Circulating tumour DNA - looking beyond the blood

Liquid Biopsy on Microfluidics: From Existing Endogenous to Emerging Exogenous Biomarkers Analysis

Liquid biopsy is an appealing approach for early diagnosis and assessment of treatment efficacy in cancer. Typically, liquid biopsy involves the detection of endogenous biomarkers, including circulating tumor cells (CTCs), extracellular vesicles (EVs), circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), and proteins. The levels of these endogenous biomarkers are higher in cancer patients compared to those in healthy individuals. However, the clinical application of liquid biopsy using endogenous biomarker analysis faces challenges due to its low abundance and poor stability in circulation. Recently, a promising strategy involving the engineering of exogenous probes has been developed to overcome these limitations. These exogenous probes are activated within the tumor microenvironment, generating distinct exogenous markers that can be easily distinguished from background biological signals. Alternatively, these exogenous probes can be labeled with intrinsic endogenous biomarkers in vivo and detected in vitro after metabolic processes. In this review, we primarily focus on microfluidic-based liquid biopsy techniques that allow for the transition from analyzing existing endogenous biomarkers to emerging exogenous ones. First, we introduce common endogenous biomarkers, as well as synthetic exogenous ones. Next, we discuss recent advancements in microfluidic-based liquid biopsy techniques for analyzing both existing endogenous and emerging exogenous biomarkers. Lastly, we provide insights into future directions for liquid biopsy on microfluidic systems.

Multi-omics analysis identifies diagnostic circulating biomarkers and potential therapeutic targets, revealing IQGAP1 as an oncogene in gastric cancer

This study employed a multi-omics integration approach to identify circulating biomarkers for gastric cancer (GC). We analyzed plasma and tumor tissue single-cell RNA sequencing data, along with gene and protein quantitative trait loci analyses. Leveraging data from UK Biobank and FinnGen, we investigated genetic associations with GC. Through colocalization, Mendelian Randomization, and various filtering analyses, we identified four genes (IQGAP1, KRTCAP2, PARP1, MLF2) and four proteins (EGFL9 [DLK2], ECM1, PDIA5, TIMP4) as potential GC biomarkers. These were selected based on significant genetic colocation probabilities and significant associations with GC. Seven of these biomarkers demonstrated predictive capability for GC occurrence, with AUC ranging from 0.61 to 0.99. Drug prediction analysis identified seven protein biomarkers as potential targets for immunotherapy, targeted therapies, and tumor chemotherapy. Further scRNA-seq analysis revealed significant expression differences between gastric tumor and normal tissues, particularly the upregulation of IQGAP1, which highlights its role in tumor growth.

Lateral Flow Platform for Lung Cancer Diagnosis through Simultaneous Detection of ctDNA and MicroRNA

Early cancer screening is essential for reducing cancer-related mortality and improving survival rates. Simultaneous detection of multiple tumor markers can enhance the accuracy and specificity of cancer diagnosis, helping us to mitigate false-positive results associated with single-marker analysis. Here, we have developed a lateral flow detection platform that combines recombinase polymerase amplification (RPA), CRISPR Cas9, and catalyzed hairpin assembly (CHA) for the simultaneous detection of KRAS ctDNA and miRNA-223 in lung cancer. The CRISPR Cas9 system acts as a linking element, enabling specific recognition and binding to RPA amplicons of KRAS ctDNA while facilitating the capture of Au-DNA-Bio nanoparticles (NPs), thereby producing a stronger detection signal through Au NPs aggregation. The CHA system enhances this platform by providing sensitive detection of miRNA-223. Our platform was tested on a limited number of clinical saliva samples, demonstrating feasibility but requiring further validation with larger cohorts.

Enhanced the Trans-Cleavage Activity of CRISPR-Cas12a Using Metal-Organic Frameworks as Stimulants for Efficient Electrochemical Sensing of Circulating Tumor DNA

Continued development of clustered regularly interspaced short palindromic repeats (CRISPR)-powered biosensing system on the electrochemical interface is vital for accurate and timely diagnosis in clinical practice. Herein, an electrochemical biosensor based on manganese metal-organic frameworks (MOFs)-enhanced CRISPR (MME-CRISPR) is proposed that enables the efficient detection of circulating tumor DNA (ctDNA). In this design, customized enzyme stimulants (Mn2+) are co-assembled with Cas12a/crRNA to form enzyme-MOF composites, which can be released quickly under mild conditions. The MOFs-induced proximity effect can continuously provide adequate Mn2+ to sufficiently interact with Cas12a/crRNA during the release process, enhancing the trans-cleavage activity of complex available for biosensor construction. The MOFs-based enzyme biocomposites also afford efficient protection against various external stimulus. It is demonstrated that the developed biosensor can achieve ultrasensitive detection of epidermal growth factor receptor L858R mutation in ctDNA with a low detection limit of 0.28 fm without pre-amplification. Furthermore, the engineered mismatch crRNA enables the biosensor based on MME-CRISPR to detect single nucleotide variant with a high signal-to-noise ratio. More importantly, it has been successfully used to detect the targets in clinical practice, requiring low-dose samples and a short time. This strategy is believed to shed new light on the applications of cancer diagnosis, treatment, and surveillance.

2D Materials-Based Field-Effect Transistor Biosensors for Healthcare

The need for accurate point-of-care (POC) tools, driven by increasing demands for precise medical diagnostics and monitoring, has accelerated the evolution of biosensor technology. Integrable 2D materials-based field-effect transistor (2D FET) biosensors offer label-free, rapid, and ultrasensitive detection, aligning perfectly with current biosensor trends. Given these advancements, this review focuses on the progress, challenges, and future prospects in the field of 2D FET biosensors. The distinctive physical properties of 2D materials and recent achievements in scalable synthesis are highlighted that significantly improve the manufacturing process and performance of FET biosensors. Additionally, the advancements of 2D FET biosensors are investigated in fatal disease diagnosis and screening, chronic disease management, and environmental hazards monitoring, as well as their integration in flexible electronics. Their promising capabilities shown in laboratory trials accelerate the development of prototype products, while the challenges are acknowledged, related to sensitivity, stability, and scalability that continue to impede the widespread adoption and commercialization of 2D FET biosensors. Finally, current strategies are discussed to overcome these challenges and envision future implications of 2D FET biosensors, such as their potential as smart and sustainable POC biosensors, thereby advancing human healthcare.

Circulating tumor DNA in colorectal cancer: biology, methods and applications

In the practice of colorectal cancer (CRC), traditional tumor tissue analysis is limited by intratumoral and intertumoral heterogeneity and its invasive nature. Circulating tumor DNA (ctDNA) analysis, a promising liquid biopsy approach, has been increasingly explored in clinical studies. Biologically, ctDNA is characterized by tumor-specific diversity and rapid clearance from circulation, enabling real-time, dynamic, and repeatable assessments. Technologically, PCR- and NGS-based downstream analysis methods have been developed and validated. However, variables in pre-analytical and analytical procedures underscores the need for standardized protocols. Compared with clinicopathology-based risk stratification, ctDNA-based molecular residual disease detection has demonstrated significant potential in guiding treatment decisions. Qualitative and quantitative changes in ctDNA have also shown predictive and prognostic value during neoadjuvant or adjuvant treatment, as well as in later-line treatment for metastatic CRC. Specific molecular aberrations in ctDNA can not only assist in identifying candidates for targeted therapies but also reveal resistance mechanisms. Additionally, emerging research is exploring the potential of ctDNA in early cancer detection. Overall, as a novel biomarker, ctDNA holds substantial promise in advancing clinical practice. This review focuses on the biological characteristics, pre-analytical variables, and downstream analysis methods of ctDNA and summarizes its role across various clinical scenarios in CRC.

