivity without compromising specificity. SVs occur across all cancers, linked to genomic instability and tumorigenesis, with unique tumor- and patient-specific breakpoints occurring throughout the genome. SVs in breast cancer are underexplored, and their potential for ctDNA detection and monitoring has not been fully evaluated.

EXPERIMENTAL DESIGN

We retrospectively analyzed a tumor-informed SV-based ctDNA assay in a cohort of patients with early-stage breast cancer (n = 100, 568 timepoints) receiving neoadjuvant systemic therapy, evaluating ctDNA dynamics and lead times to clinical recurrence in the postoperative period.

RESULTS

ctDNA was detected in 96% (91/95) of participants at baseline with a median variant allele frequency of 0.15% (range: 0.0011%-38.7%); of these, 10% (9/91) had a variant allele frequency <0.01%. ctDNA detection at cycle 2 (C2) of neoadjuvant therapy was associated with a higher likelihood of distant recurrence (log-rank P = 0.047) and enhanced residual cancer burden prognostication (log-rank P = 0.041). ctDNA was detected prior to distant recurrence in all cases (100% sensitivity) with a median lead time of 417 days (range: 4-1,931 days).

CONCLUSIONS

These results demonstrate the clinical validity of ultrasensitive ctDNA detection and monitoring using SVs. Prospective trials are required to evaluate ctDNA-guided treatment strategies.

Liquid biopsy: An innovative tool in oncology. Where do we stand?

The Liquid Biopsy (LB) represents an ideal surrogate of tumor Tissue Biopsy (TB) when the aim is to obtain useful information on patient prognosis and personalized therapy. This technique renders it possible to isolate circulating tumor cells, circulating tumor DNA and other molecules from biological fluids. The most commonly used fluid for liquid biopsy is blood, but depending on the case it could be necessary to isolate the tumor components from other biological fluids such as urine, pleural effusion, cerebrospinal fluid, and others. The main advantages of liquid biopsy are the minimally invasive nature of the procedure and the possibility of analyzing all tumor clones. Limitations include difficulties in the isolation of tumor components and the requirement for highly sensitive analysis methods to avoid the risk of technical artifacts. In our review we will focus on describing circulating tumor biomarkers to illustrate the variety of information that can be obtained from biological fluids, particularly blood. We will then discuss the advanced biotechnological techniques suitable for the identification and analysis of Circulating Tumor DNA (ctDNA), examining both the potential and limitations of analytical methods and the clinical applicability of liquid biopsy for cancer diagnosis, monitoring, and therapeutic prediction. Additionally, we will explore strategies to enhance this valuable alternative to the more invasive tissue biopsy, with a dedicated focus on ongoing clinical studies, currently approved tests, and guideline recommendations.

Liquid Biopsy in Solid Tumours: An Overview

The advent of personalised and precision medicine has radically modified the management and the clinical outcome of cancer patients. However, the expanding number of predictive, prognostic, and diagnostic biomarkers has raised the need for simple, noninvasive, quicker, but equally efficient tests for molecular profiling. In this complex scenario, the adoption of liquid biopsy, particularly circulating tumour DNA (ctDNA), has been a real godsend for many cancer patients who would otherwise have been denied the benefits of targeted treatments. Undeniably, ctDNA analysis has several advantages over conventional tissue-based analysis. One advantage is that it can guide treatment decision making, especially when tissue samples are scarce or totally unavailable. Indeed, a simple blood test can inform clinicians on patients' response or resistance to targeted therapies, help them monitor minimal residual disease (MRD) after surgical resections, and facilitate them with early cancer detection and interception. Finally, an equally important advantage is that ctDNA analysis can help decipher temporal and spatial tumour heterogeneity, a mechanism highly responsible for therapeutic resistance. In this review, we gathered and analysed current evidence on the clinical usefulness of ctDNA analysis in solid tumours.

Sensitive detection of small extracellular vesicles using a gold nanostar-based SERS assay

Small extracellular vesicles (sEVs) are lipid bilayer-bound vesicles that carry critical biomarkers for disease detection. However, the inherent heterogeneity and complexity of sEV molecular characteristics pose significant challenges for accurate and comprehensive molecular profiling. Traditional analytical methods, including immunoblotting, enzyme-linked immunosorbent assay (ELISA), and flow cytometry, exhibit several limitations, such as being time-consuming, requiring large sample volumes, and demonstrating relatively low sensitivity. Therefore, there is an urgent need to develop a highly sensitive and specific assay for the reliable detection of sEVs. Surface-enhanced Raman scattering (SERS) assays have emerged as a promising approach for sEV detection, offering advantages including high sensitivity and specificity. In the proposed SERS assay, SERS nanotags - comprising nanoparticles coated with Raman-active molecules and conjugated with antibodies - are employed to label surface-bound molecules on sEVs. This approach facilitates the generation of a high-intensity signal from molecules present in low abundance. Recently, anisotropic nanoparticles, such as star-shaped nanostructures, have garnered interest due to their ability to significantly amplify generated SERS signals for ultra-sensitive biomarker detection. In this study, we explore the application of gold nanostars (AuNSs) as SERS nanotags for the detection of sEVs. In principle, AuNS-based SERS nanotags were used to label the EpCAM protein, which can be found on the surface of cancer cell derived sEVs, and then sEV labelled SERS nanotags were captured by CD9-conjugated magnetic beads to form an immunocomplex, which exhibits a SERS signal. Our results demonstrate that the proposed SERS assay utilizing AuNSs provides high specificity and sensitivity, with a detection limit as low as 2.47 × 103 particles per μL. Furthermore, the assay was tested with spiked plasma samples (cancer cell-derived sEVs spiked into healthy plasma), showing that its specificity remains unaffected by the presence of plasma. These findings suggest that the SERS assay incorporating AuNSs holds significant promise as an effective and reliable detection method for potential clinical applications.

Advancing Personalized Medicine in Alzheimer's Disease: Liquid Biopsy Epigenomics Unveil APOE ε4-Linked Methylation Signatures

Recent studies show that patients with Alzheimer's disease (AD) harbor specific methylation marks in the brain that, if accessible, could be used as epigenetic biomarkers. Liquid biopsy enables the study of circulating cell-free DNA (cfDNA) fragments originated from dead cells, including neurons affected by neurodegenerative processes. Here, we isolated and epigenetically characterized plasma cfDNA from 35 patients with AD and 35 cognitively healthy controls by using the Infinium® MethylationEPIC BeadChip array. Bioinformatics analysis was performed to identify differential methylation positions (DMPs) and regions (DMRs), including APOE ε4 genotype stratified analysis. Plasma pTau181 (Simoa) and cerebrospinal fluid (CSF) core biomarkers (Fujirebio) were also measured and correlated with differential methylation marks. Validation was performed with bisulfite pyrosequencing and bisulfite cloning sequencing. Epigenome-wide cfDNA analysis identified 102 DMPs associated with AD status. Most DMPs correlated with clinical cognitive and functional tests including 60% for Mini-Mental State Examination (MMSE) and 80% for Global Deterioration Scale (GDS), and with AD blood and CSF biomarkers. In silico functional analysis connected 30 DMPs to neurological processes, identifying key regulators such as SPTBN4 and APOE genes. Several DMRs were annotated to genes previously reported to harbor epigenetic brain changes in AD (HKR1, ZNF154, HOXA5, TRIM40, ATG16L2, ADAMST2) and were linked to APOE ε4 genotypes. Notably, a DMR in the HKR1 gene, previously shown to be hypermethylated in the AD hippocampus, was validated in cfDNA from an orthogonal perspective. These results support the feasibility of studying cfDNA to identify potential epigenetic biomarkers in AD. Thus, liquid biopsy could improve non-invasive AD diagnosis and aid personalized medicine by detecting epigenetic brain markers in blood.

