Circulating tumor nucleic acids: biology, release mechanisms, and clinical relevance

The biological and technical challenges facing utilizing circulating tumor DNA in non-metastatic breast cancer patients

Breast cancer is one of the most prevalent cancers and has emerged as a major global challenge. Circulating tumor DNA (ctDNA), a liquid biopsy method, overcomes the accessibility limitations of tissue-based testing and is widely used for monitoring minimal residual disease and molecular relapse, predicting prognosis, evaluating the response of neoadjuvant therapy, and optimizing treatment decisions in non-metastatic breast cancer. However, the application of ctDNA still faces many challenges. Here, we survey the clinical applications of ctDNA in non-metastatic breast cancer and discuss the significant biological and technical challenges of utilizing ctDNA. Importantly, we investigate potential avenues for addressing the challenges. In addition, emerging technologies, including fragmentomics detection, methylation sequencing, and long-read sequencing, have clinical potential and could be a future direction. Proper utilization of machine learning facilitates the identification of meaningful patterns from complex fragment and methylation profiles of ctDNA. There is still a lack of clinical trials focused on the subsets of ctDNA (e.g., circulating mitochondrial DNA), ctDNA-inferred drug-resistant clonal evolution, tumor heterogeneity, and ctDNA-guided clinical decision-making in non-metastatic breast cancer. Due to regional differences in the number of registered clinical trials, it is essential to enhance communication and foster global collaboration to advance the field.

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.

Exosomes: from basic research to clinical diagnostic and therapeutic applications in cancer

Cancer continues to pose a global threat despite potent anticancer drugs, often accompanied by undesired side effects. To enhance patient outcomes, sophisticated multifunctional approaches are imperative. Small extracellular vesicles (EVs), a diverse family of naturally occurring vesicles derived from cells, offer advantages over synthetic carriers. Among the EVs, the exosomes are facilitating intercellular communication with minimal toxicity, high biocompatibility, and low immunogenicity. Their tissue-specific targeting ability, mediated by surface molecules, enables precise transport of biomolecules to cancer cells. Here, we explore the potential of exosomes as innovative therapeutic agents, including cancer vaccines, and their clinical relevance as biomarkers for clinical diagnosis. We highlight the cargo possibilities, including nucleic acids and drugs, which make them a good delivery system for targeted cancer treatment and contrast agents for disease monitoring. Other general aspects, sources, and the methodology associated with therapeutic cancer applications are also reviewed. Additionally, the challenges associated with translating exosome-based therapies into clinical practice are discussed, together with the future prospects for this innovative approach.

Longitudinal Tracking of ALK-Rearranged NSCLC From Plasma Using Circulating Tumor RNA and Circulating Tumor DNA

Background

Although the administration of tyrosine-kinase inhibitors in ALK-rearranged NSCLC has revolutionized precision medicine, the detection of gene rearrangements from liquid biopsies remains challenging. RNA-based detection has revealed promising sensitivity for rearrangement detection and thus we hypothesize that a liquid biopsy assay analyzing circulating tumor RNA (ctRNA) in addition to circulating tumor DNA (ctDNA) will improve detection. Furthermore, we hypothesize that the detection of gene fusions at baseline will correlate with clinical outcomes.

Methods

We retrospectively analyzed 86 plasma samples from 33 patients enrolled in the BRIGHTSTAR clinical trial assessing local consolidative therapy (LCT) and brigatinib in patients with stage IV or recurrent NSCLC and confirmed ALK rearrangement (NCT03707938) using a targeted next-generation sequencing assay that analyzes ctDNA to detect gene rearrangements and mutations in 80 genes and ctRNA to detect gene arrangements in 36 genes.

Results

ALK rearrangements were detected in 15 of 28 patients (54%) at baseline, of which eight were detected in both ctDNA and ctRNA. ALK rearrangements were detected in two patients pre-LCT, exclusively in ctRNA, but cleared completely post-LCT. The detection of ALK fusion at baseline was associated with significantly worse progression-free survival (p = 0.033). Plasma cell-free DNA concentrations for patients with detectable ALK rearrangements at baseline were significantly higher than for those without detectable gene fusions (12.3 ng/mL versus 20.2 ng/mL, p = 0.0046).

Conclusions

The inclusion of ctRNA in liquid biopsies increased detection of ALK rearrangements and detection at baseline was associated with significantly worse progression-free survival highlighting the added benefit of ctRNA.

Circulating tumor DNA in endometrial cancer: clinical significance and implications

Circulating tumor DNA (ctDNA) is a promising non-invasive tool that has been demonstrated to be a clinically useful biomarker in several tumor types for risk stratification, prognosis, and early detection of recurrence. However, there are limited data on the clinical utility of ctDNA in endometrial cancer (EC) compared with other solid tumors. The evolution of EC management through the integration of molecular characterization into the treatment algorithm has intensified the need to develop more effective predictive biomarkers to optimize treatment and reduce clinical toxicities. Given its non-invasive nature and its ability to represent and complement tumor multiclonal spatial and temporal heterogeneity, ctDNA could act as a valid surrogate for tissue sampling. In addition to plasma ctDNA detection being associated with clinicopathologic features of tumor aggressiveness at pre-operative assessment, an association with reduced disease-free survival and overall survival has been observed in patients with detectable ctDNA. Moreover, the half-life of ctDNA is significantly shorter than CA125, and plasma levels are reported to be completely cleared from the blood within 1 week from surgical debulking. Therefore, ctDNA may serve as a dynamic biomarker for occult microscopic residual disease when assessed within the first 4 to 8 weeks after eradicative surgery. Few studies have reported high sensitivity of ctDNA in detecting disease recurrence at longitudinal follow-up, although there are limited data comparing ctDNA and traditional serum biomarkers (CA125 and HE4) in identifying recurrence. In the perspective of personalized oncology, ctDNA may potentially help improve adjuvant therapeutic management by escalating/de-escalating treatment based on ctDNA detection after surgery, during maintenance, or in the recurrent/metastatic setting, in addition to acting as a sensitive biomarker for early detection of recurrence. Several challenges hinder the use of ctDNA in EC, including the lack of standardized protocols, the low mutational burden, tumor heterogeneity, and background normal DNA, which limit assay sensitivity and specificity. In addition, the high cost of ctDNA analysis, particularly, next-generation sequencing, restricts its accessibility. Future trials should focus on cost-effective approaches to ensure sustainability and efficient resource allocation.

Multifunctional biomimetic liposomal nucleic acid scavengers inhibit the growth and metastasis of breast cancer

Chemotherapy and surgery, though effective in cancer treatment, trigger the release of nucleic acid-containing pro-inflammatory compounds from damaged tumor cells, known as nucleic acid-associated damage-associated molecular patterns (NA-DAMPs). This inflammation promotes tumor metastasis, and currently, no effective treatment exists for this treatment-induced inflammation and subsequent tumor metastasis. To address this challenge, we developed a biomimetic liposome complex (Lipo-Rh2) incorporating a hybrid structure of liposomes and dendritic polymers, mimicking cell membrane morphology. Lipo-Rh2 leverages the multivalent surface properties of dendritic polymers to clear cell-free nucleic acids while serving as both a structural stabilizer and targeting ligand via embedded ginsenoside Rh2. Experimental data show that Lipo-Rh2 effectively reduces free nucleic acids in mouse serum through charge interactions, downregulates Toll-like receptor expression, decreases inflammatory cytokine secretion, and inhibits both primary tumor growth and metastasis. Compared to the current nucleic acid scavenger PAMAM-G3, Lipo-Rh2 demonstrates stronger antitumor effects, lower toxicity, and enhanced targeting capabilities. This biomimetic liposome-based nucleic acid scavenger represents a novel approach to nucleic acid clearance, expanding the framework for designing effective therapeutic agents.

Somatic Copy Number Alterations in Circulating Cell-Free DNA as a Prognostic Biomarker for Hepatocellular Carcinoma: Insights from a Proof-of-Concept Study

BACKGROUND/OBJECTIVES

Despite advances in hepatocellular carcinoma (HCC) management, prognosis remains poor. Advanced-stage diagnosis often excludes curative treatments, and current biomarkers (e.g., alpha-fetoprotein [AFP]) have limited utility in early detection. Liquid biopsy has emerged as a promising cancer detection tool, with circulating cell-free DNA (ccfDNA) showing significant diagnostic potential. This proof-of-concept study aimed to investigate the potential role of tumor fraction (TF) within ccfDNA as a biomarker in HCC patients.