Circulating tumor DNA: a revolutionary approach for early detection and personalized treatment of bladder cancer

Bladder cancer is a malignant tumor with a high global incidence and recurrence rate. Traditional diagnostic methods, such as cystoscopy and urine cytology, have limitations in sensitivity and specificity, particularly in detecting low-grade bladder cancer. Circulating tumor DNA (ctDNA) offers a non-invasive alternative, reflecting tumor genetic characteristics through blood samples. It demonstrates high sensitivity and repeatability, making it a promising tool for early detection, recurrence monitoring, and treatment evaluation. Clinical studies have shown that ctDNA not only detects tumor burden but also captures dynamic tumor mutations, aiding in personalized treatment strategies. Despite its potential, clinical implementation of ctDNA faces challenges, including optimization of detection techniques, standardization, and the cost of testing. This paper explores the role of ctDNA in advancing bladder cancer diagnosis and treatment, with a focus on refining its clinical application and guiding future research toward improved patient outcomes.

Utilizing ctDNA to discover mechanisms of resistance to targeted therapies in patients with metastatic NSCLC: towards more informative trials

Advances in targeted therapies for patients with non-small-cell lung cancer have substantially improved the outcomes of those with actionable alterations in certain oncogenic driver genes. However, acquired resistance to these targeted therapies remains a major challenge. Understanding the mechanisms underlying acquired resistance will be crucial for the development of strategies that might either overcome this effect or delay the onset. Circulating tumour DNA, owing to the need for only minimally invasive sampling and a potential role as both a prognostic and predictive biomarker, is increasingly being used in both research and clinical practice. Several studies have explored the landscape of acquired resistance to targeted therapies using this approach. However, the methodologies of the published studies vary widely, and several major challenges remain in addressing the practical difficulties associated with these methods. These challenges currently limit the depth of research insight provided by the available data. In this Perspective, we review clinical reports describing the use of circulating tumour DNA to detect mechanisms of acquired resistance to targeted therapies, predominantly in patients with advanced-stage non-small-cell lung cancer, and highlight key unresolved questions with the aim of moving towards more-informative research studies.

Genomic and fragmentomic landscapes of cell-free DNA for early cancer detection

Genomic analyses of cell-free DNA (cfDNA) in plasma are enabling noninvasive blood-based biomarker approaches to cancer detection and disease monitoring. Current approaches for identification of circulating tumour DNA typically use targeted tumour-specific mutations or methylation analyses. An emerging approach is based on the recognition of altered genome-wide cfDNA fragmentation in patients with cancer. Recent studies have revealed a multitude of characteristics that can affect the compendium of cfDNA fragments across the genome, collectively called the 'cfDNA fragmentome'. These changes result from genomic, epigenomic, transcriptomic and chromatin states of an individual and affect the size, position, coverage, mutation, structural and methylation characteristics of cfDNA. Identifying and monitoring these changes has the potential to improve early detection of cancer, especially using highly sensitive multi-feature machine learning approaches that would be amenable to broad use in populations at increased risk. This Review highlights the rapidly evolving field of genome-wide analyses of cfDNA characteristics, their comparison to existing cfDNA methods, and recent related innovations at the intersection of large-scale sequencing and artificial intelligence. As the breadth of clinical applications of cfDNA fragmentome methods have enormous public health implications for cancer screening and personalized approaches for clinical management of patients with cancer, we outline the challenges and opportunities ahead.

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.

Liquid biopsy in gastric cancer: A snapshot of the current state of the art

Circulating tumor DNA (ctDNA) is nowadays considered a robust source to search for druggable tumoral genetic alterations, and in some specific settings liquid biopsy (LB) is already part of the diagnostics scenario and it has successfully implemented in the everyday practice. Three strengths make LB an extraordinary tool: i) to represent the complex molecular mosaicism that characterizes spatially heterogeneous malignancies; ii) to monitor in real-time the tumoral molecular landscape (i.e. to depict the longitudinal/temporal tumor evolution); iii) to ensure molecular profiling even in those cases in which tissue sampling is not feasible or not adequate. This review provides a snapshot of the current state of the art concerning ctDNA assay utility in gastric cancer (GC), testing its robustness as marker and seeking to understand the reasons for the delay in its application in clinical practice.

Unleashing the power of urine‑based biomarkers in diagnosis, prognosis and monitoring of bladder cancer (Review)

Bladder cancer (BCa) is a prevalent malignant neoplasm of the urinary tract with high incidence rate, frequent recurrence and rapid disease progression. Conventional approaches for diagnosing, prognosticating and monitoring BCa often rely on invasive procedures such as cystoscopy and tissue biopsy, which are associated with high costs and low patient compliance for follow‑up. Liquid biopsies have advantages, such as being non‑invasive, real‑time, and reproducible, in obtaining diverse biomarkers derived from cellular, molecular, proteomic and genetic signatures in urine or plasma samples. Although plasma‑based biomarkers have been clinically validated, urine provides greater specificity for directly assessing biological materials from urological sources. The present review summarizes advancements and current limitations in urinary protein, genetic and epigenetic biomarkers for disease progression and treatment response of BC, compares performance and application scenarios of urine and blood biomarkers and explores how urinary biomarkers may serve as an alternative or complementary tool to traditional diagnostic methods. The integration of urine‑based or plasma‑based biomarkers into existing diagnostic workflows offers promising avenues for improving accuracy and efficiency of diagnosis in the management of BCa. Notably, the emergence of synthetic biomarkers and urine metabolites, combined with artificial intelligence or bioinformatic technologies, has promise in the screening of potential targets. Continued research and validation efforts are needed to translate these findings into routine clinical practice, ultimately improving patient outcomes and decreasing the burden of BCa.

Single Nucleotide Polymorphism Highlighted via Heterogeneous Light-Induced Dissipative Structure

The unique characteristics of biological structures depend on the behavior of DNA sequences confined in a microscale cell under environmental fluctuations and dissipation. Here, we report a prominent difference in fluorescence from dye-modified single-stranded DNA in a light-induced assembly of DNA-functionalized heterogeneous probe particles in a microwell of several microliters in volume. Strong optical forces from the Mie scattering of microparticles accelerated hybridization, and the photothermal effect from the localized surface plasmons in gold nanoparticles enhanced specificity to reduce the fluorescence intensity of dye-modified DNA to a few %, even in a one-base mismatched sequence, enabling us to clearly highlight the single nucleotide polymorphisms in DNA. Fluorescence intensity was positively correlated with complementary DNA concentrations ranging in several tens fg/μL after only 5 min of laser irradiation. Remarkably, a total amount of DNA in an optically assembled structure of heterogeneous probe particles was estimated between 2.36 ymol (2.36 × 10-24 mol) and 2.36 amol (2.36 × 10-18 mol) in the observed concentration range. These findings can promote an innovative production method of nanocomposite structures via biological molecules and biological sensing with simple strategies avoiding genetic amplification in a PCR-free manner.

Cerebrospinal fluid circulating tumor DNA profiling for risk stratification and matched treatment of central nervous system metastases

Genomic profiling of central nervous system (CNS) metastases has the potential to guide treatments. In the present study, we included 584 patients with non-small-cell lung cancer and CNS metastases and performed a comprehensive analysis of cerebrospinal fluid (CSF) circulating tumor DNA (ctDNA) with clinicopathological annotation. CSF ctDNA-positive detection was independently associated with shorter survival than negative detection (hazard ratio (HR) = 1.9, 95% confidence interval (CI) = 1.56-2.39; P < 0.0001). Matched tumor-CSF analysis characterized the CSF private molecular features causing poor survival (HR = 1.64, 95% CI = 1.15-2.32, P = 0.006). A multimetric CSF ctDNA prognostic model integrating CSF ctDNA features and clinical factors was developed for risk-stratifying CNS metastases and validated in an independent cohort. Among patients with treatment histories available, those positive for a driver alteration by CSF ctDNA showed a survival benefit from CSF-matched therapy (HR = 0.78, 95% CI = 0.65-0.92, P = 0.003). Longitudinal monitoring by CSF identified CNS-specific resistant mechanisms and a second matched targeted therapy indicating improved survival (HR = 0.56, 95% CI = 0.35-0.91, P = 0.018). These findings support the clinical value of CSF ctDNA for risk-stratifying CNS metastases and guiding therapy.

Circulating Tumour DNA for Ovarian Cancer Diagnosis and Treatment Monitoring: What Perspectives for Clinical Use?