Circulating tumor DNA- and cancer tissue-based next-generation sequencing reveals comparable consistency in targeted gene mutations for advanced or metastatic non-small cell lung cancer

BACKGROUND

Molecular subtyping is an essential complementarity after pathological analyses for targeted therapy. This study aimed to investigate the consistency of next-generation sequencing (NGS) results between circulating tumor DNA (ctDNA)-based and tissue-based in non-small cell lung cancer (NSCLC) and identify the patient characteristics that favor ctDNA testing.

METHODS

Patients who diagnosed with NSCLC and received both ctDNA- and cancer tissue-based NGS before surgery or systemic treatment in Lung Cancer Center, Sichuan University West China Hospital between December 2017 and August 2022 were enrolled. A 425-cancer panel with a HiSeq 4000 NGS platform was used for NGS. The unweighted Cohen's kappa coefficient was employed to discriminate the high-concordance group from the low-concordance group with a cutoff value of 0.6. Six machine learning models were used to identify patient characteristics that relate to high concordance between ctDNA-based and tissue-based NGS.

RESULTS

A total of 85 patients were enrolled, of which 22.4% (19/85) had stage III disease and 56.5% (48/85) had stage IV disease. Forty-four patients (51.8%) showed consistent gene mutation types between ctDNA-based and tissue-based NGS, while one patient (1.2%) tested negative in both approaches. Patients with advanced diseases and metastases to other organs would be suitable for the ctDNA-based NGS, and the generalized linear model showed that T stage, M stage, and tumor mutation burden were the critical discriminators to predict the consistency of results between ctDNA-based and tissue-based NGS.

CONCLUSION

ctDNA-based NGS showed comparable detection performance in the targeted gene mutations compared with tissue-based NGS, and it could be considered in advanced or metastatic NSCLC.

Protocol for Extracting Circulating Cell-Free DNA from Murine Saliva: Insights into Oral and Systemic Disease Research

Circulating cell-free DNA (cfDNA) consists of small fragments of extracellular DNA from mammalian and bacterial cells found in bodily fluids such as blood and saliva, and it has been strongly recognized as a critical biomarker for various disease diagnoses, prognoses, and therapeutic monitoring. In this study, we present a reproducible protocol for efficiently isolating cfDNA from murine saliva using an innovative swabbing method in conjunction with the QIAamp MinElute ccfDNA Mini Kit. The quantification of isolated cfDNA is detected by a Qubit Fluorometer. Moreover, qualification assessment is conducted through BioAnalyzer analysis. This protocol facilitates research on saliva-derived cfDNA in the context of oral and systemic diseases in murine models.

Circulating blood biomarkers for minimal residual disease in hepatocellular carcinoma: A systematic review

BACKGROUND

Relapse after radical treatment remains a major concern in hepatocellular carcinoma (HCC), affecting 50-75 % of early-stage cases within 5 years. Early recurrence prediction is a clinical unmet need. Circulating blood biomarkers could provide a minimally invasive approach to detect minimal residual disease (MRD) post-intervention. Although alpha-fetoprotein has been the primary biomarker in this setting, its MRD sensitivity is limited to 50-70 %. This systematic review aims to summarize available evidence regarding the clinical validity and potential utility of emerging circulating blood biomarkers for MRD detection in HCC patients.

METHODS

We searched PubMed and Embase for peer-reviewed articles and abstracts published up to 2025, and ClinicalTrials.gov for ongoing trials on circulating blood biomarkers for MRD in HCC.

RESULTS

A total of 91 studies (74 with results and 17 ongoing, out of 2,386) were retrieved. We evaluated various blood biomarkers, including circulating DNA (cDNA, N = 24), circulating tumor cells (CTCs, N = 20), circulating RNA (cRNA, N = 8), and other miscellaneous (N = 22) for MRD detection in HCC. These biomarkers demonstrated encouraging results, albeit with notable heterogeneity. In particular, circulating tumor DNA (ctDNA) and CTCs stand as the most robust novel approaches, with 50-80 % sensitivity and specificity up to 94 %. Nonetheless, none of the 17 ongoing studies involve biomarker-driven intervention to prove clinical utility.

CONCLUSIONS

Novel circulating blood biomarkers are mature for MRD detection in HCC. However, variability in methodologies and results highlights the need for further validation. We encourage the investigation of CTCs and/or ctDNA in interventional trials to assess clinical utility. This biomarker-driven approach may enhance adjuvant treatment effectiveness in MRD-positive cases while minimizing toxicity in MRD-negative patients.

Circulating microRNAs: A remarkable opportunity as non-invasive biomarkers from adult to pediatric brain tumor patients

Central nervous system (CNS) tumors represent the most frequent solid tumors among adolescents and children, and the leading cause of cancer-related death in men < 40 and women < 20 years of age. Brain tumors are challenging to diagnose, monitor, and treat. The current diagnostic approach involves magnetic resonance imaging (MRI), tumor histology, molecular characterization and cytologic analysis of cerebrospinal fluid (CSF). However, surgical procedures pose potential risks to the patient's health, not achieving good accuracy. For these reasons, it is crucial to identify new non-invasive disease biomarkers to improve patients' stratification at diagnosis and during follow-up and prognosis. MicroRNAs (miRNAs) are a class of short RNA molecules that have been demonstrated in numerous studies to be dysregulated in brain tumor patients. As a result, they may be used as biomarkers of brain tumors. Additionally, miRNAs can be analyzed in liquid biopsy samples, such as blood and CSF, providing a non-invasive source of biomolecular data on patients' disease status. This review aims to highlight the role of miRNAs in liquid biopsy, also known as circulating miRNAs, as potential non-invasive cancer biomarkers in both adult and pediatric populations and to suggest their potential impact on clinical trials.

The promising role of nanopore sequencing in cancer diagnostics and treatment

Cancer arises from genetic alterations that impact both the genome and transcriptome. The utilization of nanopore sequencing offers a powerful means of detecting these alterations due to its unique capacity for long single-molecule sequencing. In the context of DNA analysis, nanopore sequencing excels in identifying structural variations (SVs), copy number variations (CNVs), gene fusions within SVs, and mutations in specific genes, including those involving DNA modifications and DNA adducts. In the field of RNA research, nanopore sequencing proves invaluable in discerning differentially expressed transcripts, uncovering novel elements linked to transcriptional regulation, and identifying alternative splicing events and RNA modifications at the single-molecule level. Furthermore, nanopore sequencing extends its reach to detecting microorganisms, encompassing bacteria and viruses, that are intricately associated with tumorigenesis and the development of cancer. Consequently, the application prospects of nanopore sequencing in tumor diagnosis and personalized treatment are expansive, encompassing tasks such as tumor identification and classification, the tailoring of treatment strategies, and the screening of prospective patients. In essence, this technology stands poised to unearth novel mechanisms underlying tumorigenesis while providing dependable support for the diagnosis and treatment of cancer.