METHODS

A total of sixty patients were recruited, including thirteen with chronic liver disease (CLD), twenty-four with cirrhosis, and twenty-three with HCC. Plasma samples were collected, and ccfDNA was extracted for shallow whole genome sequencing (sWGS) analysis. The TF was calculated by focusing on somatic copy number alterations (SCNAs) within the ccfDNA.

RESULTS

Among patients with CLD and cirrhosis (n = 37), ctDNA was undetectable in all but one cirrhotic patient who exhibited a significant tumor fraction (TF) of 17% and subsequently developed HCC. Conversely, five out of twenty-three HCC patients (21.7%) displayed detectable ctDNA with TF levels ranging from 3.0% to 32.6%. Patients with detectable ctDNA were characterized by more aggressive oncological features, including a higher number of nodules (p = 0.005), advanced-stage disease (60% BCLC C, p = 0.010), and poorer response to therapy (80% PD, p = 0.001). Moreover, the overall survival (OS) was significantly reduced in patients with detectable ctDNA (median OS: 17 months; CI 95% 4.5-26.5) compared to those without (median OS: 24.0 months; CI 95% 7.0-66.0; log-rank p = 0.002).

CONCLUSIONS

Our results suggest that the analysis of TF by sWGS is a promising non-invasive tool for the identification of HCC with aggressive clinical behavior, whereas it is not sensitive enough for early HCC detection. This molecular assay can improve prognostic stratification in HCC patients.

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.

Liquid biopsy for guiding breast cancer immunotherapy

Liquid biopsy is a laboratory test used to detect and analyze circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and other tumor-derived components, in a blood sample. In the context of breast cancer (BC), liquid biopsies hold significant promise for guiding the use of immune checkpoint inhibitors and immune-based combinations, offering real-time insights into tumor dynamics, treatment response, and resistance mechanisms. This review explores the role of liquid biopsy in BC immunotherapy, focusing on its applications, benefits, issues, and current and future research directions.

Catching cancer signals in the blood: Innovative pathways for early esophageal cancer diagnosis

In recent years, significant progress has been made in the application of DNA methylation for the early detection of esophageal cancer (EC). As an epigenetic modification, DNA methylation allows for noninvasive screening by detecting the methylation status of circulating tumor DNA. Studies have shown that the methylation of genes such as SHOX2, SEPTIN9, EPO, and RNF180 significantly improves diagnostic sensitivity and specificity. Currently, SEPTIN9 has been approved by the Food and Drug Administration for colorectal cancer screening, while SHOX2 and EPO show promising results in EC, and RNF180 has potential in gastrointestinal tumors. This editorial reviews the study by Liu et al, which demonstrated the potential of combining the methylation of these four genes for early EC screening. In addition to their roles in early diagnosis, DNA methylation markers are gaining attention because of their roles in predicting recurrence and in postoperative follow-up. By monitoring changes in methylation levels, these markers can provide valuable insights into treatment efficacy and long-term management. As research progresses, liquid biopsy technology is expected to become an essential tool in the precision diagnosis and treatment of EC, benefiting patients significantly.

CRISPR-Cas12a/Cas13a Multiplex Bioassay for ctDNA and miRNA by Mass Spectrometry

The CRISPR-Cas system, particularly CRISPR-Cas12a and CRISPR-Cas13a, has been widely utilized in constructing various biosensors due to their "trans-cleavage" ability as a means of signal amplification. However, this universal "trans-cleavage" characteristic also presents a challenge for realizing CRISPR-Cas multiplexed bioanalysis. Besides, potential signal cascading interference and complicated design are notable obstacles in CRISPR-Cas multiplexed bioanalysis. Herein, we propose a mass spectrometry method that leverages the CRISPR-Cas12a/13a system to achieve simultaneous detection of ctDNA and miRNA. Based on the properties of the CRISPR-Cas12a/13a system, two types of nanoparticle reporter probes have been engineered, using cancer-related biomarkers ctDNA and miR-21 as our model analytes. The nanoparticle tags, which intrinsically incorporated millions of detectable atoms, combined with the CRISPR-Cas12a/Cas13a system's "trans-cleavage" ability, allow the proposed mass spectrometry strategy to achieve fmol-level detection limits without any nucleic acid amplification procedures. The assay was successfully applied to human serum samples, demonstrating its potential for early disease diagnosis and progression tracking.

Circulating tumour DNA in early stage and locally advanced NSCLC: ready for clinical implementation?

Circulating tumour DNA (ctDNA) can be released by cancer cells into biological fluids through apoptosis, necrosis or active release. In patients with non-small-cell lung cancer (NSCLC), ctDNA levels correlate with clinical and pathological factors, including histology, tumour size and proliferative status. Currently, ctDNA analysis is recommended for molecular profiling in patients with advanced-stage NSCLC. In this Review, we summarize the increasing evidence suggesting that ctDNA has potential clinical applications in the management of patients with early stage and locally advanced NSCLC. In those with early stage NSCLC, detection of ctDNA before and/or after surgery is associated with a greater risk of disease recurrence. Longitudinal monitoring after surgery can further increase the prognostic value of ctDNA testing and enables detection of disease recurrence earlier than the assessment of clinical or radiological progression. In patients with locally advanced NSCLC, the detection of ctDNA after chemoradiotherapy is also associated with a greater risk of disease progression. Owing to the limited number of patients enrolled and the different technologies used for ctDNA testing in most of the clinical studies performed thus far, their results are not sufficient to currently support the routine clinical use of ctDNA monitoring in patients with early stage or locally advanced NSCLC. Therefore, we discuss the need for interventional studies to provide evidence for implementing ctDNA testing in this setting.

Dynamic Monitoring of Circulating Tumor DNA to Predict the Risk of Non In Situ Recurrence of Postoperative Glioma: A Prospective Cohort Study

BACKGROUND

Glioma recurrence can be divided into in situ recurrence and non-in situ recurrence, and the mutation evolution of gliomas with different recurrence patterns is still unknown. We used sequential sequencing of circulating tumor DNA (ctDNA) to compare the somatic mutation profile and clonal evolution of gliomas with different recurrence patterns. To investigate the value of ctDNA in predicting early postoperative tumor recurrence and guiding prognosis stratification in patients with glioma.

METHODS

We prospectively recruited 92 patients with near-total resection of gliomas from our center. Two hundred and thirty-four postoperative tissue and Tumor In Situ Fluid (TISF) samples from 69 eligible patients were included in ctDNA analysis.

RESULTS

Among the 69 patients, 37 glioblastoma (GBM) patients experienced recurrence, and the median progression-free survival (mPFS) was not significantly different between the situ recurrence group and the non-in situ recurrence group (8.6 vs. 6.1 months). The ctDNA of recurrent tissue and TISF were significantly consistent. Before and after initial treatment, TISF-ctDNA mutant allele fraction (MAF), subclonal mutation, and alterations in related pathways (lysine degradation and PI3K pathway) were negatively correlated with treatment response and PFS. Among recurrent GBM patients, EGFR mutations were the most common. Mutations related to the RTK-RAS pathway (NF1) were most common in patients with situ recurrent GBM, while mutations in the MUC family and TP53 pathway (MUC16, CHEK2) were prevalent and continuously increased in patients with non-in situ recurrent GBM.

CONCLUSIONS

In glioma patients undergoing primary surgery, dynamic monitoring of ctDNA and genotyping can be used for early risk stratification, efficacy monitoring, and early recurrence detection, and provide a basis for clinical research to evaluate early therapeutic intervention.