Globally, ovarian cancer (OC) is the eighth most common malignant tumour in women. Unfortunately, its symptoms-especially at the early stages-are vague and non-specific, and, thus, most patients are diagnosed at the advanced stages of the disease (stage III and IV) when treatment is not curative. The currently available approved biomarkers are not sufficient for effective screening, prognosis, or monitoring of OC. Liquid biopsy tests such as circulating tumour DNA (ctDNA) analysis has the advantage of monitoring response to treatment in real time and providing a comprehensive genotypic profile of primary, metastatic, and recurrent tumours. Thus, ctDNA analysis can be used as a complementary test for effective diagnosis and monitoring of OC. We comprehensively review current studies (2019-2024) on OC, critically highlighting recent developments and applications of ctDNA for the diagnosis and management of the disease.

A scoping review of factors influencing the implementation of liquid biopsy for cancer care

BACKGROUND

Liquid biopsy (LB) offers a promising, minimally invasive alternative to traditional tissue biopsies in cancer care, enabling real-time monitoring and personalized treatment. Despite its potential, the routine implementation of LB in clinical practice faces significant challenges. This scoping review examines the barriers and facilitators influencing the implementation of liquid biopsies into standard cancer care.

METHODS

Four academic databases (PubMed, Scopus, Embase, and Web of Science) were systematically searched without language restrictions. We included peer-reviewed articles that were published between January 2019 and March 2024 that focused on the implementation of LB in cancer care or described barriers and facilitators to its implementation. Data relevant to the review objective, including key article characteristics; barriers and facilitators of implementation; and recommendations for advancement or optimisation; were extracted and analysed using thematic and visual network analyses.

RESULTS

The majority of the included articles were narrative review articles (84%), with most from China (24.2%) and the United States (20%). Thematic analysis identified four main categories and their associated barriers and facilitators to the implementation of LB in cancer care: (1) Laboratory and personnel requirements; (2) Disease specificity; (3) Biomarker-based liquid biopsy; and (4) Policy and regulation. The majority of barriers identified were concentrated in the pre-analytical phase, highlighting the lack of standardization in LB technologies and outcomes.

CONCLUSIONS

Through a thematic analysis of the barriers and facilitators to LB implementation, we present an integrated tool designed to encourage the standardization of testing methods for clinical practice guidelines in the field.

Plasma ctDNA kinetics as a predictor of systemic therapy response for advanced non-small cell lung cancer: a systematic review and meta-analysis

BACKGROUND

Predicting early treatment response in advanced non-small cell lung cancer (NSCLC) is challenging. Longitudinal monitoring of circulating tumor DNA (ctDNA) can track tumor response to treatments like immune checkpoint blockade (ICB) and correlate with outcomes. This meta-analysis evaluated whether ctDNA clearance or decrease is associated with improved survival across various settings in NSCLC.

METHODS

A systematic review of MEDLINE, EMBASE, and Cochrane databases (up to April 2024) identified studies evaluating the impact of ctDNA kinetics on survival outcomes in non-curative NSCLC settings. Pooled hazard ratios (HR) for progression-free survival (PFS) and overall survival (OS) were calculated using a random effects model.

RESULTS

We included 32 studies with 3047 NSCLC patients receiving systemic therapies such as targeted therapy (TT), ICB, and chemotherapy. Meta-analysis of 31 studies showed that ctDNA decrease/clearance was linked to improved PFS (HR: 0.32 [0.26, 0.40], I² = 63%, P < .01). Subgroup analysis indicated strong PFS benefits from ctDNA clearance (HR: 0.27 [0.20, 0.36]). Similar improvements were seen across patients undergoing targeted therapy (HR: 0.34) and ICB (HR: 0.33). Analysis of 25 studies revealed a significant association between ctDNA reduction and better OS (HR: 0.31 [0.23, 0.42], I² = 47%, P < .01). Subgroup findings were consistent for both TT (HR: 0.41) and ICB (HR: 0.32). Sensitivity analysis demonstrated that ctDNA clearance/decrease was consistently associated with improved PFS across study designs and ctDNA analysis methods. There was no significant variation in hazard ratios for PFS based on NSCLC subtypes, smoking status, or sex.

CONCLUSION

Plasma ctDNA kinetics was associated with improved survival outcomes in patients diagnosed with advanced NSCLC undergoing treatment with TT and ICB.

Frontiers in pancreatic cancer on biomarkers, microenvironment, and immunotherapy

Pancreatic cancer remains one of the most challenging malignancies to treat due to its late-stage diagnosis, aggressive progression, and high resistance to existing therapies. This review examines the latest advancements in early detection, and therapeutic strategies, with a focus on emerging biomarkers, tumor microenvironment (TME) modulation, and the integration of artificial intelligence (AI) in data analysis. We highlight promising biomarkers, including microRNAs (miRNAs) and circulating tumor DNA (ctDNA), that offer enhanced sensitivity and specificity for early-stage diagnosis when combined with multi-omics panels. A detailed analysis of the TME reveals how components such as cancer-associated fibroblasts (CAFs), immune cells, and the extracellular matrix (ECM) contribute to therapy resistance by creating immunosuppressive barriers. We also discuss therapeutic interventions that target these TME components, aiming to improve drug delivery and overcome immune evasion. Furthermore, AI-driven analyses are explored for their potential to interpret complex multi-omics data, enabling personalized treatment strategies and real-time monitoring of treatment response. We conclude by identifying key areas for future research, including the clinical validation of biomarkers, regulatory frameworks for AI applications, and equitable access to innovative therapies. This comprehensive approach underscores the need for integrated, personalized strategies to improve outcomes in pancreatic cancer.

Enhancing Cancer Screening and Early Diagnosis in India: Overcoming Challenges and Leveraging Emerging Technologies

This review addresses the significant challenges and technological developments in cancer screening and early diagnosis in the context of India's diverse and resource-constrained healthcare landscape. Selected cancers like breast, cervical, oral, lung, and colorectal cancers are focused on, and established screening methods such as clinical breast examination (CBE), mammography, visual inspection with acetic acid (VIA), HPV DNA testing, and oral visual inspection (OVI) are reviewed. These are cost-effective strategies that are proven to reduce mortality. However, they face systemic barriers, including low awareness, socio-cultural stigma, and discontinuous healthcare access. Emerging technologies in cancer screening like liquid biopsy (detecting circulating tumor DNA), artificial intelligence (AI)-driven imaging (enhancing radiological accuracy), next-generation sequencing (identifying genetic mutations), and methylation-based ctDNA analysis (epigenetic profiling) are considered to be transformative in cancer management. Digital pathology and telemedicine are also found to improve diagnostic precision and rural/remote outreach. However, high costs, technical complexity, and limited validation in Indian settings are the major challenges that hinder their widespread adoption. The review emphasizes the need for culturally tailored awareness campaigns, integration of screening with the already existing public health programs, and increased investments in indigenous research to address genetic and environmental risk factors. It specifically advocates for strengthening the primary healthcare infrastructure, training community health workers, and leveraging mobile screening units to bridge urban-rural disparities. A combination of scalable low-resource methods and strategic adoption of emerging technologies can help in mitigating India's growing cancer burden. This aligns with global targets to reduce premature non-communicable disease (NCD) mortality by 2030. This synthesis of evidence-based practices and innovative strategies offers a roadmap for policymakers and stakeholders to enhance equitable cancer care delivery nationwide.