Role of exosomes in diagnosis, prognostication, and treatment of pediatric solid tumors

Cancer is the second leading cause of death in children, and solid tumors make up 30% of childhood cancers. Molecular profiling of pediatric solid tumors allows a personalized approach to therapy, but this approach mostly relies on surgical biopsy, which is invasive and carries the risk of complications. Liquid biopsy serves as a reliable alternative and a minimally invasive tool for diagnosing, prognosticating, and residual disease monitoring in childhood cancers. This review outlines the potential of exosomes as informative liquid biopsies in pediatric solid tumors. Studies highlighting the potential applications and clinical utility of exosomes and their molecular constituents as prognosticators and therapies in common childhood solid tumors, including neuroblastoma, medulloblastoma, sarcoma, and hepatoblastoma, have been overviewed. We also discuss the limitations and technical challenges of utilizing exosomes for pediatric solid tumors.

Optimization of Pre-Analytical Handling to Maintain DNA Integrity in Diagnostic Papanicolaou Tests

Cell-free DNA (cfDNA) of ovarian carcinoma origin can be detected in samples from the gynecologic tract. This study aims to evaluate how pre-analytical handling affects DNA profile and integrity in Papanicolaou (Pap) tests, to optimize their potential for detection of ovarian cancers (OCs). Analysis of archived Pap tests from patients with OC, kept at room temperature for 48 hours and stored at -80°C, was complemented by in vitro experiments. Temperature-associated effects on DNA fragmentation were evaluated in samples stored at 4°C, -20°C, or -80°C. Time-dependent DNA degradation at room temperature was evaluated in comparison to storage at 4°C. Results were validated in prospectively collected Pap tests. The DNA integrity was assessed by fragment analysis. Accumulation of short DNA fragments was observed in archived Pap tests from patients with OC. In vitro, fragments of 100 to 350 bp increased 11.5-fold within 48 hours at room temperature compared with 1.7-fold when stored at 4°C. Consistent with the in vitro findings, prospectively collected samples showed reduced fragmentation when stored at 4°C compared with room temperature (P = 0.007). Long-term storage at 4°C had a significant negative effect on DNA stability (P = 0.013), whereas freezing slowed down fragmentation. Immediate storage at 4°C after sampling markedly reduces DNA degradation, suggesting a simple way to optimize pre-analytical handling and decrease unwanted fragmentation for cfDNA analysis in Pap tests.

Pathological diagnosis of central nervous system tumours in adults: what's new?

In the course of the last decade, the pathological diagnosis of many tumours of the central nervous system (CNS) has transitioned from a purely histological to a combined histological and molecular approach, resulting in a more precise 'histomolecular diagnosis'. Unfortunately, translation of this refinement in CNS tumour diagnostics into more effective treatment strategies is lagging behind. There is hope though that incorporating the assessment of predictive markers in the pathological evaluation of CNS tumours will help to improve this situation. The present review discusses some novel aspects with regard to the pathological diagnosis of the most common CNS tumours in adults. After a brief update on recognition of clinically meaningful subgroups in adult-type diffuse gliomas and the value of assessing predictive markers in these tumours, more detailed information is provided on predictive markers of (potential) relevance for immunotherapy especially for glioblastomas, IDH-wildtype. Furthermore, recommendations for improved grading of meningiomas by using molecular markers are briefly summarised, and an overview is given on (predictive) markers of interest in metastatic CNS tumours. In the last part of this review, some 'emerging new CNS tumour types' that may occur especially in adults are presented in a table. Hopefully, this review provides useful information on 'what's new' for practising pathologists diagnosing CNS tumours in adults.

Demystifying EV heterogeneity: emerging microfluidic technologies for isolation and multiplexed profiling of extracellular vesicles

Extracellular vesicles (EVs) are heterogeneous lipid containers carrying complex molecular cargoes, including proteins, nucleic acids, glycans, etc. These vesicles are closely associated with specific physiological characteristics, which makes them invaluable in the detection and monitoring of various diseases. However, traditional isolation methods are often labour-intensive, inefficient, and time-consuming. In addition, single biomarker analyses are no longer accurate enough to meet diagnostic needs. Routine isolation and molecular analysis of high-purity EVs in clinical applications is even more challenging. In this review, we discuss a promising solution, microfluidic-based techniques, that combine efficient isolation and multiplex detection of EVs, to further demystify EV heterogeneity. These microfluidic-based EV multiplexing platforms will hopefully facilitate development of liquid biopsies and offer promising opportunities for personalised therapy.

Harnessing ferroptosis for precision oncology: challenges and prospects

The discovery of diverse molecular mechanisms of regulated cell death has opened new avenues for cancer therapy. Ferroptosis, a unique form of cell death driven by iron-catalyzed peroxidation of membrane phospholipids, holds particular promise for targeting resistant cancer types. This review critically examines current literature on ferroptosis, focusing on its defining features and therapeutic potential. We discuss how molecular profiling of tumors and liquid biopsies can generate extensive multi-omics datasets, which can be leveraged through machine learning-based analytical approaches for patient stratification. Addressing these challenges is essential for advancing the clinical integration of ferroptosis-driven treatments in cancer care.

Longitudinal evaluation of circulating tumor DNA in patients undergoing neoadjuvant therapy for early breast cancer using a tumor-informed assay

Circulating tumor DNA (ctDNA) is an emerging biomarker for the treatment of early breast cancer (EBC). We sought to evaluate a highly sensitive tumor-informed ctDNA assay in a real-world cohort of patients receiving neoadjuvant therapy (NAT) to assess clinical validity and explore prognostic outcomes. ctDNA is detected in 77.2% (88/114) of participants at baseline, with 18/88 (20.5%) having a baseline estimated variant allele frequency (eVAF) of <0.01%. Persistent detection of ctDNA, measured midway through NAT (mid-NAT), is associated with disease recurrence in all participants, reaching statistical significance in those with HER2-negative disease. Stratified analyses demonstrate that ctDNA detected mid-NAT enhances the prognostic accuracy of the residual cancer burden (RCB) score for disease recurrence. Postoperative or follow-up detection of ctDNA demonstrates a 100% positive predictive value for disease recurrence, with a median lead time of 374 days (range: 13-1010 days). These data suggest that assays with high analytical sensitivity may improve baseline ctDNA detection in patients with EBC. The ability to replicate the prognostic association of ctDNA dynamics in a real-world cohort supports further investigation. Prospective trials incorporating ctDNA testing are warranted to assess and develop the clinical utility of ctDNA-guided treatment strategies.

Clinical implications of Alu-based cell-free DNA and serum onco-piRNA monitoring in colorectal cancer management

BACKGROUND

Colorectal cancer (CRC) remains a significant global health challenge, characterized by high morbidity and mortality rates. This study explores the potential of Alu-based cell-free DNA (cfDNA) and specific PIWI-interacting RNAs (piRNAs) as innovative biomarkers for monitoring treatment responses in CRC patients.

METHODS

We analyzed plasma samples from 70 CRC patients, equally divided between those undergoing chemotherapy and surgical interventions.

RESULTS

Our findings reveal that certain piRNAs, particularly piRNA-823, piRNA-54265, and piRNA-1245, exhibit significant prognostic value, with notable expression changes observed in the chemotherapy group compared to the surgery group. Furthermore, the levels of ALU-based cfDNA fragments showed a marked decrease post-chemotherapy, suggesting their utility in assessing therapeutic efficacy.

CONCLUSIONS

This research underscores the importance of integrating these molecular tools particularly piRNA-823 and ALU-based cfDNA into clinical practice, potentially enhancing the management strategies for CRC patients and improving their outcomes.