Circulating Biomarkers of Thyroid Cancer: An Appraisal

Thyroid cancer is the most prevalent endocrine cancer. The prognosis depends on the type and stage at diagnosis. Thyroid cancer treatments involve surgery, possibly followed by additional therapeutic options such as hormone therapy, radiation therapy, targeted therapy and chemotherapy. Besides the well-known thyroid tumor biomarkers, new circulating biomarkers are now emerging. Advances in genomic, transcriptomic and proteomic technologies have allowed the development of novel tumor biomarkers. This review explores the current literature data to critically analyze the benefits and limitations of routinely measured circulating biomarkers for the diagnosis and monitoring of thyroid cancer. The review also sheds light on new circulating biomarkers, focusing on the challenges of their use in the clinical management of thyroid cancer, underlining the need for the identification of a new generation of circulating biomarkers.

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.

Circulating Tumor DNA Dynamics and Clinical Outcome in Metastatic Colorectal Cancer Patients Undergoing Front-Line Chemotherapy

PURPOSE

We tested whether circulating tumor DNA (ctDNA) changes may be used to assess early response and clinical outcomes in patients with metastatic colorectal cancer (mCRC) undergoing first-line systemic anticancer therapy (SACT).

EXPERIMENTAL DESIGN

Eight hundred sixty-two plasma samples were collected 4-weekly from baseline (BL) until disease progression in patients with mCRC receiving first-line SACT. ctDNA was tested using tissue-agnostic next-generation sequencing panels. ctDNA normalization was defined as ≥99% clearance after 1 month of therapy (Mo1) in the three variants with the highest allele frequency in BL ctDNA.

RESULTS

Eighty-three paired samples from 75 patients were available for analysis. Twelve pairs (14.4%) showed no variants in either BL or Mo1. In the remaining 71 comparisons (65 patients), 37 (52.1%) showed ctDNA normalization at Mo1. Patients who cleared ctDNA had significantly longer overall (45.6 months) and progression-free survival (13.9 months) compared with nonnormalized patients [overall survival = 22.6 months (log-rank P = 0.01) and progression-free survival = 10.7 months (log-rank P = 0.036), respectively]. In addition, a higher response rate was observed in patients with ctDNA clearance (72.9%) compared with nonnormalized cases (38.2%). Longitudinal sequencing of at least four time points in patients with a progression-free survival of >10 months showed emerging variants in 47.8% of cases; in all these patients, the trajectory of these new "outlier" variants seemed in stark contrast with the clinical-radiological course of disease and the trend in other mutations.

CONCLUSIONS

ctDNA clearance represents an early indicator of benefit from SACT in patients with mCRC; serial tracking of multiple variants is warranted to improve specificity and avoid misleading information due to the emergence of mutations of unknown clinical significance.

Enhancing Electrochemical Biosensing of Circulating Nucleic Acids at the Electrode-Biomolecule-Electrolyte Interfaces

The detection and analysis of circulating cell-free nucleic acid (ccfNA) biomolecules are redefining a new era of molecular targeted cancer therapies. However, the clinical translation of electrochemical ccfNA biosensing remains hindered by unresolved challenges in analytical specificity and sensitivity. In this Perspective, we present a novel electrochemical framework for improving ccfNA biosensor performance by optimizing the critical electrode-biomolecules-electrolyte interfaces. We highlight and elucidate related research works on modification-free electrode sensor surfaces, nucleic acids as biological scaffolds, and redesigning redox reporter systems. We conclude by providing an outlook into the future research developments of ccfNA electrochemical biosensing, emphasizing the potential to overcome current analytical limitations by controlling the complex interplay of target biomolecules and redox species at the electrode surface. These advances are poised to significantly impact the development of electrochemical ccfNA technologies, improving both cancer diagnostics and therapeutic monitoring.

Circulating DNA in Rectal Cancer to Unravel the Prognostic Potential for Radiation Oncologist: A Meta-analysis

OBJECTIVES

Liquid biopsy, with its noninvasive nature and ability to detect tumor-specific genetic alterations, emerges as an ideal biomarker for monitoring recurrences for locally advanced rectal cancer (LARC). Completed studies have small sample sizes and different experimental methods. To consolidate and assess the collective evidence regarding the prognostic role of circulating DNA (ctDNA) detection in LARC patients undergoing neoadjuvant chemoradiotherapy (nCRT).

METHODS

Computerized bibliographic searches of MEDLINE and CANCERLIT (2000 to 2023) were supplemented with hand searches of reference lists. Study selection: studies evaluating oncological outcomes of patients with LARC treated with a nCRT comparing patients with positive and negative liquid biopsy at baseline and after nCRT. Data extraction: data on population, intervention, and outcomes were extracted from each study, in accordance with the intention to treat method, by 2 independent observers, and combined using the DerSimonian method and Laird method.

RESULTS

Nine studies follow inclusion criteria including 678 patients treated with nCRT. The pooled RD rate of ctDNA negative between measure at baseline and after nCRT is statistically significant 61% (95% CI: 53-70, P =0.0002). The hazard ratio (HR) of progression-free survival between ct-DNA negative and positive is significant 7.41 (95% CI: 4.87-11.289, P <0.00001).

CONCLUSIONS

ctDNA can identify patients with different recurrence risks following nCRT and assess prognosis in patients with LARC. Further prospective study is necessary to determine the utility of ctDNA in personalised therapy for patients with LARC.

Molecular diagnosis of nasopharyngeal carcinoma: Past and future

Nasopharyngeal carcinoma (NPC) is a malignant tumor originated from the nasopharynx epithelial cells and has been linked with Epstein-Barr virus (EBV) infection, dietary habits, environmental and genetic factors. It is a common malignancy in Southeast Asia, especially with gender preference among men. Due to its non-specific symptoms, NPC is often diagnosed at a late stage. Thus, the molecular diagnosis of NPC plays a crucial role in early detection, treatment selection, disease monitoring, and prognosis prediction. This review aims to provide a summary of the current state and the latest emerging molecular diagnostic techniques for NPC, including EBV-related biomarkers, gene mutations, liquid biopsy, and DNA methylation. Challenges and potential future directions of NPC molecular diagnosis will be discussed.

CircRNA-miRNA-mRNA interactome analysis in endometrial cancer

In recent years, exploring the potential of miRNAs as novel diagnostic, prognostic and diagnostic markers have gained much attention. In current study, we conducted an in-depth circRNA-miRNA-mRNA interactome to reveal significant molecular processes and biological pathways putatively associated with endometrial cancer (EC). Firstly, we retrieved two circRNAs from circad, hsa_circ_0002577 & hsa_circ_0109046, based on their association with the EC. Subsequently, we predicted miRNAs sponging sites in the two circRNAs and the potential target mRNAs of the predicted miRNAs. Sequestered miRNAs target a number of oncogenes (CBL, MET, KRAS), tumor suppressor (CFT R), receptor protein kinases & GT Pase (MET, KRAS, RAB1B), methyltransferases (SET D8), receptors associated factors (T RAF2, GRB2), growth factors (FGF20), autophagy (BECN1, AT G14), apoptotic regulators (BCL2), transcription factors (T Fs) (CREB1, RUNX1, RUNX2) and gene regulators (CCND1, HIF1A); and others, including some novel gene candidates (CREB1, FGF20, IFI27), that have never been implicated in EC earlier. The expression of hsa-miR-433-3p showed significant predictive relevance (Fold Change = 1.8, AUC = 0.736, Mann-Whitney test p-value = 6.1 e- 14) suggesting its predictive relevance in assessing patients' response to chemotherapy. The hsamiR- 188-3p targets autophagic and apoptotic regulators and its upregulation in endometriosis may be used as for the early stage diagnostic purpose. The hsa-miR-502-5p targets SET D8, T RAF2 and others and suggests additional genomic/epigenomic molecular targets for promising therapeutic interventions in EC. Predicted miRNAs target a number of mRNAs having varied functional impacts and offer an in-depth mechanistic insights for expatiating the biological and regulatory role in EC.Communicated by Ramaswamy H. Sarma.