Minimally invasive biomarkers for triaging lung nodules-challenges and future perspectives

CT chest scans are commonly performed worldwide, either in routine clinical practice for a wide range of indications or as part of lung cancer screening programs. Many of these scans detect lung nodules, which are small, rounded opacities measuring 8-30 mm. While the concern about nodules is that they may represent early lung cancer, in screening programs, only 1% of such nodules turn out to be cancer. This leads to a series of complex decisions and, at times, unnecessary biopsies for nodules that are ultimately determined to be benign. Additionally, patients may be anxious about the status of detected lung nodules. The high rate of false positive lung nodule detections has driven advancements in biomarker-based research aimed at triaging lung nodules (benign versus malignant) to identify truly malignant nodules better. Biomarkers found in biofluids and breath hold promise owing to their minimally invasive sampling methods, ease of use, and cost-effectiveness. Although several biomarkers have demonstrated clinical utility, their sensitivity and specificity are still relatively low. Combining multiple biomarkers could enhance the characterisation of small pulmonary nodules by addressing the limitations of individual biomarkers. This approach may help reduce unnecessary invasive procedures and accelerate diagnosis in the future. This review offers a thorough overview of emerging minimally invasive biomarkers for triaging lung nodules, emphasising key challenges and proposing potential solutions for biomarker-based nodule differentiation. It focuses on diagnosis rather than screening, analysing research published primarily in the past five years with some exceptions. The incorporation of biomarkers into clinical practice will facilitate the early detection of malignant nodules, leading to timely interventions and improved outcomes. Further efforts are needed to increase the cost-effectiveness and practicality of many of these applications in clinical settings. However, the range of technologies is advancing rapidly, and they may soon be implemented in clinics in the near future.

The urinary eccDNA landscape in prostate cancer reveals associations with genome instability and vital roles in cancer progression

INTRODUCTION

Extrachromosomal circular DNA (eccDNA) plays significant roles in cancer progression and prognosis. However, it remains unclear whether cell-free eccDNA, considered more stable than linear DNA, possesses cancer-specific genomic features. Furthermore, the biogenesis and function of eccDNAs are not yet fully understood.

OBJECTIVES

This study aims to characterize the genomic landscape of urinary cell-free eccDNAs in prostate cancer (PCa) and non-cancer (NC) individuals, elucidate their biogenesis and PCa-specific genomic features, and investigate their roles in PCa progression.

METHODS

We conducted urine Circle-seq for 21 PCa patients and 16 NC individuals, performed integrated analysis with other omics datasets, and finally validated the function of eccDNA by in vitro transfection and RNA-seq.

RESULTS

We pioneered the profiling of urinary cell-free eccDNAs landscape in PCa and uncovered a high association between eccDNA generation and active chromatin status as well as gene transcription. Double strand breaks and R-loops, which preferentially occur in active genomic sites and cause genome instability, can promote eccDNA generation. Genome instability frequently results in genomic mutations, and our study further established a link between eccDNA generation and oncogenic mutations. Additionally, genes specifically exhibiting high eccDNA generation frequency (HFGs) in PCa contributed to PCa progression and were associated with poorer survival outcomes in PCa patients. Finally, we demonstrated that eccDNAs derived from PCa-specific HFGs, in contrast to intergenic eccDNAs, could suppress PCa cell proliferation and migration, which was independent of their host gene expression.

CONCLUSION

Our study illustrated the biogenesis of eccDNAs from DSBs in active genes, revealed PCa-specific eccDNA features and suggested new mechanisms underlying eccDNA function.

Multiple time points for detecting circulating tumor DNA to monitor the response to neoadjuvant therapy in breast cancer: a meta-analysis

BACKGROUND

Not all breast cancer (BC) patients can benefit from neoadjuvant therapy (NAT). A poor response may result in patients missing the best opportunity for treatment, ultimately leading to a poor prognosis. Thus, to identify an effective predictor that can assess and predict patient response at early time points, we focused on circulating tumor DNA (ctDNA), which is a vital noninvasive liquid biopsy biomarker. We performed a meta-analysis to explore the predictive value of response by monitoring ctDNA at four time points of NAT using pathologic complete response (pCR) and residual cancer burden (RCB).

METHODS

By searching Embase, PubMed, the Cochrane Library, and the Web of Science until December 24, 2023, we selected studies concerning the relationship between ctDNA and response or prognosis. We analysed the results at the following various time points: baseline (T0), first cycle of NAT (T1), mid-treatment (MT), and end of NAT (EOT). pCR and RCB were used to evaluate the response as the primary endpoint. The secondary endpoint was to investigate the relationship between ctDNA and prognosis. Odds ratios (ORs) and hazard ratios (HRs) were used as effect indicators.

RESULTS

Thirteen reports from twelve studies were eligible for inclusion in this meta-analysis. The results demonstrated that ctDNA negativity was associated with pCR at T1 (OR = 0.34; 95% CI: 0.21-0.57), MT (OR = 0.35; 95% CI: 0.20-0.60), and EOT (OR = 0.38; 95% CI: 0.22-0.66). When RCB was used to evaluate responses, ctDNA negativity was associated with RCB-0/I at the MT (OR = 0.34; 95% CI: 0.21-0.55) and EOT (OR = 0.26; 95% CI: 0.15-0.46). Furthermore, ctDNA positivity at T1 predicted a worse prognosis for patients (HR = 2.73; 95% CI: 1.29-5.75). We also performed a subgroup analysis to more accurately assess the predictive value of ctDNA for triple-negative breast cancer.

CONCLUSIONS

Our meta-analysis suggested that the ctDNA status at the early stage of NAT can predict patient response, which provides evidence for adjusting personalized treatment strategies and improving patient survival.

PROSPERO REGISTRATION NUMBER

CRD42024496465.

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.

Low-Pass Whole Genome Sequencing of Cell-Free DNA from Cerebrospinal Fluid: A Focus on Pediatric Central Nervous System Tumors

BACKGROUND

Cell-free DNA (cfDNA) technology has allowed for cerebrospinal fluid (CSF), a previously underutilized biofluid, to be analyzed in new ways. The interrogation of CSF-derived cfDNA is giving rise to novel molecular insights, particularly in pediatric central nervous system (CNS) tumors, where invasive tumor tissue acquisition may be challenging. Contemporary disease monitoring is currently restricted to radiographic surveillance by magnetic resonance imaging and CSF cytology to directly detect abnormal cells and cell clusters. Alternatively, cfDNA is often present in the CSF from pediatric patients with both malignant and nonmalignant CNS tumors and can be accessed by minimally invasive lumbar puncture and other CSF-liberating procedures, offering a promising alternative for longitudinal molecular disease analysis and surveillance.

CONTENT

This review explores the use of low-pass whole genome sequencing (LP-WGS) to analyze cfDNA from the CSF of pediatric patients with CNS tumors. This platform is uniquely poised for the detection of tumors harboring copy number variants, which are prevalent in this population. The utility and sensitivity of LP-WGS as a clinical tool is explored and discussed in the context of alternative CSF liquid biopsy interrogation modalities, including nanopore sequencing and methylation array.

SUMMARY

Analysis of CSF-derived cfDNA by LP-WGS has broad diagnostic, prognostic, and clinical implications for pediatric patients with CNS tumors. Careful interpretation of LP-WGS results may aid in therapeutic targeting of pediatric CNS tumors and may provide insight into tumor heterogeneity and evolution over time, without the need for invasive and potentially risky tissue sampling.

Minimal residual disease as a target for liquid biopsy in patients with solid tumours

Metastasis is the leading cause of cancer-related death in patients with solid tumours. Current imaging technologies are not sufficiently sensitive to detect minimal residual disease (MRD; also known as measurable or molecular residual disease) after initial surgery or chemotherapy, pointing to the need for more sensitive tests to detect remaining traces of cancer in the body. Liquid biopsy, or the analysis of tumour-derived or tumour-induced cells or cellular products in the blood or other body fluids, has opened a new diagnostic avenue to detect and monitor MRD. Liquid biopsy is already used in clinical decision making for patients with haematological malignancies. Here, we review current knowledge on the use of circulating tumour DNA (ctDNA) to detect and monitor MRD in patients with solid tumours. We also discuss how ctDNA-guided MRD detection and characterization could herald a new era of novel 'post-adjuvant therapies' with the potential to eliminate MRD and cure patients before terminal metastatic disease is evident on imaging.