Rapid in situ mutation detection in extracellular vesicle DNA

Aim: A PCR- and sequencing-free mutation detection assay facilitates cancer diagnosis and reduces over-reliance on specialized equipment. This benefit was highlighted during the pandemic when high demand for viral nucleic acid testing often sidelined mutation analysis. This shift led to substantial challenges for patients on targeted therapy in tracking mutations. Here, we report a 30-min DNA mutation detection technique using Cas12a-loaded liposomes in a microplate reader, a fundamental laboratory tool. Methods: CRISPR-Cas12a complex and fluorescence-quenching (FQ) probes are introduced into tumor-derived extracellular vesicles (EV) through membrane fusion. When CRISPR-RNA hybridizes with the DNA target, activated Cas12a can trans-cleave FQ probes, resulting in fluorescence signals for the quantification of DNA mutation. Results: This method enables the detection of EGFR L858R mutation in EV DNA within 30 min. Laborious extraction, purification, and other preparation steps for EV DNA are eliminated. The need for advanced data processing is also dispensed with. In a cohort study involving 10 healthy donors and 30 patients with advanced non-small cell lung cancer (NSCLC), the assay achieved a sensitivity of 86.7%, a specificity of 90%, and an accuracy of 87.5%. Conclusion: The limit of detection of our Cas12 assay was ~ 8 × 105 EVs, corresponding to a mutation allele frequency (MAF) of ~ 10%. The MAF in late-stage cancers varies widely but often falls within 5%-50%. Therefore, without amplification of targets, this Cas12 assay can detect mutations in patients with advanced lung cancer. Future advancements in multiplex and high-throughput mutation detection using this assay will streamline self-diagnosis and treatment monitoring at home.

Circulating RNA Markers Associated with Adenoma-Carcinoma Sequence in Colorectal Cancer

Colorectal cancer progresses through a well-defined adenoma-carcinoma sequence (ACS), which is pivotal for early detection and intervention. While ACS-based surveillance has been instrumental, its reliance on tissue sampling limits accurate staging. Liquid biopsies, including circulating tumor DNA (ctDNA) and extracellular RNA, have emerged as non-invasive alternatives, yet they primarily detect genetic alterations or passive RNA release rather than active biological processes. Thus, there is a need for biomarkers that reflect real-time immune responses and tumor-microenvironment interactions during ACS progression. This study aimed to identify circulating RNA biomarkers associated with ACS by analyzing blood samples from 160 individuals across five groups: colorectal cancer, advanced adenoma, non-advanced adenoma, symptomatic non-disease control, and healthy control. RNA sequencing coupled with gene ontology and protein-protein interaction analyses identified stage-specific circulating transcripts. Notably, IFI27 was linked to the symptomatic non-disease control group, DEFA4 to the non-advanced adenoma group, MPO to the advanced adenoma group, and CD177 to the colorectal cancer group. These findings suggest that colorectal-cancer-related circulating RNA markers reflect host immune responses during ACS progression, supporting their potential role in early detection and non-invasive diagnoses. By addressing critical gaps in early colorectal cancer detection, this study advances the utility of circulating RNA biomarkers and liquid biopsies in colorectal cancer screening and clinical management.

Preoperative circulating tumor cells level is associated with lymph node metastasis in patients with unifocal papillary thyroid carcinoma

OBJECTIVE

Unifocal papillary thyroid carcinoma (PTC) refers to thyroid cancer that has only one isolated lesion, it has also the possibility of lymph node metastasis (LNM). Circulating tumor cell (CTC) has been used to assist in the assessment of tumor progression, but the relationship between CTCs levels and LNM in unifocal PTC patients is unclear.

METHODS

The clinical records (age, gender, Hashimoto's thyroiditis, thyroid function, tumor size, invaded capsule (thyroid cancer penetrating the capsule), clinical stage, and LNM) of unifocal PTC patients in Meizhou People's Hospital were analyzed retrospectively. Receiver operating characteristic (ROC) curve analysis was used to determine the cutoff value of CTCs levels to distinguish LNM. The relationship between CTCs level and clinical features was analyzed. Logistic regression analysis was used to evaluate the relationship between CTCs and LNM.

RESULTS

A total of 507 unifocal PTC patients were included, and 198(39.1%) patients with LNM. The critical value of CTCs was 9.25 FU/3mL by ROC analysis, and 288(56.8%) unifocal PTC patients with preoperative CTC-positive(≥ 9.25 FU/3mL). The patients with positive CTCs had higher proportions of normal thyroid function (91.3% vs. 84.5%, p = 0.018), and LNM (44.1% vs. 32.4%, p = 0.008) than patients with negative. High preoperative CTCs level (≥ 9.25/<9.25 FU/3mL, odds ratio(OR): 1.653, 95% confidence interval(CI): 1.115-2.451, p = 0.012), tumor size > 1 cm (OR: 3.189, 95% CI: 2.069-4.913, p < 0.001), and invaded capsule (OR: 1.521, 95% CI: 1.005-2.302, p = 0.047) were associated with LNM among unifocal PTC in multivariate logistic regression analysis.

CONCLUSIONS

High preoperative CTCs level (≥ 9.25 FU/3mL), tumor size > 1 cm, and invaded capsule were associated with LNM among unifocal PTC.

Circulating microRNA panels for multi-cancer detection and gastric cancer screening: leveraging a network biology approach

BACKGROUND

Screening tests, particularly liquid biopsy with circulating miRNAs, hold significant potential for non-invasive cancer detection before symptoms manifest.

METHODS

This study aimed to identify biomarkers with high sensitivity and specificity for multiple and specific cancer screening. 972 Serum miRNA profiles were compared across thirteen cancer types and healthy individuals using weighted miRNA co-expression network analysis. To prioritize miRNAs, module membership measure and miRNA trait significance were employed. Subsequently, for specific cancer screening, gastric cancer was focused on, using a similar strategy and a further step of preservation analysis. Machine learning techniques were then applied to evaluate two distinct miRNA panels: one for multi-cancer screening and another for gastric cancer classification.

RESULTS

The first panel (hsa-miR-8073, hsa-miR-614, hsa-miR-548ah-5p, hsa-miR-1258) achieved 96.1% accuracy, 96% specificity, and 98.6% sensitivity in multi-cancer screening. The second panel (hsa-miR-1228-5p, hsa-miR-1343-3p, hsa-miR-6765-5p, hsa-miR-6787-5p) showed promise in detecting gastric cancer with 87% accuracy, 90% specificity, and 89% sensitivity.

CONCLUSIONS

Both panels exhibit potential for patient classification in diagnostic and prognostic applications, highlighting the significance of liquid biopsy in advancing cancer screening methodologies.

FGFR2 fusions assessed by NGS, FISH, and immunohistochemistry in intrahepatic cholangiocarcinoma

BACKGROUND

FGFR2 fusion has become a promising therapeutic target in iCCAs; however, the procedure for screening FGFR2 fusion has not been conventionally developed.

METHODS

FGFR2 fusion was identified using DNA + RNA-based NGS and FISH, and the concordance between DNA + RNA-based NGS, FISH, and IHC was compared.

RESULTS

FGFR2 fusions were detected in 9 out of 76 iCCAs (11.8%). The consistency of FISH and DNA + RNA-based NGS for FGFR2 fusions was high (κ value = 0.867, P = 0.001), while the consistency of IHC and DNA + RNA-based NGS was lower (κ value = 0.464, P = 0.072). All nine FGFR2 fusion-positive iCCAs were MSS with a median TMB of 2.1 mut/Mb, and only one had a CPS (PD-L1) above 5. Two FGFR2 fusion-positive iCCA patients were treated with and benefited from FGFR inhibitor therapy.