The role of ctDNA from liquid biopsy in predicting survival outcomes in HPV-negative head and neck cancer: A meta-analysis

The incidence of head and neck cancer (HNC) is on the rise, making it a significant clinical challenge. Human papillomavirus (HPV)-related and HPV-negative HNC exhibit distinct etiopathogenesis and prognoses, requiring targeted approaches for effective management. Conventional tissue biopsies are essential for confirming the diagnosis and locating solid tumors. However, they have limitations in detecting microscopic disease, tracking treatment response, and capturing the dynamic heterogeneity of the mutational profile within the tumor. Liquid biopsy using circulating tumor DNA (ctDNA) analysis has emerged as a promising non-invasive tool to overcome the drawbacks of conventional biopsy for comprehensive molecular profiling. This meta-analysis aims to colligate available evidence on the clinical utility of ctDNA analysis in predicting survival outcomes, specifically in HPV-negative HNC. Our systematic search of six electronic databases identified eight publications (N = 886 patients) meeting the inclusion criteria. The included studies reported data from HPV-negative HNC patients, employing ctDNA analysis to report survival outcomes. Our findings reveal a significant association between mutation or methylation in ctDNA and worsened survival outcomes in HPV-negative HNC cases. The presence of ctDNA mutations in TP53 and methylation of SEPT9 and SHOX2 was linked to reduced overall survival, disease-free survival, and progression-free survival. Subgroup analyses demonstrated consistent associations across different survival outcomes, ctDNA detection methods, and blood collection tubes used. Our study underscores the need for future research endeavors prioritizing larger, well-designed prospective studies with standardized methodologies to further elucidate the role of ctDNA analysis in guiding personalized treatment approaches and optimizing patient care in this specific HNC cohort.

Cell-free epigenomes enhanced fragmentomics-based model for early detection of lung cancer

BACKGROUND

Lung cancer is a leading cause of cancer mortality, highlighting the need for innovative non-invasive early detection methods. Although cell-free DNA (cfDNA) analysis shows promise, its sensitivity in early-stage lung cancer patients remains a challenge. This study aimed to integrate insights from epigenetic modifications and fragmentomic features of cfDNA using machine learning to develop a more accurate lung cancer detection model.

METHODS

To address this issue, a multi-centre prospective cohort study was conducted, with participants harbouring suspicious malignant lung nodules and healthy volunteers recruited from two clinical centres. Plasma cfDNA was analysed for its epigenetic and fragmentomic profiles using chromatin immunoprecipitation sequencing, reduced representation bisulphite sequencing and low-pass whole-genome sequencing. Machine learning algorithms were then employed to integrate the multi-omics data, aiding in the development of a precise lung cancer detection model.

RESULTS

Cancer-related changes in cfDNA fragmentomics were significantly enriched in specific genes marked by cell-free epigenomes. A total of 609 genes were identified, and the corresponding cfDNA fragmentomic features were utilised to construct the ensemble model. This model achieved a sensitivity of 90.4% and a specificity of 83.1%, with an AUC of 0.94 in the independent validation set. Notably, the model demonstrated exceptional sensitivity for stage I lung cancer cases, achieving 95.1%. It also showed remarkable performance in detecting minimally invasive adenocarcinoma, with a sensitivity of 96.2%, highlighting its potential for early detection in clinical settings.

CONCLUSIONS

With feature selection guided by multiple epigenetic sequencing approaches, the cfDNA fragmentomics-based machine learning model demonstrated outstanding performance in the independent validation cohort. These findings highlight its potential as an effective non-invasive strategy for the early detection of lung cancer.

KEYPOINTS

Our study elucidated the regulatory relationships between epigenetic modifications and their effects on fragmentomic features. Identifying epigenetically regulated genes provided a critical foundation for developing the cfDNA fragmentomics-based machine learning model. The model demonstrated exceptional clinical performance, highlighting its substantial potential for translational application in clinical practice.

All-In-One Entropy-Driven DNA Nanomachine for Tumor Cell-Selective Fluorescence/SERS Dual-Mode Imaging of MicroRNA

An entropy-driven catalysis (EDC) strategy is appealing for amplified bioimaging of microRNAs in living cells; yet, complex operation procedures, lacking of cell selectivity, and insufficient accuracy hamper its further applications. Here, we introduce an ingenious all-in-one entropy-driven DNA nanomachine (termed as AIO-EDN), which can be triggered by endogenous apurinic/apyrimidinic endonuclease 1 (APE1) to achieve tumor cell-selective dual-mode imaging of microRNA. Compared with the traditional EDC strategy, the integrated design of AIO-EDN achieves autocatalytic signal amplification without extra fuel strands. Moreover, the AIO-EDN leverages an endogenous APE1 overexpressed in cancer cells to activate the EDC reaction, which, however, exerts no target sensing activity in normal cells. Combining fluorescence- and surface-enhanced Raman scattering (FL/SERS) dual-mode imaging techniques, this DNA nanomachine exhibits significantly improved accuracy and tumor cell selectivity for microRNA imaging in living cells. This study provides a new paradigm to develop an integrated EDC-based platform and shows great potential in in-depth cancer diagnosis with high precision.

Dual Biomarker Strategies for Liquid Biopsy: Integrating Circulating Tumor Cells and Circulating Tumor DNA for Enhanced Tumor Monitoring

The liquid biopsy has gained significant attention in cancer diagnostics, with circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) being recognized as key biomarkers for tumor detection and monitoring. However, each biomarker possesses inherent limitations that restrict its standalone clinical utility, such as the rarity and heterogeneity of CTCs and the variable sensitivity and specificity of ctDNA assays. This highlights the necessity of integrating both biomarkers to maximize diagnostic and prognostic potential, offering a more comprehensive understanding of the tumor biology and therapeutic response. In this review, we summarize clinical studies that have explored the combined analysis of CTCs and ctDNA as biomarkers, providing insights into their synergistic value in diverse tumor types. Specifically, this paper examines the individual advantages and limitations of CTCs and ctDNA, details the findings of combined biomarker studies across various cancers, highlights the benefits of dual biomarker approaches over single-biomarker strategies, and discusses future prospects for advancing personalized oncology through liquid biopsies. By offering a comprehensive overview of clinical studies combining CTCs and ctDNA, this review serves as a guideline for researchers and clinicians aiming to enhance biomarker-based strategies in oncology and informs biosensor design for improved biomarker detection.

Predictive value of preoperative circulating tumor cells combined with hematological indexes for liver metastasis after radical resection of colorectal cancer

Colorectal cancer is one of the most common malignant tumors in the world, and about 50% of its advanced patients will have liver metastasis. Preoperative assessment of the risk of liver metastasis in patients with colorectal cancer is of great significance for making individualized treatment plans. Traditional imaging examinations and tumor markers have some limitations in predicting the risk of liver metastasis. Therefore, it is of great clinical value to explore more sensitive and specific predictive indicators for improving early detection and treatment effect. In recent years, circulating tumor cells (CTCs), as a new biomarker, have attracted much attention because of their close relationship with tumor metastasis and prognosis. The purpose of this study is to collect and analyze the data of colorectal cancer patients treated in our hospital, so as to determine the predictive value of circulating tumor cells before operation and related hematological indexes for liver metastasis after radical resection of colorectal cancer, and to establish the corresponding prediction model to provide gastrointestinal surgeons with more accurate identification of high-risk patients and guidance for treatment. A total of 88 patients were included in this study, and 26 of whom developed liver metastasis after colorectal cancer surgery. The possible related factors are included in the single factor logistic regression, and the results are obtained after analysis. Body mass index, carcinoembryonic antigen (CEA), carbohydrate antigen 19-9, tumor marker CA72-4 (CA72-4), cytokeratin-7 (CK-7), CTC count, and neutrophil-to-lymphocyte ratio (P < .2) are risk factors for liver metastasis after radical resection of colorectal cancer. Furthermore, the data obtained were included in multivariate regression analysis, and CEA, CA72-4, CK-7, and CTC counts were independent risk factors for liver metastasis after radical resection of colorectal cancer (P < .05). This study confirmed that CEA, CA72-4, CK-7, and CTC counts are independent risk factors for liver metastasis after radical resection of colorectal cancer. In addition, the prediction model of this study can help gastrointestinal surgeons accurately identify patients who are prone to liver metastasis after colorectal cancer surgery.

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.