Efficiency of electrochemical immuno- vs. apta(geno)sensors for multiple cancer biomarkers detection

The interest in biosensors technology has been constantly growing over the last few years. It is still the biggest challenge to design biosensors able to detect two or more analytes in a single measurement. Electrochemical methods are frequently used for this purpose, mainly due to the possibility of applying two or more different redox labels characterized by independent and distinguished electrochemical signals. In addition to antibodies, nucleic acids (aptamers) have been increasingly used as bioreceptors in the construction of such sensors. Within this review paper, we have collected the examples of electrochemical immuno- and geno(apta)sensors for simultaneous detection of multiple analytes. Based on many published literature examples, we have emphasized the recent application of multiplexed platforms for detection of cancer biomarkers. It has allowed us to compare the progress in design strategies, including novel nanomaterials and amplification of signals, to get as low as possible limits of detection. We have focused on multi-electrode and multi-label strategies based on redox-active labels, such as ferrocene, anthraquinone, methylene blue, thionine, hemin and quantum dots, or metal ions such as Ag+, Pb2+, Cd2+, Zn2+, Cu2+ and others. We have finally discussed the possible way of development, challenges and prospects in the area of multianalyte electrochemical immuno- and geno(apta)sensors.

Current and Future Role of Circulating DNA in the Diagnosis and Management of Urothelial Carcinoma

The growing sophistication of tumor molecular profiling has helped to slowly transition oncologic care toward a more personalized approach in different tumor types, including in bladder cancer. The National Comprehensive Cancer Network recommends that all patients with stage IVA and stage IVB urothelial carcinoma have molecular analysis that integrates at least FGFR3 testing to help facilitate the selection of future therapeutic options. Sequencing of tumor-derived tissue is the mainstay to obtain this genomic testing, but as in other cancers, there has been extensive research into the integration of liquid biopsies in longitudinal management. Liquid biopsies broadly refer to the isolation of both cellular and noncellular tumor components including proteins and nucleic acids such as mRNA and circulating free DNA within a liquid sample. Although protein-based testing and testing of circulating tumor cells are options, the bulk of promising research in bladder cancer is investigating the role of plasma-based circulating tumor DNA (ctDNA). Currently, a universal consensus on optimal preanalytic and analytic approaches has not been fully defined, and the exact role that liquid biopsies should have in screening, diagnosis, prognostication, treatment selection, and monitoring is not yet known. Still, it can be expected that ctDNA testing will be a part of appropriate management of muscle-invasive bladder cancer and metastatic bladder cancer in the near future. In this review, the goal is to provide a practical overview of the current and future role of ctDNA in bladder cancer including ongoing trials.

Immunogenicity of cell death and cancer immunotherapy with immune checkpoint inhibitors

While immunotherapy with immune checkpoint inhibitors (ICIs) has revolutionized the clinical management of various malignancies, a large fraction of patients are refractory to ICIs employed as standalone therapeutics, necessitating the development of combinatorial treatment strategies. Immunogenic cell death (ICD) inducers have attracted considerable interest as combinatorial partners for ICIs, at least in part owing to their ability to initiate a tumor-targeting adaptive immune response. However, compared with either approach alone, combinatorial regimens involving ICD inducers and ICIs have not always shown superior clinical activity. Here, we discuss accumulating evidence on the therapeutic interactions between ICD inducers and immunotherapy with ICIs in oncological settings, identify key factors that may explain discrepancies between preclinical and clinical findings, and propose strategies that address existing challenges to increase the efficacy of these combinations in patients with cancer.

Integration of circulating tumor DNA in biliary tract cancer: the emerging landscape

Precision medicine has emerged as a cornerstone in cancer treatment revolutionizing our approach across malignancies. Molecular profiling of biliary tract cancers (BTCs) has changed the treatment landscape positively by prolonging survival in an aggressively fatal malignancy in its advanced stages. The acquisition of tissue tumor DNA for genomic analysis in BTC is often anatomically challenging, limited by quantity and quality. In response, ctDNA has emerged as a noninvasive means of molecular profiling. The utility of both plasma and bile ctDNA has been explored in several studies demonstrating the high mutation detection rates and the ability to isolate targetable mutations when present. In addition, the concordance between plasma and tissue DNA provides validity in utilizing ctDNA results to infer treatment decisions. Analysis of ctDNA in BTC has also provided prognostic information and facilitated evaluation of clonal evolution with ease of serial measurements. Insight into novel mechanisms of resistance to targeted therapies are being uncovered in ctDNA. As research endeavors continue to deepen our understanding in the field particularly in the space of ctDNA surveillance after curative intent, the tremendous progress made so far has enabled integration of ctDNA into the clinical practice of BTCs.

Modulating cell-free DNA biology as the next frontier in liquid biopsies

Technical advances over the past two decades have enabled robust detection of cell-free DNA (cfDNA) in biological samples. Yet, higher clinical sensitivity is required to realize the full potential of liquid biopsies. This opinion article argues that to overcome current limitations, the abundance of informative cfDNA molecules - such as circulating tumor DNA (ctDNA) - collected in a sample needs to increase. To accomplish this, new methods to modulate the biological processes that govern cfDNA production, trafficking, and clearance in the body are needed, informed by a deeper understanding of cfDNA biology. Successful development of such methods could enable a major leap in the performance of liquid biopsies and vastly expand their utility across the spectrum of clinical care.

Elements of liquid biopsies: isolation, analysis, and clinical application in cancer diagnosis to prognosis

INTRODUCTION

The liquid biopsy is a breakthrough in the field of medical diagnostics. It serves as a sentinel that can quietly detect even the subtlest aberrations that indicate the presence of disease. They make it possible to uncover relevant genetic factors of tumors with minimal to no risk to cancer patients. Liquid biopsies allow detailed diagnosis, dynamic treatment monitoring, and accurate prognosis. They are also invaluable in diagnosing other diseases such as infectious diseases and aberrant gene mutations.

AREAS COVERED

The present review undertakes an in-depth analysis of the existing status of liquid biopsy diagnostic tools, focusing on their principal components. Furthermore, the review highlights pertinent and recent research in this field to provide a comprehensive understanding of the current state of this technology and its prospects.

EXPERT OPINION

Despite new and upcoming research in liquid biopsies, multiple areas need to be further explored before the viable transition into the clinical arena. With the advancements in tools such as artificial intelligence and machine learning and the integration of these technologies with liquid biopsies, these challenges are being addressed and will eventually lead to the development of a highly evolved liquid biopsy diagnostic tools.

Deciphering the role of exosomal derived regulatory noncoding RNAs as potential biomarkers for diabetic retinopathy: a systematic review

About one-third of individuals with diabetes develop diabetic retinopathy (DR), with one-tenth experiencing vision-threatening conditions such as diabetic macular edema (DME) or proliferative diabetic retinopathy (PDR). Current treatments only show recovery in 50% of cases, and the disease often remains asymptomatic. Therefore, novel early detection methods and new biomarkers are crucial. Our study aims to summarise evidence on the role of altered exosomal regulatory noncoding RNAs in DR, based on human studies. Observational studies delineating the different exosomal noncoding RNAs in DR were searched systematically from inception to June 2024 in PubMed-MEDLINE and SCOPUS databases. Preferred Reporting Items of Systematic Reviews and Meta-analysis (PRISMA) 2020 guidelines was used to conduct this systematic review (Prospero ID: CRD42023406724). We synthesised data from 13 human studies that assessed the expression of exosomal regulatory ncRNAs from individuals with DR. Among the 13 studies, nine focused on miRNA, while three examined lncRNA and one on circRNA. Although no common genes were identified across the studies, the review underscores the critical roles of exosomal noncoding RNAs in the pathogenesis of diabetic retinopathy, highlighting their potential as therapeutic targets. Future studies should aim for a unified approach in terms of sample selection, RNA analysis, and appropriate controls for a comprehension of exosomal expression patterns for early diagnosis of DR.

The Diagnostic Utility of cfDNA and ctDNA in Liquid Biopsies for Gastrointestinal Cancers over the Last Decade

BACKGROUND

Cell-free DNA (cfDNA) is a fragmented DNA that is released into the blood through necrosis, apoptosis, phagocytosis, or active secretion. cfDNA includes a subclass called circulating tumor DNA (ctDNA) released from cancer cells and constitutes a varied proportion of the total cfDNA. Both cfDNA and ctDNA hold significant potential as diagnostic biomarkers in gastrointestinal cancers.