CONCLUSIONS

FGFR2 fusion should be assessed for advanced iCCA patients. We recommend DNA + RNA-based NGS as the preferred option to supply all possible therapeutic targets. FISH should be preferred if the tumor sample is insufficient for NGS or if the patient is inclined to receive FGFR inhibitors promptly. Although IHC is not the preferred method to identify FGFR2 fusion, it might be used as preliminary screening for FGFR2 alterations if the hospital cannot offer NGS or FISH, and the results need to be validated before FGFR2 inhibitors treatment.

Circulating Tumor DNA in Conjunctival Melanoma: Landscape and Surveillance Value

PURPOSE

To evaluate the surveillance value of circulating tumor DNA (ctDNA) for detecting distant metastasis and indicating systemic therapeutic efficacy in conjunctival melanoma (CoM).

DESIGN

Retrospective, observational case series.

METHODS

From July 2021 to June 2023, 30 CoM patients in our center underwent plasma ctDNA assessment, out of which 12 individuals presented with distant metastases. We employed a 437-gene panel containing common mutations in CoM and common drug-sensitive mutations using next-generation sequencing (NGS) technology to analyze ctDNA mutations in plasma. Clinical and radiological records were used to assess tumor status. The relationship between ctDNA characteristics, tissue gene mutations, and clinical manifestations were explored.

RESULTS

CoM-related driver mutations were detected in ctDNA of 11 patients with distant metastasis. The ctDNA were highly consistent with tissue sequencing, mutual driver mutation including BRAF, NRAS, KRAS, NF1, CTNNB1, and TP53 mutation. those with a higher VAF had shorter progression-free survival (PFS, p = .0475) and overall survival (OS, p = .0043). The ctDNA variant allele fraction (VAF) was not correlated with the sum of the longest diameters (SLD, p = .8192) in distant metastasis patients.

CONCLUSIONS

Positive plasma ctDNA reflected the presence of metastases. The ctDNA could be used as a complement or alternative to tissue sequencing. High VAF ctDNA might indicate rapid disease progression in distant metastasis patients.

Evaluation of circulating tumor DNA as a prognostic and predictive biomarker in BRAF V600E mutated colorectal cancer-results from the FIRE-4.5 study

The randomized FIRE-4.5 (AIO KRK0116) trial compared first-line therapy with FOLFOXIRI (folinic acid, fluorouracil, oxaliplatin, and irinotecan) plus either cetuximab or bevacizumab in B-Raf proto-oncogene, serine/threonine kinase (BRAF) V600E-mutant metastatic colorectal cancer (mCRC) patients. This study was accompanied by a prospective translational project analyzing cell-free circulating tumor DNA (ctDNA) in plasma to test whether ctDNA analysis may help to guide clinical treatment decision making. FIRE-4.5 included mCRC patients with BRAF V600E mutation detected by tissue-based analyses. Liquid biopsies (LBs) were collected at baseline (pre-treatment) and during therapy. Digital droplet PCR (ddPCR) technology was applied for determination of BRAF mutations and the in vitro diagnostics (IVD)-certified ONCOBEAM RAS procedure for analysis of RAS mutations. The BRAF V600E variants in ctDNA were analyzable in 66 patients at start of the therapy, at baseline. No BRAF V600E mutations were detected in 26% (17/66) of patients and was associated with a significantly longer progression-free survival (PFS: 13.2 vs 6.5 months; HR 0.47; P = 0.014) and overall survival (OS: 36.8 vs 13.2 months; HR 0.35; P = 0.02) as compared to ctDNA mutant patients. Patients with detectable BRAF mutations showed a clear superiority of FOLFOXIRI plus bevacizumab with regard to PFS (10.4 vs 5.7 months; HR 0.4; P = 0.009) and OS (16.6 vs 11.6 months; HR 0.5; P = 0.15), while this was not the case for BRAF wild-type patients. Follow-up LBs were obtained from 51 patients. Patients converting from BRAF V600E mutant to a BRAF V600 wild-type status (36%, N = 18) had a superior PFS (8.6 vs 2.3 months; P = 0.0002) and OS (17.4 vs 5.1 months; P < 0.0001) compared to patients with stable or increased mutational allele frequency (12%, N = 6). Those patients also achieved a significantly greater disease control rate (89% vs 20%; P = 0.008). In conclusion, LB evaluating ctDNA is informative and may help to guide treatment in patients with BRAF V600E-mutated mCRC.

The Role of Liquid Biopsy in Neuroblastoma: A Scoping Review

BACKGROUND

Neuroblastoma (NBL), is the most common, non-CNS solid tumor of childhood. This disease presents with unique biological and clinical challenges necessitating accurate diagnosis, prognosis assessment, treatment, and vigilant monitoring. Liquid biopsy is an upcoming, innovative, and non-invasive diagnostic modality. It has the potential to detect tumors and perform therapeutic monitoring through the analysis of circulating biomarkers in blood, urine, saliva, and other bodily fluids.

METHODOLOGY

This scoping review offers an in-depth exploration, of the current landscape of liquid biopsy-based biomarkers in NBL. The review looks at the clinical implications, prevalent challenges, and future outlook of their clinical applications in NBL. The scoping review adhered to the guidelines of the PRISMA extension for scoping reviews, known as PRISMA-ScR, as the skeletal framework. The review involved comprehensive searches for liquid biopsy-based biomarkers in NBL across multiple databases, including PUBMED, EMBASE, SCOPUS, and WEB of Science, without restrictions.

RESULTS

The scoping review process uncovered a significant body of literature (n = 201) that underwent meticulous scrutiny, ultimately leading to the final selection of studies (n = 15). The liquid biopsy biomarkers included circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), exosomes, and other entities in bodily fluids. Their evaluation focused on associations with clinical outcomes such as overall survival, event-free survival, and risk stratification in NBL.

CONCLUSION

Our findings highlight the potential of liquid biopsy biomarkers to revolutionize NBL diagnosis and therapeutic monitoring. This rapidly evolving frontier in pediatric oncology suggests significant advancements in precision medicine for the management of NBL.

Exosomes as a Therapeutic Strategy in Cancer: Potential Roles as Drug Carriers and Immune Modulators

Exosome-based cancer immunotherapy is advancing quickly on the concept of artificially activating the immune system to combat cancer. They can mechanistically change the tumor microenvironment, increase immune responses, and function as efficient drug delivery vehicles because of their inherent bioactivity, low toxicity, and immunogenicity. Accurate identification of the mechanisms of action of exosomes in tumor environments, along with optimization of their isolation, purification, and characterization methods, is necessary to increase clinical applications. Exosomes can be modified through cargo loading and surface modification to enhance their therapeutic applications, either before or after the donor cells' isolation. These engineered exosomes can directly target tumor cells at the tumor site or indirectly activate innate and adaptive immune responses in the tumor microenvironment. This approach is particularly effective when combined with traditional cancer immunotherapy techniques such as vaccines, immune checkpoints, and CAR-T cells. It can improve anti-tumor responses, induce long-term immunity, and address the limitations of traditional therapies, such as poor penetration in solid tumors and immunosuppressive environments. This review aims to provide a comprehensive and detailed overview of the direct role of engineered exosomes as drug delivery systems and their immunomodulatory effects on tumors as an indirect approach to fighting cancer. Additionally, it will discuss novel immunotherapy options.