18F-FDG PET/CT for early prediction of pathological complete response in breast cancer neoadjuvant therapy: a retrospective analysis

BACKGROUND

Neoadjuvant treatment has been developed as a systematic approach for patients with early breast cancer and has resulted in improved breast-conserving rate and survival. However, identifying treatment-sensitive patients at the early phase of therapy remains a problem, hampering disease management and raising the possibility of disease progression during treatment.

METHODS

In this retrospective analysis, we collected 2-deoxy-2-[F-18] fluoro-d-glucose (18F-FDG) positron emission tomography (PET)/computed tomography (CT) images of primary tumor sites and axillary areas and reciprocal clinical pathological data from 121 patients who underwent neoadjuvant treatment and surgery in our center. The univariate and multivariate logistic regression analyses were performed to investigate features associated with pathological complete response (pCR). An 18F-FDG PET/CT-based prediction model was trained, and the performance was evaluated by receiver operating characteristic curves (ROC).

RESULTS

The maximum standard uptake values (SUVmax) of 18F-FDG PET/CT were a powerful indicator of tumor status. The SUVmax values of axillary areas were closely related to metastatic lymph node counts (R = 0.62). Moreover, the early SUVmax reduction rates (between baseline and second cycle of neoadjuvant treatment) were statistically different between pCR and non-pCR patients. The early SUVmax reduction rates-based model showed great ability to predict pCR (AUC = 0.89), with all molecular subtypes (HR+HER2-, HR+HER2+, HR-HER2+, and HR-HER2-) considered.

CONCLUSION

Our research proved that the SUVmax reduction rate of 18F-FDG PET/CT contributed to the early prediction of pCR, providing rationales for utilizing PET/CT in NAT in the future.

The role of circulating tumor DNA in melanomas of the uveal tract

Melanoma of the uveal tract or uveal melanoma (UM) originates from melanocytes of the eye and is the most common intraocular malignancy in adults. Despite considerable advances in diagnostic procedures and treatments, prognosis remains poor in those with advanced disease. Accordingly, although current treatments have an excellent local disease control rate, approximately 50% of patients develop metastatic relapse within 10 years. The high risk for metastatic disease with a variable and often long latency period is thought to be due to early spread of cancer cells disseminating into organs such as the liver, followed by a period of dormancy, before the eventual emergence of radiologically measurable disease. Early detection of disease relapse or metastasis is therefore crucial to allow timely treatment and ultimately improve patient outcome. Recently, advances in minimally-invasive liquid biopsy techniques and biomarkers such as circulating tumor DNA (ctDNA) have demonstrated potential to transform the field of cancer care by aiding diagnosis, prognosis and monitoring of various cancer types. UM is particularly suitable for ctDNA-based approaches due to the relatively well-characterized spectrum of genetic mutations, along with the inherent difficulties and risks associated with getting sufficient tumor samples via traditional biopsy methods. Key potential advantage of ctDNA are the detection of molecular residual disease (MRD) in patients post definitive treatment, and in the early identification of metastasis. This is particularly relevant contemporarily with the recent demonstration of tebentafusp improving survival in metastatic UM patients, and opens avenues for further research to investigate the potential utilization of tebentafusp combined with ctDNA-based strategies in adjuvant settings and early intervention for MRD. The present review illustrates the current understanding of ctDNA-based strategies in UM, discusses the potential clinical applications, explores the potential of utilizing ctDNA in UM MRD in the context of an ongoing clinical trial, and highlights the challenges that need to be overcome prior to routine clinical implementation.

Efficacy and Safety of KRASG12C Inhibitor IBI351 Monotherapy in Patients With Advanced NSCLC: Results From a Phase 2 Pivotal Study

INTRODUCTION

KRAS glycine-to-cysteine substitution at codon 12 (G12C) mutation is a well-recognized and increasingly promising therapeutic target with huge unmet clinical needs in NSCLC patients. IBI351 is a potent covalent and irreversible inhibitor of KRAS G12C. Here, we present the efficacy and safety of IBI351 from an open-label, single-arm, phase 2 pivotal study.

METHODS

Eligible patients with NSCLC with KRAS G12C who failed standard therapy were enrolled. IBI351 was orally administered at a dose of 600 mg twice daily. The primary endpoint was confirmed objective response rate assessed by an independent radiological review committee (IRRC) as per Response Evaluation Criteria in Solid Tumors v1.1. Other endpoints were safety, IRRC-confirmed disease control rate, duration of response, progression-free survival (PFS), and overall survival.

RESULTS

As of December 13, 2023, 116 patients were enrolled (Eastern Cooperative Oncology Group Performance Status 1: 91.4%; brain metastasis: 30.2%; prior treatments with both anti-PD-1 or anti-PD-L1 inhibitors and platinum-based chemotherapy: 84.5%). As per the IRRC assessment, the confirmed objective response rate was 49.1% (95% confidence interval [CI]: 39.7-58.6), and the disease control rate was 90.5% (95% CI: 83.7-95.2). The median duration of response was not reached whereas disease progression or death events occurred in 22 patients (38.6%), and the median PFS was 9.7 months (95% CI: 5.6-11.0). overall survival data was immature. Treatment-related adverse events (TRAEs) occurred in 107 patients (92.2%) whereas 48 patients (41.4%) had equal to or higher than grade three TRAEs. Common TRAEs were anemia (44.8%), increased alanine aminotransferase (28.4%), increased aspartate aminotransferase (27.6%), asthenia (26.7%) and presence of protein in urine (25.0%). TRAEs leading to treatment discontinuation occurred in nine patients (7.8%). In biomarker evaluable patients (n = 95), all patients had positive KRAS G12C in tissue whereas 72 patients were blood-positive and 23 were blood-negative for KRAS G12C. Patients with KRAS G12C in both blood and tissue had higher tumor burden at baseline (p < 0.05) and worse PFS (p < 0.05). Tumor mutation profiling identified tumor protein p53 (45.3%), serine/threonine kinase 11 (STK11) (30.5%), and kelch-like ECH-associated protein 1 (21.1%) as the most common genes co-mutated with KRAS G12C. Among 13 genes with mutation frequency equal to or higher than 5%, mutations of six genes (STK11, kelch-like ECH-associated protein 1, phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma, DNA polymerase epsilon, SMAD family member 4, and BMP/retinoic acid-inducible neural-specific protein 3) were significantly associated with worse PFS (p < 0.05). Mutation in STK11 was also found to have a significant association with higher tumor burden at baseline and lower response rate (p < 0.05).

CONCLUSIONS

IBI351 monotherapy demonstrated promising and sustained efficacy with manageable safety, supporting its potential as a new treatment option for KRAS G12C-mutant NSCLC.

Liquid biopsy: paving a new avenue for cancer research

The current constraints associated with cancer diagnosis and molecular profiling, which rely on invasive tissue biopsies or clinical imaging, have spurred the emergence of the liquid biopsy field. Liquid biopsy involves the extraction of circulating tumor cells (CTCs), circulating free or circulating tumor DNA (cfDNA or ctDNA), circulating cell-free RNA (cfRNA), extracellular vesicles (EVs), and tumor-educated platelets (TEPs) from bodily fluid samples. Subsequently, these components undergo molecular characterization to identify biomarkers that are critical for early cancer detection, prognosis, therapeutic assessment, and post-treatment monitoring. These innovative biosources exhibit characteristics analogous to those of the primary tumor from which they originate or interact. This review comprehensively explores the diverse technologies and methodologies employed for processing these biosources, along with their principal clinical applications.

NCI workshop on ctDNA in cancer treatment and clinical care

Detection of cell-free circulating tumor DNA (ctDNA) from solid tumors is a fast-evolving field with significant potential for improving patient treatment outcomes. The spectrum of applications for ctDNA assays is broad and includes very diverse intended uses that will require different strategies to demonstrate utility. On September 14-15, 2023, the National Cancer Institute held an in-person workshop in Rockville, MD titled "ctDNA in Cancer Treatment and Clinical Care." The goal of the workshop was to examine what is currently known and what needs to be determined for various ctDNA liquid biopsy use cases related to treatment and management of patients with solid tumors and to explore how the community can best assess the value of ctDNA assays and technology. Additionally, new approaches were presented that may show promise in the future. The information exchanged in this workshop will provide the community with a better understanding of this field and its potential to affect and benefit decision-making in the treatment of patients with solid tumors.