SUMMARY

cfDNA and ctDNA are promising diagnostic biomarkers for gastrointestinal cancers with varied diagnostic values in different types of cancers. cfDNA offers higher sensitivity that makes it more suitable for screening methods and constant monitoring, particularly in integration with conventional biomarkers or in a multimarker model. On the contrary, ctDNA gives a real-time picture of tumor genetics and is more suitable for definitive diagnosis due to its specificity for tumor-associated alterations. Different types of samples and methods of detection can influence sensitivity, and the amount of cfDNA is higher in serum but plasma is used for cfDNA analysis because it contains less cellular contamination. In summary, cfDNA is more sensitive than ctDNA, although they have comparable or slightly lower specificity.

KEY MESSAGE

Further studies are needed to create common guidelines, minimize the cost of analysis, and perform extensive clinical trials to demonstrate the utility of circulating cfDNA and ctDNA in the vast majority of gastrointestinal cancer stages. Therefore, with the advancement in these technologies, cfDNA and ctDNA will be highly beneficial and evolve cancer diagnostics and therapy.

BRCA1 & BRCA2 methylation as a prognostic and predictive biomarker in cancer: Implementation in liquid biopsy in the era of precision medicine

BACKGROUND

BReast CAncer gene 1 (BRCA1) and BReast CAncer gene 2 (BRCA2) encode for tumor suppressor proteins which are critical regulators of the Homologous Recombination (HR) pathway, the most precise and important DNA damage response mechanism. Dysfunctional HR proteins cannot repair double-stranded DNA breaks in mammalian cells, a situation called HR deficiency. Since their identification, pathogenic variants and other alterations of BRCA1 and BRCA2 genes have been associated with an increased risk of developing mainly breast and ovarian cancer. Interestingly, HR deficiency is also detected in tumors not carrying BRCA1/2 mutations, a condition termed "BRCAness".

MAIN TEXT

One of the main mechanisms causing the BRCAness phenotype is the methylation of the BRCA1/2 promoters, and this epigenetic modification is associated with carcinogenesis and poor prognosis mainly among patients with breast and ovarian cancer. BRCA1 promoter methylation has been suggested as an emerging biomarker of great predictive significance, especially concerning Poly (ADP-ribose) Polymerase inhibitors (PARP inhibitor-PARPi) responsiveness, along with or beyond BRCA1/2 mutations. However, as its clinical exploitation is still insufficient, the impact of BRCA1/2 promoter methylation status needs to be further evaluated. The current review aims to gather the latest findings about the mechanisms that underline BRCA1/2 function as well as the molecular characteristics of tumors associated with BRCA1/2 defects, by focusing on DNA methylation. Furthermore, we critically analyze their translational meaning and the validity of BRCA methylation biomarkers in predicting treatment response.

CONCLUSIONS

We believe that BRCA1/2 methylation alone or combined with other biomarkers in a clinical setting is expected to change the scenery in prognosis and predicting treatment response in multiple cancer types and is worthy of further attention. The quantitative BRCA1 promoter methylation assessment might predict treatment response in PARPi and analysis of BRCA1/2 methylation in liquid biopsy might define patient subgroups at different time points that may benefit from PARPi. Finally, we suggest a pipeline that could be implemented in liquid biopsy to aid precision pharmacotherapy in BRCA-associated tumors.

Circulating tumor DNA fraction predicts residual cancer burden post-neoadjuvant chemotherapy in triple negative breast cancer

Purpose

Pathologic response after preoperative/neoadjuvant chemotherapy (NAC) is a continuum that can range from complete pathologic response (pCR) to extensive residual disease (RD). We hypothesized that post-NAC plasma circulating tumor DNA (ctDNA) fraction (TF) reflect pathologic response as continuum measured by the residual cancer burden (RCB) score.

Methods

ctDNA was assessed using the PredicineBEACON assay, that interrogates up to 50 personalized tumor variants and 500 hot-spot mutations, in 3 mL archived plasma isolated from EDTA tubes collected post-NAC but before surgery from 44 patients with stage I/III triple negative breast cancer (TNBC) who received durvalumab and weekly nab-paclitaxel followed by doxorubicin/cyclophosphamide on a clinical trial (NCT02489448). Circulating free tumor DNA methylation profiling was performed using PredicineEPIC assay in paired pre- and post-NAC plasma (N = 30). Youden's J-statistics was used to define optimal thresholds.

Results

We observed a significant positive correlation (r = 0.45, p = 0.004) between RCB scores and post-NAC TF. The median TF was significantly lower in pCR (RCB0) compared to RD patients (0.06 % vs. 0.3 %, p = 0.02). Using a TF positivity threshold of ≥0.05 %, PredicineBEACON had 58 % sensitivity at 83 % specificity for identifying RD. TF was higher in patients who experienced recurrence (n = 9) compared to those without recurrence (n = 35) (0.17 % vs. 0.05 % TF, p = 0.029). There was significant decrease in methylation signal in post-compared to pre-NAC samples, but post-treatment methylation signal was lower in cases with pCR vs RD.

Conclusions

Post-NAC plasma tumor fraction and change in tumor-derived methylation signal predict the extent of RD and recurrence in TNBC patients.

5-Hydroxymethylcytosine Profiles of cfDNA in Urine as Diagnostic, Differential Diagnosis and Prognostic Markers for Multiple Myeloma

BACKGROUND

An effective urine-based method for the diagnosis, differential diagnosis and prognosis of multiple myeloma (MM) has not yet been developed. Urine cell-free DNA (cfDNA) carrying cancer-specific genetic and epigenetic aberrations may enable a noninvasive "liquid biopsy" for diagnosis and monitoring of cancer.

METHODS

We first identified MM-specific hydroxymethylcytosine signatures by comparing 64 MM patients, 23 amyloidosis (AM) patients and 59 healthy cohort. Then, we applied a machine learning algorithm to develop diagnostic and differential diagnosis model. Finally, the prognosis of MM patients was predicted based on their survival time at the last follow-up.

RESULTS

We identified 11 5hmC markers using logistic regression algorithm could effectively diagnosis MM (AUC = 0.902), and achieved 85.00% specificity and 85.71% sensitivity. These 11 markers could also effectively differential diagnosis MM (AUC = 0.805) with 88.89% specificity and 73.08% sensitivity. In addition, the prognostic prediction model also effectively predicted the prognosis of patients with MM (p < 0.01), of which 4 differential markers (RAPGEF2, BRD1, TET2, TRAF3IP2) could independently predict the prognosis of MM.

CONCLUSIONS

Together, our findings showed the value of urine cfDNA hydroxymethylcytosine markers in the diagnosis, differential diagnosis and prognosis of MM. Meantime, our study provides a promising and completely non-invasive method for the diagnosis, differential diagnosis and prognosis prediction of MM.

Mapping the Future: A Comprehensive Bibliometric Analysis of Circulating Tumor DNA in Colorectal Cancer

Purpose

Colorectal cancer (CRC) is among the most prevalent malignancies worldwide, with rising incidence and mortality rates presenting substantial public health challenges. Traditional detection methods have inherent limitations, which has led to growing interest in liquid biopsy technologies for the identification of circulating tumor DNA (ctDNA). The aim of this study is to explore the developmental trends and future prospects of ctDNA in colorectal cancer through bibliometric analysis.

Methods

This bibliometric analysis examines the literature on ctDNA in CRC from 2004 to 2024, utilizing the Web of Science Core Collection database to identify research trends, key areas of interest, and potential future directions. The R package "bibliometrix" and VOSviewer software were employed for bibliometric analysis and visualization. The analysis encompassed an evaluation of publication volume, contributing authors, influential journals, country and institutional contributions, and citation metrics.

Results

The analysis encompassed a total of 1,054 publications, demonstrating a marked escalation in research activity since 2015. The journal "Cancers" has been identified as the most prolific publisher within this domain. Prominent researchers, including Bardelli A and Sartore-Bianchi A, have made substantial contributions to the field. The United States is the leading country in terms of both publication volume and citation frequency, followed by China and Italy. A keyword analysis identified seven conceptual clusters, with "circulating tumor DNA" and "liquid biopsy" emerging as predominant themes.