Advancing Veterinary Oncology: Next-Generation Diagnostics for Early Cancer Detection and Clinical Implementation

Cancer is a leading cause of death among companion animals, with many cases diagnosed at advanced stages when clinical signs have appeared, and prognosis is poor. Emerging diagnostic technologies, including Artificial Intelligence (AI)-enhanced imaging, liquid biopsies, molecular diagnostics, and nematode-based screening, can improve early detection capabilities in veterinary medicine. These tools offer non-invasive or minimally invasive methods to facilitate earlier detection and treatment planning, addressing the limitations of traditional diagnostics, such as radiography and tissue biopsies. Recent advancements in comparative oncology, which leverage the biological similarities between human and companion animal cancers, underscore their translational value in improving outcomes across species. Technological advances in genomics, bioinformatics, and machine learning are driving a shift toward precision medicine, enabling earlier detection, personalized treatments, and monitoring of disease progression. Liquid biopsy testing detects circulating tumor DNA and tumor cells, providing actionable insights into tumor genetics without invasive procedures. Imaging systems enhance diagnostic precision, offering consistent and accurate tumor identification across veterinary practices, while portable innovations like Caenorhabditis elegans-based screening provide accessible options for underserved regions. As these technologies migrate from human medicine to veterinary applications, they are poised to redefine cancer care for companion animals. This review highlights key advancements in diagnostic technologies and their application in veterinary oncology, with a focus on enhancing early detection, accessibility, and precision in cancer care. By fostering the adoption of these innovations, veterinary oncology can achieve a new standard of care, improving outcomes for both animals and humans through the lens of comparative oncology.

Integrating machine learning-predicted circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) in metastatic breast cancer: A proof of principle study on endocrine resistance profiling

The study explored endocrine resistance by leveraging machine learning to establish the prognostic stratification of predicted Circulating tumor cells (CTCs), assessing its integration with circulating tumor DNA (ctDNA) features and contextually evaluate the potential of CTCs-based transcriptomics. 1118 patients with a diagnosis of luminal-like Metastatic Breast Cancer (MBC) were characterized for ctDNA through NGS before treatment start, predicted CTCs were computed through a K nearest neighbor algorithm. Differences across subgroups were analyzed through chi square or Fisher's exact test according to sample size and corrected for False Discovery Rate. Differences in survival were tested by log-rank test and uni- and multivariable Cox regression. CTCs transcriptomics was performed through RNAseq after sorting with DEPArray NxT. Univariable and multivariable analysis adjusted for ctDNA alterations revealed a significant impact of CTCs predictive stratification on both progression-free survival (PFS) and overall survival (OS). Alterations in RTK and ER pathways were significantly correlated with predicted-Stage IVaggressive. The combined impact of CTCs stratification and RTK/ER pathway alterations influenced patient outcomes, with predicted-Stage IVaggressive having a negative impact on PFS regardless of the mutational status. The pilot exploratory CTCs transcriptomics analysis showed transcriptional changes linked to cell proliferation such as under expression of MALAT1 and overexpression of GREM1, GPR85 and OCM. Our data underline the potential of an integration between ctDNA and CTCs, both through quantification and transcriptomic analysis, for a deeper understanding of tumor biology and treatment response in HR-positive, HER2-negative MBC.

Immunolipid magnetic bead-based circulating tumor cell sorting: a novel approach for pathological staging of colorectal cancer

Objective

This study aimed to assess whether circulating tumor cells (CTCs) from colorectal cancer (CRC) could be used as an alternative to tissue samples for genetic mutation testing, overcoming the challenge of difficult tumor tissue acquisition.

Methods

We developed an immunolipid magnetic bead (IMB) system modified with antibodies against epithelial cell adhesion molecule (EpCAM) and vimentin to efficiently separate CTCs. We prepared EpCAM-modified IMBs (Ep-IMBs) and vimentin-modified IMBs (Vi-IMBs). The separation efficiency of the system was evaluated via in vitro experiments and by capturing and counting CTCs in blood samples from 23 CRC patients and 20 healthy controls. Hotspot mutations in patient tissue samples were identified via next-generation sequencing (NGS), whereas mutations in blood CTCs were detected via Sanger sequencing. The concordance between hotspot mutations in tumor tissue and blood CTCs was analyzed.

Results

The CTC sorting system exhibited good dispersion, stability, and low cytotoxicity, with a specificity of 90.54% and a sensitivity of 89.07%. CRC patients had an average of 8.39 CTCs per 7.5 mL of blood, whereas healthy controls had 0.09 per 7.5 mL of blood. The consistency of gene mutations was as follows: TP53 (91.31%), PIK3CA (76.00%), KRAS (85.36%), BRAF (51.00%), APC (65.67%), and EGFR (74.00%), with an overall gene mutation consistency of 85.06%.

Conclusion

Our CTC sorting system, which is based on Ep-IMBs and Vi-IMBs, effectively captures CTCs in the peripheral blood of CRC patients and enables clinical hotspot gene mutation testing via these enriched CTCs. This system partially solves the problem of difficult tumor tissue sample collection and provides a reference for gene mutation testing in early diagnosis, therapeutic efficacy evaluation, prognosis assessment, and minimal metastasis detection in CRC patients, showing significant potential for clinical application, especially in targeted therapy gene testing for CRC.

Circulating Extracellular Vesicles as Promising Biomarkers for Precession Diagnostics: A Perspective on Lung Cancer

Extracellular vesicles (EVs) have emerged as promising biomarkers in liquid biopsy, owing to their ubiquitous presence in bodily fluids and their ability to carry disease-related cargo. Recognizing their significance in disease diagnosis and treatment, substantial efforts have been dedicated to developing efficient methods for EV isolation, detection, and analysis. EVs, heterogeneous membrane-encapsulated vesicles secreted by all cells, contain bioactive substances capable of modulating recipient cell biology upon internalization, including proteins, lipids, DNA, and various RNAs. Their prevalence across bodily fluids has positioned them as pivotal mediators in physiological and pathological processes, notably in cancer, where they hold potential as straightforward tumor biomarkers. This review offers a comprehensive examination of advanced nanotechnology-based techniques for detecting lung cancer through EV analysis. It begins by providing a brief overview of exosomes and their role in lung cancer progression. Furthermore, this review explores the evolving landscape of EV isolation and cargo analysis, highlighting the importance of characterizing specific biomolecular signatures within EVs for improved diagnostic accuracy in lung cancer patients. Innovative strategies for enhancing the sensitivity and specificity of EV isolation and detection, including the integration of microfluidic platforms and multiplexed biosensing technologies are summarized. The discussion then extends to key challenges associated with EV-based liquid biopsies, such as the standardization of isolation and detection protocols and the establishment of robust analytical platforms for clinical translation. This review highlights the transformative impact of EV-based liquid biopsy in lung cancer diagnosis, heralding a new era of personalized medicine and improved patient care.

Precision medicine in diagnosis, prognosis, and disease monitoring of bone and soft tissue sarcomas using liquid biopsy: a systematic review

INTRODUCTION

Liquid biopsy as a non-invasive method to investigate cancer biology and monitor residual disease has gained significance in clinical practice over the years. Whilst its applicability in carcinomas is well established, the low incidence and heterogeneity of bone and soft tissue sarcomas explains the less well-established knowledge considering liquid biopsy in these highly malignant mesenchymal neoplasms.