High level of circulating cell-free tumor DNA at diagnosis correlates with disease spreading and defines multiple myeloma patients with poor prognosis

Multiple myeloma (MM) is a plasma cell (PC) disorder characterized by skeletal involvement at the time of diagnosis. Recently, cell-free DNA (cfDNA) has been proven to recapitulate the heterogeneity of bone marrow (BM) disease. Our aim was to evaluate the prognostic role of cfDNA at diagnosis according to disease distribution, and to investigate the role of the MM microenvironment inflammatory state in supplying the release of cfDNA. A total of 162 newly diagnosed MM patients were screened using 18F-FDG PET/CT and assessed by ultra low-pass whole genome sequencing (ULP-WGS). High cfDNA tumor fraction (ctDNA) levels were correlated with different tumor mass markers, and patients with high ctDNA levels at diagnosis were more likely to present with metabolically active paraskeletal (PS) and extramedullary (EM) lesions. Moreover, we demonstrated that microenvironment cancer-associated fibroblast (CAFs)-mediated inflammation might correlate with high ctDNA levels. Indeed, a high cfDNA TF level at diagnosis predicted a poorer prognosis, independent of R-ISS III and 1q amplification; the inclusion of >12% ctDNA in the current R-ISS risk score enables a better identification of high-risk patients. ctDNA can be a reliable and less invasive marker for disease characterization, and can refine patient risk.

Considering Biomarkers of Neurodegeneration in Alzheimer's Disease: The Potential of Circulating Cell-Free DNA in Precision Neurology

Neurodegenerative diseases, such as Alzheimer's disease (AD), are a growing public health crisis, exacerbated by an aging global population and the lack of effective early disease-modifying therapies. Early detection of neurodegenerative disorders is critical to delaying symptom onset and mitigating disease progression, but current diagnostic tools often rely on detecting pathology once clinical symptoms have emerged and significant neuronal damage has already occurred. While disease-specific biomarkers, such as amyloid-beta and tau in AD, offer precise insights, they are too limited in scope for broader neurodegeneration screening for these conditions. Conversely, general biomarkers like neurofilament light chain (NfL) provide valuable staging information but lack targeted insights. Circulating cell-free DNA (cfDNA), released during cell death, is emerging as a promising biomarker for early detection. Derived from dying cells, cfDNA can capture both general neurodegenerative signals and disease-specific insights, offering multi-layered genomic and epigenomic information. Though its clinical potential remains under investigation, advances in cfDNA detection sensitivity, standardized protocols, and reference ranges could establish cfDNA as a valuable tool for early screening. cfDNA methylation signatures, in particular, show great promise for identifying tissue-of-origin and disease-specific changes, offering a minimally invasive biomarker that could transform precision neurology. However, further research is required to address technological challenges and validate cfDNA's utility in clinical settings. Here, we review recent work assessing cfDNA as a potential early biomarker in AD. With continued advances, cfDNA could play a pivotal role in shifting care from reactive to proactive, improving diagnostic timelines and patient outcomes.

Establishment of liquid biopsy procedure for the analysis of circulating cell free DNA, exosomes, RNA and proteins in colorectal cancer and adenoma patients

Liquid biopsy has an underexplored diagnostic potential in colorectal cancer (CRC). Sufficient quantity and quality of its elements (circulating cell-free DNA (ccfDNA), exosomes and exosomal RNA) are essential for accurate results. The present study aims to establish the optimal protocol for handling liquid biopsy samples. Samples were obtained by collecting peripheral blood from colorectal adenoma patients in CellSave tubes. Plasma was separated within six hours using differential centrifugation and aliquots stored at - 20/- 80 °C until further processing. Three methods for isolation of ccfDNA, and two combinations of kits for isolation of exosomes and exosomal RNA were tested. The quality and quantity of ccfDNA isolates were evaluated. Exosomes were characterised by determining size, concentration, and total and specific protein content. Expression of chosen microRNAs, miR-19a-3p and miR-92-3p, which have been implicated in CRC progression, were determined. The vacuum-column-based kit showed the highest quantities of isolated ccfDNA (P-value < 0.001). Kits for exosome isolation significantly differed in size (P-value = 0.016), concentration (P-value = 0.016) and protein content (P-value = 0.016). There was no significant difference in expressions of miR-19a-3p (P-value = 0.219) and miR-92a-3p (P-value = 0.094) between the two isolation kits. The new, adapted protocol described, enables simultaneous analysis of multiple elements when investigating potential biomarkers of CRC.

Excitation/emission-enhanced heterostructure photonic crystal array synergizing with "DD-A" FRET entropy-driven circuit for high-resolution and ultrasensitive analysis of ctDNA

Circulating tumor DNA (ctDNA) is an emerging biomarker of liquid biopsy for cancer. But it remains a challenge to achieve simple, sensitive and specific detection of ctDNA because of low abundance and single-base mutation. In this work, an excitation/emission-enhanced heterostructure photonic crystal (PC) array synergizing with entropy-driven circuit (EDC) was developed for high-resolution and ultrasensitive analysis of ctDNA. The donor donor-acceptor FÖrster resonance energy transfer ("DD-A" FRET) was integrated in EDC based on the introduction of simple auxiliary strand, which exhibited higher sensitivity than that of traditional EDC. The heterostructure PC array was constructed with the bilayer periodic nanostructures of nanospheres. Because the heterostructure PC has the adjustable dual photonic band gaps (PBGs) by changing nanosphere sizes, and the "DD-A" FRET can offer the excitation and emission peak with enough distance, it helps the successful matches between the dual PBGs of heterostructure PC and the excitation/emission peaks of "DD-A" FRET; thus, the fluorescence from EDC can be enhanced effectively from both of excitation and emission processes on heterostructure PC array. Besides, high-resolution of single-base mutation was obtained through the strict recognition of EDC. Benefiting from the specific spectrum-matched and synergetic amplification of heterostructure PC and EDC with "DD-A" FRET, the proposed array obtained ultrasensitive detection of ctDNA with LOD of 12.9 fM, and achieved the analysis of mutation frequency as low as 0.01%. Therefore, the proposed strategy has the advantages of simple operation, mild conditions (enzyme-free and isothermal), high-sensitivity, high-resolution and high-throughput analysis, showing potential in bioassay and clinical application.

The ctDNA revolution: Insights on cancer care: A narrative review

Circulating tumor DNA (ctDNA) is a revolutionary tool in the detection and monitoring of cancer: a minimally invasive, highly sensitive approach to analysing tumor-specific DNA in the bloodstream. Therefore, it is of interest to explore the current and evolving landscape of cancer genomics as precision tools in quantifying tumor dynamics. Thus, the role of ctDNA in tracking minimum residual disease, relapse, recurrence and the tailoring of therapeutic strategies for effective management of tumours is reviewed.

Advances and challenges in the use of liquid biopsy in gynaecological oncology

Ovarian cancer, endometrial cancer, and cervical cancer are the three primary gynaecological cancers that pose a significant threat to women's health on a global scale. Enhancing global cancer survival rates necessitates advancements in illness detection and monitoring, with the goal of improving early diagnosis and prognostication of disease recurrence. Conventional methods for identifying and tracking malignancies rely primarily on imaging techniques and, when possible, protein biomarkers found in blood, many of which lack specificity. The process of collecting tumour samples necessitates intrusive treatments that are not suitable for specific purposes, such as screening, predicting, or evaluating the effectiveness of treatment, monitoring the presence of remaining illness, and promptly detecting relapse. Advancements in treatment are being made by the detection of genetic abnormalities in tumours, both inherited and acquired. Newly designed therapeutic approaches can specifically address some of these abnormalities. Liquid biopsy is an innovative technique for collecting samples that examine specific cancer components that are discharged into the bloodstream, such as circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), cell-free RNA (cfRNA), tumour-educated platelets (TEPs), and exosomes. Mounting data indicates that liquid biopsy has the potential to improve the clinical management of gynaecological cancers through enhanced early diagnosis, prognosis prediction, recurrence detection, and therapy response monitoring. Understanding the distinct genetic composition of tumours can also inform therapy choices and the identification of suitable targeted treatments. The main benefits of liquid biopsy are its non-invasive characteristics and practicality, enabling the collection of several samples and the continuous monitoring of tumour changes over time. This review aims to provide an overview of the data supporting the therapeutic usefulness of each component of liquid biopsy. Additionally, it will assess the benefits and existing constraints associated with the use of liquid biopsy in the management of gynaecological malignancies. In addition, we emphasise future prospects in light of the existing difficulties and investigate areas where further research is necessary to clarify its rising clinical capabilities.