Conclusion

This study emphasizes the evolving emphasis on the clinical applications of ctDNA, encompassing early detection, treatment monitoring, and prognostic assessment in CRC, thereby underscoring its potential as a non-invasive biomarker in oncology.

Atomic force microscopy as a nanomechanical tool for cancer liquid biopsy

Liquid biopsies have been receiving tremendous attention for their potential to reshape cancer management. Though current studies of cancer liquid biopsy primarily focus on applying biochemical assays to characterize the genetic/molecular profiles of circulating tumor cells (CTCs) and their secondary products shed from tumor sites in bodily fluids, delineating the nanomechanical properties of tumor-associated materials in liquid biopsy specimens yields complementary insights into the biology of tumor dissemination and evolution. Particularly, atomic force microscopy (AFM) has become a standard and versatile toolbox for characterizing the mechanical properties of living biological systems at the micro/nanoscale, and AFM has been increasingly utilized to probe the nanomechanical properties of various tumor-derived analytes in liquid biopsies, including CTCs, tumor-associated cells, circulating tumor DNA (ctDNA) molecules, and extracellular vesicles (EVs), offering additional possibilities for understanding cancer pathogenesis from the perspective of mechanobiology. Herein, the applications of AFM in cancer liquid biopsy are summarized, and the challenges and future directions of AFM as a nanomechanical analysis tool in cancer liquid biopsy towards clinical utility are discussed and envisioned.

Clinical applications of circulating tumor DNA in hematological malignancies: From past to the future

Liquid biopsy, particularly circulating tumor DNA (ctDNA), has drawn a lot of attention as a non- or minimal-invasive detection approach for clinical applications in patients with cancer. Many hematological malignancies are well suited for serial and repeated ctDNA surveillance due to relatively high ctDNA concentrations and high loads of tumor-specific genetic and epigenetic abnormalities. Progress of detecting technology in recent years has improved sensitivity and specificity significantly, thus broadening and strengthening the potential utilities of ctDNA including early diagnosis, prognosis estimation, treatment response evaluation, minimal residual disease monitoring, targeted therapy selection, and immunotherapy surveillance. This manuscript reviews the detection methodologies, clinical application and future challenges of ctDNA in hematological malignancies, especially for lymphomas, myeloma and leukemias.

Unveiling the impact of circulating tumor cells: Two decades of discovery and clinical advancements in solid tumors

Circulating tumor cells (CTCs) enumeration and molecular profiling hold promise in revolutionizing the management of solid tumors. Their understanding has evolved significantly over the past two decades, encompassing pivotal biological discoveries and clinical studies across various malignancies. While for some tumor types, such as breast, prostate, and colorectal cancer, CTCs are ready to enter clinical practice, for others, additional research is required. CTCs serve as versatile biomarkers, offering insights into tumor biology, metastatic progression, and treatment response. This review summarizes the latest advancements in CTC research and highlights future directions of investigation. Special attention is given to concurrent evaluations of CTCs and other circulating biomarkers, particularly circulating tumor DNA. Multi-analyte assessment holds the potential to unlock the full clinical capabilities of liquid biopsy. In conclusion, CTCs represent a transformative biomarker in precision oncology, offering extraordinary opportunities to translate scientific discoveries into tangible improvements in patient care.

Monitoring Response Using Circulating Tumor DNA in Undifferentiated Pleomorphic Sarcoma: A Case Report

Circulating tumor DNA (ctDNA) can be used to assess treatment response in patients with undifferentiated pleomorphic sarcoma (UPS). The importance of this is explored in our case of a 75-year-old man who was diagnosed with UPS of the right kidney. After a right nephrectomy and tumor resection, the patient was recovering well with initially undetectable, and then slightly elevated, circulating tumor DNA. Abdominal pain started shortly before a scheduled magnetic resonance imaging (MRI) which revealed a large mass in the resection bed invading the liver. The patient was treated with gemcitabine and docetaxel chemotherapy, and the ctDNA level rose dramatically before gradually decreasing and eventually becoming undetectable. At surgery, pathologic examination of the re-resection specimen revealed a complete pathological response. ctDNA monitoring may be a useful tool for early detection of response to chemotherapy in patients with UPS.

Diversity of the Circulating Tumor Markers: Perspectives of a Multimodal Liquid Biopsy

Over the past decade, liquid biopsy (LB) has become a routine diagnostic test essential for the treatment of malignant tumors of various localizations. Its capabilities include early diagnosis, molecular genotyping, prognosis, prediction, and monitoring of tumor response. Typically, liquid biopsy involves the extraction of a single type of tumor-derived molecules or cellular elements from blood and subsequent molecular analysis. These elements may include circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), circulating tumor RNA (ctRNA), or contents of extracellular vesicles (exosomes). Despite the technical sophistication of molecular analysis methods for circulating biomarkers, this diagnostic approach has limited relevance. In a significant proportion of cancer patients (ranging from 10 to 50%, depending on the tumor type), none of these analytes can be detected and analyzed, even in the presence of large, progressing neoplastic foci in the body. It seems reasonable to suggest that heterogeneous fractions of the circulating tumor-specific biomarkers complement each other, thus simultaneous analysis of several fractions will not only increase sensitivity of the method but also more accurately characterize and predict the clinical situation. This review examines the possibilities and advantages of applying a combined multiparametric approach to liquid biopsy, which involves testing multiple circulating analytes in a single blood sample.

Sensitive and Specific Droplet Digital PCR Assays for Circulating Tumor HPV DNA: Development, Validation, and Clinical Application in HPV-Associated Cancers

BACKGROUND

Human papillomavirus (HPV) has emerged as a significant contributor to cancer incidence globally, particularly in the context of oropharyngeal squamous cell carcinoma (OPSCC) and cancer of unknown primary (HNCUP). This study aimed to develop and validate droplet digital PCR (ddPCR) assays for the detection of circulating tumor HPV DNA (ctHPV-DNA) in plasma, focusing on high-risk HPV genotypes associated with these cancers.

METHODS

ddPCR assays for HPV16, 18, 33, 35, 56, and 59 were developed and tested using gBlocks, HPV cell-free DNA, fragmented tumor HPV+ DNA, and plasma samples from patients with HPV+ OPSCC (n = 110) and HNCUP (n = 9).

RESULTS

Assays demonstrated robust technical sensitivity across all tested HPV genotypes. Clinical application of the assays on a cohort of patients with HPV+ OPSCC and HNCUP revealed high sensitivity (91.6%) and wide variability in ctHPV-DNA levels. Analyses revealed correlations between ctHPV-DNA levels and TNM stage and tumor viral load. The association between ctHPV-DNA and tumor viral load persisted even after adjusting for TNM stage. At posttreatment, 72.5% of samples had reached undetectable ctHPV-DNA levels. Having detectable ctHPV-DNA posttreatment was associated with a higher ctHPV-DNA level at diagnosis and higher viral load at diagnosis.

CONCLUSION

The findings underscore the potential of ctHPV-DNA as a biomarker for monitoring HPV+ cancers and offer insights into tumor dynamics. Implementation of these assays in clinical practice could enhance no-invasive treatment monitoring and recurrence detection in HPV-associated cancers.

CLINICAL TRIALS

NCT05904327.

Liquid biopsy: Comprehensive overview of circulating tumor DNA (Review)

Traditional tumor diagnosis methods rely on tissue biopsy, which can be invasive and unsuitable for long-term monitoring of tumor dynamics. The advent of liquid biopsy has notably improved the overall management of patients with cancer. Liquid biopsy techniques primarily involve detection of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA). The present review focuses on ctDNA because of its significance in tumor diagnosis, monitoring and treatment. The use of ctDNA-based liquid biopsy offers several advantages, including non-invasive or minimally invasive collection methods, the ability to conduct repeated assessment and comprehensive insights into tumor biology. It serves crucial roles in disease management by facilitating screening of high-risk patients, dynamically monitoring therapeutic responses and diagnosis. Furthermore, ctDNA can be used to demonstrate pseudo-progression, monitor postoperative tumor status and guide adaptive treatment plans. The present study provides a comprehensive review of ctDNA, exploring its origins, metabolism, detection methods, clinical role and the current challenges associated with its application.