MATERIALS AND METHODS

A systematic literature review adhering to the PRISMA guidelines initially identified 920 studies, of whom 68 original articles could be finally included, all dealing with clinical applicability of liquid biopsy in sarcoma. Studies were discussed within two main chapters, i.e. translocation-associated and complex-karyotype sarcomas.

RESULTS

Overall, data on clinical applicability of liquid biopsy in 2636 patients with > 10 different entities of bone and soft tissue sarcomas could be summarised. The five most frequent tumour entities included osteosarcoma (n = 602), Ewing sarcoma (n = 384), gastrointestinal stromal tumour (GIST; n = 203), rhabdomyosarcoma (n = 193), and leiomyosarcoma (n = 145). Of 11 liquid biopsy analytes, largest evidence was present for ctDNA and cfDNA, investigated in 26 and 18 studies, respectively.

CONCLUSIONS

This systematic literature review provides an extensive up-to-date overview about the current and potential future uses of different liquid biopsy modalities as diagnostic, prognostic, and disease monitoring markers in sarcoma.

Liquid Biopsy and Challenge of Assay Heterogeneity for Minimal Residual Disease Assessment in Colon Cancer Treatment

This review provides a comprehensive overview of the evolving role of minimal residual disease (MRD) for patients with Colon Cancer (CC). Currently, the standard of care for patients with non-metastatic CC is adjuvant chemotherapy (ACT) for all patients with stage III and high-risk stage II CC following surgical intervention. Despite a 5-20% improvement in long-term survival outcomes, this approach also results in a significant proportion of patients receiving ACT without any therapeutic benefit and being unnecessarily exposed to the risks of secondary side effects. This underscores an unmet clinical need for more precise stratification to distinguish patients who necessitate ACT from those who can be treated with surgery alone. By employing liquid biopsy, it is possible to discern MRD enabling the categorization of patients as MRD-positive or MRD-negative, potentially revolutionizing the management of ACT. This review aimed to examine the heterogeneity of methodologies currently available for MRD detection, encompassing the state-of-the-art technologies, their respective advantages, limitations, and the technological challenges and multi-omic approaches that can be utilized to enhance assay performance. Furthermore, a discussion was held regarding the clinical trials that employ an MRD assay focusing on the heterogeneity of the assays used. These differences in methodology, target selection, and performance risk producing inconsistent results that may not solely reflect biological/clinical differences but may be the consequence of the preferential use of particular products in studies conducted in different countries. Standardization and harmonization of MRD assays will be crucial to ensure the liquid revolution delivers reliable and clinically actionable outcomes for patients.

Longitudinal genomic profiling using liquid biopsies in metastatic nonsquamous NSCLC following first line immunotherapy

Tumor genomic profiling is often limited to one or two timepoints due to the invasiveness of tissue biopsies, but longitudinal profiling may provide deeper clinical insights. Using ctDNA data from IMpower150 study, we examined genetic changes in metastatic non-squamous NSCLC post-first-line immunotherapy. Mutations were most frequently detected in TP53, KRAS, SPTA1, FAT3, and LRP1B at baseline and during treatment. Mutation levels rose prior to radiographic progression in most progressing patients, with specific mutations (SPTA1, STK11, KEAP1, SMARCA4, TBX3, CDH2, and MLL3) significantly enriched in those with progression or nondurable response. However, ctDNA's role in detecting hyperprogression and pseudoprogression remains uncertain. STK11, SMARCA4, KRAS, SLT2, and KEAP1 mutations showed the strongest correlation with poorer overall survival, while SMARCA4, STK11, SPTA1, TBX3, and KEAP1 mutations correlated with shorter progression-free survival. Overall, longitudinal liquid biopsy profiling provided valuable insights into lung cancer biology post-immunotherapy, potentially guiding personalized therapies and future drug development.

Precision medicine using molecular-target drugs in psoriatic arthritis

Psoriatic arthritis (PsA) presents various clinical manifestations, including skin lesions, peripheral arthritis, axial involvement, enthesitis, nail involvement, dactylitis, and uveitis. In addition, it causes a high incidence of lifestyle-related diseases and an increase in cerebrovascular and cardiovascular events. As the pathology of PsA has been clarified, molecular-targeted drugs targeting tumor necrosis factor-α, interleukin (IL)-17A, IL-17A/F, IL-17 receptor, IL-12/23(p40), IL-23p19, Cytotoxic T-lymphocyte Antigen-4 (CTLA-4), Janus kinase, and phosphodiesterase-4 have been developed and are widely used in clinical practice. PsA is clinically and molecularly heterogeneous, and it is necessary to improve various clinical symptoms with limited treatment options simultaneously; therefore, rheumatologists sometimes encounter difficult situations in clinical practice. Hence, the development of precision medicine may improve treatment outcomes. Recently, the strategic use of molecular-targeted drugs based on the stratification of patients with PsA by peripheral blood lymphocyte phenotyping and serum cytokine concentrations has been reported to possibly lead to a higher therapeutic response. A randomized controlled trial was initiated to verify the efficacy of this treatment strategy. However, to make precision medicine in PsA feasible, shifting from conventional clinical trials to clinical trials based on biomarker profiles and accumulating further data are necessary.

Electrical and fluorescence in situ monitoring of tumor microenvironment-based pH-responsive polymer dot coated surface

A boronate-ester structure forming a pH-responsive polymer dot (Plu-PD) coated biosensor between carbonized-sp2 rich dopamine-alginate [PD(Alg)] and boronic acid-grafted Pluronic (BA-Pluronic) was developed for the electrochemical and fluorescence detection of cancer cells. The reduced fluorescence (FL) resulting from fluorescence resonance energy transfer (FRET) mediated by π-π interactions within Plu-PD was successfully reinvigorated through the specific cleavage of the boronate-ester bond, triggered by the acidic conditions prevailing in the cancer microenvironment. The anomalous variations in extracellular pH levels observed in cancer (pH ∼6.8), as opposed to the normal cellular pH range of approximately 7.4, serve as robust indicators for discerning cancer cells from their healthy counterparts. Moreover, the Plu-PD coated surface demonstrated remarkable adaptability in modulating its surface structure, concurrently exhibiting tunable electroconductivity under reduced pH conditions, thereby imparting selective responsiveness to cancer cells. The pH-modulated conductivity change was validated by a reduction in resistance from 211 ± 9.7 kΩ at pH 7.4 to 73.9 ± 9.4 kΩ and 61.5 ± 11.5 kΩ at pH 6.8 and 6.0, respectively. The controllable electrochemical characteristics were corroborated through in vitro treatment of cancer cells (HeLa, B16F10, and SNU-C2A) via LED experiments and wireless output analysis. In contrast, identical treatments yielded a limited response in normal cell line (CHO-K1). Notably, the Plu-PD coated surface can be seamlessly integrated with a wireless system to facilitate real-time monitoring of the sensing performance in the presence of cancer and normal cells, enabling rapid and accurate cancer diagnosis using a smartphone.