DNA demethylation triggers cell free DNA release in colorectal cancer cells

BACKGROUND

Liquid biopsy based on cell-free DNA (cfDNA) analysis holds significant promise as a minimally invasive approach for the diagnosis, genotyping, and monitoring of solid malignancies. Human tumors release cfDNA in the bloodstream through a combination of events, including cell death, active and passive release. However, the precise mechanisms leading to cfDNA shedding remain to be characterized. Addressing this question in patients is confounded by several factors, such as tumor burden extent, anatomical and vasculature barriers, and release of nucleic acids from normal cells. In this work, we exploited cancer models to dissect basic mechanisms of DNA release.

METHODS

We measured cell loss ratio, doubling time, and cfDNA release in the supernatant of a colorectal cancer (CRC) cell line collection (N = 76) representative of the molecular subtypes previously identified in cancer patients. Association analyses between quantitative parameters of cfDNA release, cell proliferation, and molecular features were evaluated. Functional experiments were performed to test the impact of modulating DNA methylation on cfDNA release.

RESULTS

Higher levels of supernatant cfDNA were significantly associated with slower cell cycling and increased cell death. In addition, a higher cfDNA shedding was found in non-CpG Island Methylator Phenotype (CIMP) models. These results indicate a positive correlation between lower methylation and increased cfDNA levels. To explore this further, we exploited methylation microarrays to identify a subset of probes significantly associated with cfDNA shedding and derive a methylation signature capable of discriminating high from low cfDNA releasers. We applied this signature to an independent set of 176 CRC cell lines and patient derived organoids to select 14 models predicted to be low or high releasers. The methylation profile successfully predicted the amount of cfDNA released in the supernatant. At the functional level, genetic ablation of DNA methyl-transferases increased chromatin accessibility and DNA fragmentation, leading to increased cfDNA release in isogenic CRC cell lines. Furthermore, in vitro treatment of five low releaser CRC cells with a demethylating agent was able to induce a significant increase in cfDNA shedding.

CONCLUSIONS

Methylation status of cancer cell lines contributes to the variability of cfDNA shedding in vitro. Changes in methylation pattern are associated with cfDNA release levels and might be exploited to increase sensitivity of liquid biopsy assays.

Molecular characterization and biomarker identification in paediatric B-cell acute lymphoblastic leukaemia

B-cell acute lymphoblastic leukaemia (B-ALL) is the most prevalent hematologic malignancy in children and a leading cause of mortality. Managing B-ALL remains challenging due to its heterogeneity and relapse risk. This study aimed to delineate the molecular features of paediatric B-ALL and explore the clinical utility of circulating tumour DNA (ctDNA). We analysed 146 patients with paediatric B-ALL who received systemic chemotherapy. The mutational landscape was profiled in bone marrow (BM) and plasma samples using next-generation sequencing. Minimal residual disease (MRD) testing on day 19 of induction therapy evaluated treatment efficacy. RNA sequencing identified gene fusions in 61% of patients, including 37 novel fusions. Specifically, the KMT2A-TRIM29 novel fusion was validated in a boy who responded well to initial therapy but relapsed after 1 year. Elevated mutation counts and maximum variant allele frequency in baseline BM were associated with significantly poorer chemotherapy response (p = 0.0012 and 0.028, respectively). MRD-negative patients exhibited upregulation of immune-related pathways (p < 0.01) and increased CD8+ T cell infiltration (p = 0.047). Baseline plasma ctDNA exhibited high mutational concordance with the paired BM samples and was significantly associated with chemotherapy efficacy. These findings suggest that ctDNA and BM profiling offer promising prognostic insights for paediatric B-ALL management.

Homologous Recombination Repair Testing Patterns and Outcomes in mCRPC by Alteration Status and Race

Background

Alterations in DNA damage repair genes in advanced prostate cancer (PC) may impact responses to therapy and clinical outcomes. This study described homologous recombination repair (HRR) testing patterns and clinical outcomes among patients with metastatic castration-resistant prostate cancer (mCRPC) by HRR alteration status and race in the United States (US).

Methods

Clinical data in the nationwide (US-based) Flatiron Health-Foundation Medicine, Inc. (FMI) Metastatic PC Clinico-Genomic Database were evaluated (01/01/2011-12/31/2022). Patients initiating first-line (1L) mCRPC therapy on or after mCRPC diagnosis were included. Testing patterns, time-to-next treatment, overall survival (OS), and time-to-prostate specific antigen response were described.

Results

Of the 1367 patients with mCRPC and at least one HRR panel test prior to or on the date of 1L mCRPC therapy initiation, 332 (24.3%) were HRR positive (White patients: n = 219 [66.0%]; Black patients: n = 37 [11.1%]) and 1035 (75.7%) were HRR negative (White patients: n = 702 [67.8%]; Black patients: n = 84 [8.1%]). The mean time between first positive test and 1L mCRPC therapy initiation date was 588 days (White patients: 589 days; Black patients: 639 days). Among HRR positive relative to negative patients, trends for faster progression (respective 12-month rate overall: 71.1% and 63.7%; White patients: 72.5% and 64.0%; Black patients: 65.4% and 56.4%), shorter OS (respective 24-month rate overall: 46.8% and 51.9%; White patients: 48.6% and 46.2%; Black patients: 52.8% and 54.1%), and decreased treatment response (respective 12-month rate overall: 24.3% and 37.9%; White patients: 24.5% and 35.2%; Black patients: 17.0% and 43.9%) were observed.

Conclusion

Patients with mCRPC positive for HRR alterations tended to exhibit poorer treatment responses and clinical outcomes than those with a negative status. These findings highlight the importance of timely genetic testing in mCRPC, particularly among Black patients, and the need for improved 1L targeted therapies to address the unmet need in HRR positive mCRPC.

Turning the tide: pembrolizumab's triumph in adjuvant RCC therapy

In recent years, kidney cancer has shown an increased worldwide incidence of more than 400 000 novel cases annually. Although more than half of patients are diagnosed at a localised stage, this disease presents a high-risk of relapse after surgery. Thus, there is a need for adjuvant therapy post-resection to reduce cancer recurrence and prolong disease-free and overall survival. Thorough investigation of adjuvant drugs for renal cell carcinoma (RCC) has shown little promise in the last fifty years, with no recorded overall survival benefits. This was the case until pembrolizumab, an immune checkpoint inhibitor, was introduced into the adjuvant RCC space through the KEYNOTE-564 trial. The adjuvant administration of this novel anti-PD-1 drug demonstrated a significant overall survival benefit which has led to an update in the current treatment guidelines of RCC. This substantial change in the standard of care also caused an investigation of possible treatment combinations and an adoption of innovative predictive biomarkers. In this review, we will present the evolution of past adjuvant ICI trials for the treatment of RCC, the implications of pembrolizumab's overall survival benefits and a discussion of future directions concerning new RCC drug trials and liquid biopsy-based biomarkers.

Circulating Tumor DNA and Survival in Metastatic Breast Cancer: A Systematic Review and Meta-Analysis

Importance

Metastatic breast cancer (MBC) poses a substantial clinical challenge despite advancements in diagnosis and treatment. While tissue biopsies offer a static snapshot of disease, liquid biopsy-through detection of circulating tumor DNA (ctDNA)-provides minimally invasive, real-time insight into tumor biology.

Objective

To determine the association between ctDNA and survival outcomes in patients with MBC.

Data Sources

An electronic search was performed in 5 databases (CINAHL, Cochrane Library, Embase, Medline, and Web of Science) and included all articles published from inception until October 23, 2023.