Circulating tumor DNA: current implementation issues and future challenges for clinical utility

Over the past decades, liquid biopsy, especially circulating tumor DNA (ctDNA), has received tremendous attention as a noninvasive detection approach for clinical applications, including early diagnosis of cancer and relapse, real-time therapeutic efficacy monitoring, potential target selection and investigation of drug resistance mechanisms. In recent years, the application of next-generation sequencing technology combined with AI technology has significantly improved the accuracy and sensitivity of liquid biopsy, enhancing its potential in solid tumors. However, the increasing integration of such promising tests to improve therapy decision making by oncologists still has complexities and challenges. Here, we propose a conceptual framework of ctDNA technologies and clinical utilities based on bibliometrics and highlight current challenges and future directions, especially in clinical applications such as early detection, minimal residual disease detection, targeted therapy, and immunotherapy. We also discuss the necessities of developing a dynamic field of translational cancer research and rigorous clinical studies that may support therapeutic strategy decision making in the near future.

Circulating tumor DNA methylation: a promising clinical tool for cancer diagnosis and management

Cancer continues to pose significant challenges to the medical community. Early detection, accurate molecular profiling, and adequate assessment of treatment response are critical factors in improving the quality of life and survival of cancer patients. Accumulating evidence shows that circulating tumor DNA (ctDNA) shed by tumors into the peripheral blood preserves the genetic and epigenetic information of primary tumors. Notably, DNA methylation, an essential and stable epigenetic modification, exhibits both cancer- and tissue-specific patterns. As a result, ctDNA methylation has emerged as a promising molecular marker for noninvasive testing in cancer clinics. In this review, we summarize the existing techniques for ctDNA methylation detection, describe the current research status of ctDNA methylation, and present the potential applications of ctDNA-based assays in the clinic. The insights presented in this article could serve as a roadmap for future research and clinical applications of ctDNA methylation.

Aggregation-Induced Emission Luminogen: Role in Biopsy for Precision Medicine

Biopsy, including tissue and liquid biopsy, offers comprehensive and real-time physiological and pathological information for disease detection, diagnosis, and monitoring. Fluorescent probes are frequently selected to obtain adequate information on pathological processes in a rapid and minimally invasive manner based on their advantages for biopsy. However, conventional fluorescent probes have been found to show aggregation-caused quenching (ACQ) properties, impeding greater progresses in this area. Since the discovery of aggregation-induced emission luminogen (AIEgen) have promoted rapid advancements in molecular bionanomaterials owing to their unique properties, including high quantum yield (QY) and signal-to-noise ratio (SNR), etc. This review seeks to present the latest advances in AIEgen-based biofluorescent probes for biopsy in real or artificial samples, and also the key properties of these AIE probes. This review is divided into: (i) tissue biopsy based on smart AIEgens, (ii) blood sample biopsy based on smart AIEgens, (iii) urine sample biopsy based on smart AIEgens, (iv) saliva sample biopsy based on smart AIEgens, (v) biopsy of other liquid samples based on smart AIEgens, and (vi) perspectives and conclusion. This review could provide additional guidance to motivate interest and bolster more innovative ideas for further exploring the applications of various smart AIEgens in precision medicine.

Salivary diagnostics: opportunities and challenges

Saliva contains a diverse array of biomarkers indicative of various diseases. Saliva testing has been a major advancement towards non-invasive point-of-care diagnosis with clinical significance. However, there are challenges associated with salivary diagnosis from sample treatment and standardization. This review highlights the biomarkers in saliva and their role in identifying relevant diseases. It provides an overview and discussion about the current practice of saliva collection and processing, and advancements in saliva detection systems from in vitro methods to wearable oral devices. The review also addresses challenges in saliva diagnostics and proposes solutions, aiming to offer a comprehensive understanding and practical guidance for improving saliva-based detection in clinical diagnosis. Saliva diagnosis provides a rapid, effective, and safe alternative to traditional blood and urine tests for screening large populations and enhancing infectious disease diagnosis and surveillance. It meets the needs of various fields such as disease management, drug screening, and personalized healthcare with advances in saliva detection systems offering high sensitivity, fast response times, portability, and automation. Standardization of saliva collection, treatment, biomarker discovery, and detection between different laboratories needs to be implemented to obtain reliable salivary diagnosis in clinical practice.

International Society for Heart and Lung Transplantation Guidelines for the Evaluation and Care of Cardiac Transplant Candidates-2024

The "International Society for Heart and Lung Transplantation Guidelines for the Evaluation and Care of Cardiac Transplant Candidates-2024" updates and replaces the "Listing Criteria for Heart Transplantation: International Society for Heart and Lung Transplantation Guidelines for the Care of Cardiac Transplant Candidates-2006" and the "2016 International Society for Heart Lung Transplantation Listing Criteria for Heart Transplantation: A 10-year Update." The document aims to provide tools to help integrate the numerous variables involved in evaluating patients for transplantation, emphasizing updating the collaborative treatment while waiting for a transplant. There have been significant practice-changing developments in the care of heart transplant recipients since the publication of the International Society for Heart and Lung Transplantation (ISHLT) guidelines in 2006 and the 10-year update in 2016. The changes pertain to 3 aspects of heart transplantation: (1) patient selection criteria, (2) care of selected patient populations, and (3) durable mechanical support. To address these issues, 3 task forces were assembled. Each task force was cochaired by a pediatric heart transplant physician with the specific mandate to highlight issues unique to the pediatric heart transplant population and ensure their adequate representation. This guideline was harmonized with other ISHLT guidelines published through November 2023. The 2024 ISHLT guidelines for the evaluation and care of cardiac transplant candidates provide recommendations based on contemporary scientific evidence and patient management flow diagrams. The American College of Cardiology and American Heart Association modular knowledge chunk format has been implemented, allowing guideline information to be grouped into discrete packages (or modules) of information on a disease-specific topic or management issue. Aiming to improve the quality of care for heart transplant candidates, the recommendations present an evidence-based approach.

Effectiveness of peritoneal lavage fluid circulating tumour cells and circulating tumour DNA in the prediction of metachronous peritoneal metastasis of gastric cancer (pT4NxM0/pT1-3N+M0) after radical resection: protocol of a prospective single-centre clinical study

BACKGROUND

Gastric cancer (GC) is the fourth leading cause of cancer mortality worldwide. Peritoneal metastasis (PM) is a significant cause of death in patients with GC, and presents a major challenge in clinical diagnosis and treatment. Predicting the occurrence of PM in high-risk patients, and diagnosing and treating PM in advance to improve patient survival, remains an unsolved problem in clinical practice. Given the low positive rate of cytology and difficulty in diagnosing occult PM, new molecular markers and detection technologies for early diagnosis require urgent validation. The primary objective of this study is to observe and evaluate the predictive effect of intraoperative peritoneal lavage fluid (PLF) circulating tumour cells (CTC) and circulating tumour DNA (ctDNA) levels in patients with pT4NxM0/pT1-3N+M0 GC on metachronous PM after R0 resection.

METHODS AND ANALYSIS

This prospective single-centre clinical study is conducted at Renji Hospital, Shanghai Jiao Tong University School of Medicine. In this study, 200 cases of patients with pT4NxM0/pT1-3N+M0 gastric adenocarcinoma older than 18 years will be screened. Participants will undergo intraoperative PLF CTC and ctDNA testing and will be followed up for 2 years, with imaging assessments performed every 3-6 months until PM occurrs. The primary outcome is the incidence of PM 1 year after surgery, which will be estimated using Clopper-Pearson method, with 95% CIs calculated and compared between groups. Secondary outcome include the incidence of PM 2 years after surgery, overall survival and disease progression. Data will be analysed using the Kaplan-Meier method and the log-rank test.

ETHICS AND COMMUNICATION

Informed consent has been obtained from all subjects. This protocol has been approved by the Ethics Committee of Renji Hospital, Shanghai Jiao Tong University School of Medicine (LY2023-142-B). The findings will be disseminated through peer-reviewed manuscripts, reports and presentations.

TRIAL REGISTRATION NUMBER

ChiCTR2300074910.