Biological Cargo: Exosomes and their Role in Cancer Progression and Metastasis

Cancer cells are among the many types of cells that release exosomes, which are nanovesicles. Because of their many potential applications, exosomes have recently garnered much attention from cancer researchers. The bioactive substances that exosomes release as cargo have been the subject of several investigations. The substances in question may operate as biomarkers for diagnosis or affect apoptosis, the immune system, the development and spread of cancer, and other processes. Others have begun to look at exosomes in experimental therapeutic trials because they believe they may be useful in the treatment of cancer. This review started with a short description of exosome biogenesis and key features. Next, the potential of tumor-derived exosomes and oncosomes to influence the immune system throughout the development of cancer, as well as alter tumor microenvironments (TMEs) and pre-metastatic niche creation, was investigated. Finally, there was talk of exosomes' possible use in cancer treatment. Furthermore, there is emerging consensus about the potential application of exosomes to be biological reprogrammers of cancer cells, either as carriers of naturally occurring chemicals, including anticancer medications, or as carriers of anticancer vaccines for immunotherapy as well as boron neutron capture therapy (BNCT). We briefly review the key ideas and logic behind this intriguing therapy recommendation.

Ultrasensitive detection of cancer-associated nucleic acids and mutations by primer exchange reaction-based signal amplification and flow cytometry

The detection of cancer-associated nucleic acids and mutations through liquid biopsy has emerged as a highly promising non-invasive approach for early cancer detection and monitoring. In this study, we report the development of primer exchange reaction (PER) based signal amplification strategy that enables the rapid, sensitive and specific detection of nucleic acids bearing cancer specific single nucleotide mutations using flow cytometry. Using micrometer size beads as support for immobilizing oligonucleotides and programmable PER assembly for target oligonucleotide recognition and fluorescence signal amplification, we demonstrated the versatile detection of target nucleic acids including KRAS oligonucleotide, fragmented mRNAs, and miR-21. Moreover, our detection system can discriminate single base mutations frequently occurred in cancer-associated genes including KRAS, PIK3CA and P53 from cell extracts and circulating tumor DNAs (ctDNAs). The detection is highly sensitive, with a limit of detection down to 27 fM without pre-amplification. In view of a clinical application, we demonstrate the detection of single mutations after extraction and pre-amplification of ctDNAs from the plasma of breast cancer patients. Importantly, our detection strategy enabled the detection of single KRAS mutation even in the presence of 1000-fold excess of wild type (WT) DNA using multi-color flow cytometry detection approach. Overall, our strategy holds immense potential for clinical applications, offering significant improvements for early cancer detection and monitoring.

Role of circulating tumor cells in breast cancer

Circulating tumor cells (CTCs) are tumor cells that shed from the primary tumor or metastatic loci, intravasate, and circulate in the bloodstream. CTCs have been suggested to play a major role in the metastatic spread of cancer, constantly shedding from tumors during proliferation or as a result of mechanical insults. Breast cancer (BC) is one of the most representative tumors in CTC research, with several studies conducted on its clinical validity and utility in both early and advanced BC (EBC and ABC, respectively). The assessment of the number and molecular profiles of CTCs is expected to provide a more tailored therapy for patients with BC. The detection of CTCs is usually dependent on molecular markers, and epithelial cell adhesion molecules are widely used. Although the CellSearch® technology has been widely utilized for CTC detection, recent advances have led to the development of novel detection methods, facilitating further molecular analysis. In this review, we discuss the clinical applications of CTCs, current status of research, and efforts to incorporate CTC analysis into clinical practice. Additionally, we discuss potential challenges and future directions for integrating CTC analysis into clinical practice.

Integrating Multi-Cancer Early Detection (MCED) Tests with Standard Cancer Screening: System Dynamics Model Development and Feasibility Testing

BACKGROUND

Cancer screening plays a critical role in early disease detection and improving outcomes. In Australia, established screening protocols for colorectal, breast and cervical cancer have significantly contributed to timely cancer detection. However, the recent introduction of multi-cancer early detection (MCED) tests arguably can disrupt current screening, yet the extent to which these tests provide additional benefits remains uncertain. We present the development and initial validation of a system dynamics (SD) model that estimates the additional cancer detections and costs associated with MCED tests.

AIM

This article describes the development of a simulation model built to evaluate the additional patient diagnoses and the economic impact of incorporating MCED testing alongside Australia's well-established standard of care (SOC) screening programs for colorectal, breast, cervical and lung cancers. The model was designed to estimate the additional number of patients diagnosed at each cancer stage (stage I, II, III, IV, or unknown) and the associated costs. This simulation model allows for the analysis of multiple scenarios under a plausible set of assumptions regarding population-level participation rates.

METHODS

An SD model was developed to represent the existing SOC national cancer screening pathways and to integrate potential clinical pathways that could be introduced by MCED tests. The SD model was built to investigate three scenarios for the use of MCED testing: firstly, to explore the viability of MCED testing as a substitute among individuals who are not opting for SOC screening for any reason; secondly, to implement MCED testing exclusively for individuals ineligible for SOC screening, yet have high-risk characteristics; and thirdly, to employ MCED testing after SOC screening to serve as a triaging/confirmatory tool for individuals receiving inconclusive test results. The three primary scenarios were constructed by varying diagnostic accuracy and uptake rates of MCED tests.

DISCUSSION

The clinical utility and outcomes of MCED testing for screening and early detection still lack comprehensive evidence. Nonetheless, this simulation model facilitates a thorough analysis of MCED tests within the Australian healthcare context, providing insights into potential additional detections and costs to the healthcare system, which may help prioritise future evidence development. The adaptable yet novel SD model presented herein is anticipated to be of considerable interest to industry, policymakers, consumers and clinicians involved in informing clinical and economic decisions regarding integrating MCED tests as cancer screening and early detection tools. The expected results of applying this SD model will determine whether using MCED testing in conjunction with SOC screening offers any potential benefits, possibly guiding policy decisions and clinical practices towards the adoption of MCED tests.

KRAS Mutations in Cholangiocarcinoma: Prevalence, Prognostic Value, and KRAS G12/G13 Detection in Cell-Free DNA

BACKGROUND/AIM

Cholangiocarcinoma (CCA) is an aggressive hepatobiliary malignancy characterized by genomic heterogeneity. KRAS mutations play a significant role in influencing patient prognosis and guiding therapeutic decision-making. This study aimed to determine the prevalence and prognostic significance of KRAS mutations in CCA, asses the detection of KRAS G12/G13 mutations in plasma cell-free DNA (cfDNA), and evaluate the prognostic value of KRAS G12/G13 mutant allele frequency (MAF) in cfDNA in relation to clinicopathological data and patient survival.

MATERIALS AND METHODS

A retrospective analysis of 937 CCA patients was performed using data from cBioPortal to examine KRAS mutation profiles and their association with survival. Plasma from 101 CCA patients was analyzed for KRAS G12/G13 mutations in the cfDNA using droplet digital PCR, and the results were compared with tissue-based sequencing from 78 matched samples.

RESULTS

KRAS driver mutations were found in 15.6% of patients, with common variants being G12D (37.0%), G12V (24.0%) and Q61H (8.2%). Patients harboring KRAS mutations exhibited decreased overall and recurrence-free survival. KRAS G12/G13 mutations were detected in 14.9% of cfDNA samples, showing moderate concordance with tissue sequencing, and achieving 80% sensitivity and 93% specificity. Elevated KRAS G12/G13 MAF in cfDNA, combined with high CA19-9 levels, correlated with poorer survival outcomes.

CONCLUSION

The presence of KRAS mutations was associated with poor survival in CCA, underscoring the importance of KRAS mutations as prognostic markers. The detection of KRAS mutations in cfDNA demonstrated potential as a promising non-invasive alternative for mutation detection and, when combined with CA19-9 levels, may improve prognostic efficacy in CCA.