Study Selection

To be included in the meta-analysis, studies had to (1) include women diagnosed with MBC; (2) report baseline plasma ctDNA data; and (3) report overall survival, progression-free survival, or disease-free survival with associated hazards ratios.

Data Extraction and Synthesis

Titles and abstracts were screened independently by 2 authors. Data were pooled using a random-effects model. This study adhered to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guideline, and quality was assessed using the Newcastle-Ottawa Scale.

Main Outcomes and Measures

The primary study outcome was the association between detection of specific genomic alterations in ctDNA with survival outcomes. Secondary objectives were associations of study methodology with survival.

Results

Of 3162 articles reviewed, 37 met the inclusion criteria and reported data from 4264 female patients aged 20 to 94 years. Aggregated analysis revealed a significant association between ctDNA detection and worse survival (hazard ratio, 1.40; 95% CI, 1.22-1.58). Subgroup analysis identified significant associations of TP53 and ESR1 alterations with worse survival (hazard ratios, 1.58 [95% CI, 1.34-1.81] and 1.28 [95% CI, 0.96-1.60], respectively), while PIK3CA alterations were not associated with survival outcomes. Stratifying by detection method, ctDNA detection through next-generation sequencing and digital polymerase chain reaction was associated with worse survival (hazard ratios, 1.48 [95% CI, 1.22-1.74] and 1.28 [95% CI, 1.05-1.50], respectively).

Conclusions and Relevance

In this systematic review and meta-analysis, detection of specific genomic alterations in ctDNA was associated with worse overall, progression-free, and disease-free survival, suggesting its potential as a prognostic biomarker in MBC. These results may help guide the design of future studies to determine the actionability of ctDNA findings.

Unveiling the impact of corticosteroid therapy on liquid biopsy-detected cell-free DNA levels in meningioma and glioblastoma patients

The liquid biopsy era has brought several possibilities to improve precision in patient care. Among the different sources of analytes, the cfDNA has been explored as a possible disease indicator, especially in cancer. Intracranial tumors still represent a challenge for liquid biopsy due to the blood-brain barrier being able to restrain both the migrating tumor cells and the liberation of cfDNA into the blood circulation. The aim of this work was to compare the differences between the cfDNA concentration in the plasma from patients with central nervous system tumors, and for this we analyzed a cohort of 188 individuals with glioblastoma (N = 57), brain metastasis (N = 15), meningioma (N = 90) and schwannoma (N = 26). Plasma samples were obtained immediately before tumor excision, and the cfDNA was isolated from the samples and quantified. The results showed that cfDNA plasma levels vary according to the tumors analyzed, with glioblastoma and brain metastasis presenting higher median levels of cfDNA than meningiomas and schwannomas. In addition, corticosteroid treatment resulted in higher cfDNA levels in meningioma and glioblastoma patients and vasogenic brain edema resulted in higher cfDNA levels only in meningioma patients. We hypothesize that cfDNA evaluation might have clinical monitoring value and that other clinical variables, such as corticosteroid used, should be considered during the liquid biopsy clinical evaluation of intracranial tumors.

Clinical utility of repeated rebiopsy for EGFR T790M mutation detection in non-small cell lung cancer

Purpose

In cases where rebiopsy fails to find the epidermal growth factor receptor (EGFR) T790M mutation, the criteria for selecting patients for repeated rebiopsy remains unclear. This study aimed to assess the impact of repeated rebiopsy on T790M mutation detection in non-small cell lung cancer (NSCLC) patients.

Methods

Patients with advanced EGFR-mutated NSCLC between January 2018 and December 2021 at three-referral hospitals in South Korea underwent retrospective review. Of 682 patients who had rebiopsy after disease progression, T790M mutation status was assessed in plasma circulating tumor DNA (ctDNA) and/or tumor tissues.

Results

The overall T790M positivity rate increased from 40.8% after the first rebiopsy to 52.9% following multiple rebiopsies in the entire study population. Longer duration of initial EGFR TKI use (OR 1.792, ≥8 months vs. <8 months, p=0.004), better EGFR TKI responses (OR 1.611, complete or partial response vs. stable disease, p=0.006), presence of bone metastasis (OR 2.286, p<0.001) were correlated with higher T790M positivity. Longer EGFR TKI use and better responses increased T790M positivity in repeated tissue rebiopsy, while bone metastasis favored liquid rebiopsy. Additionally, T790M status has been shown to be positive over time through repeated rebiopsies ranging from several months to years, suggesting its dynamic nature.

Conclusion

In this study, among patients who initially tested negative for T790M in rebiopsy, repeated rebiopsies uncovered an additional 23.5% T790M positivity. Particularly, it is suggested that repeated rebiopsies may be valuable for patients with prolonged EGFR TKI usage, better responses to treatment, and bone metastasis.

Phenotyping Tumor Heterogeneity through Proteogenomics: Study Models and Challenges

Tumor heterogeneity refers to the diversity observed among tumor cells: both between different tumors (inter-tumor heterogeneity) and within a single tumor (intra-tumor heterogeneity). These cells can display distinct morphological and phenotypic characteristics, including variations in cellular morphology, metastatic potential and variability treatment responses among patients. Therefore, a comprehensive understanding of such heterogeneity is necessary for deciphering tumor-specific mechanisms that may be diagnostically and therapeutically valuable. Innovative and multidisciplinary approaches are needed to understand this complex feature. In this context, proteogenomics has been emerging as a significant resource for integrating omics fields such as genomics and proteomics. By combining data obtained from both Next-Generation Sequencing (NGS) technologies and mass spectrometry (MS) analyses, proteogenomics aims to provide a comprehensive view of tumor heterogeneity. This approach reveals molecular alterations and phenotypic features related to tumor subtypes, potentially identifying therapeutic biomarkers. Many achievements have been made; however, despite continuous advances in proteogenomics-based methodologies, several challenges remain: in particular the limitations in sensitivity and specificity and the lack of optimal study models. This review highlights the impact of proteogenomics on characterizing tumor phenotypes, focusing on the critical challenges and current limitations of its use in different clinical and preclinical models for tumor phenotypic characterization.

From Detection to Cure - Emerging Roles for Urinary Tumor DNA (utDNA) in Bladder Cancer

PURPOSE OF REVIEW

This review sought to define the emerging roles of urinary tumor DNA (utDNA) for diagnosis, monitoring, and treatment of bladder cancer. Building from early landmark studies the focus is on recent studies, highlighting how utDNA could aid personalized care.

RECENT FINDINGS

Recent research underscores the potential for utDNA to be the premiere biomarker in bladder cancer due to the constant interface between urine and tumor. Many studies find utDNA to be more informative than other biomarkers in bladder cancer, especially in early stages of disease. Points of emphasis include superior sensitivity over traditional urine cytology, broad genomic and epigenetic insights, and the potential for non-invasive, real-time analysis of tumor biology. utDNA shows promise for improving all phases of bladder cancer care, paving the way for personalized treatment strategies. Building from current research, future comprehensive clinical trials will validate utDNA's clinical utility, potentially revolutionizing bladder cancer management.

Detection and Characterization of Methylated Circulating Tumor DNA in Gastric Cancer

Gastric cancer is the fifth most common disease in the world and the fourth most common cause of death. It is diagnosed through esophagogastroduodenoscopy with biopsy; however, there are limitations in finding lesions in the early stages. Recently, research has been actively conducted to use liquid biopsy to diagnose various cancers, including gastric cancer. Various substances derived from cancer are reflected in the blood. By analyzing these substances, it was expected that not only the presence or absence of cancer but also the type of cancer can be diagnosed. However, the amount of these substances is extremely small, and even these have various variables depending on the characteristics of the individual or the characteristics of the cancer. To overcome these, we collected methylated DNA fragments using MeDIP and compared them with normal plasma to characterize gastric cancer tissue or patients' plasma. We attempted to diagnose gastric cancer using the characteristics of cancer reflected in the blood through the cancer tissue and patients' plasma. As a result, we confirmed that the consistency of common methylated fragments between tissue and plasma was approximately 41.2% and we found the possibility of diagnosing and characterizing cancer using the characteristics of the fragments through SFR and 5'end-motif analysis.