Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

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.

The multitiered evaluation of teaching based on improved case-based learning: A continuous survey in biochemistry and molecular biology

Contemporary undergraduate medical education has been exploring ways to effectively link basic medical curricula with clinical practice. Despite the variety of approaches, there is still no effective model or assessment method. This study examines an improved case-based learning (CBL) model that attempts to bridge the transition between basic and clinical medicine curricula. This study implanted an improved case-based learning approach in a biochemistry and molecular biology course in a clinical specialty class and evaluated the pedagogical effectiveness of this integrated approach. This study utilized a "three-tiered" teaching evaluation to assess satisfaction with teaching at three different stages of undergraduate education and to collect constructive feedback from students. We found that the satisfaction of the students in the class was significantly higher than 70% in all three dimensions of "knowledge acquisition, clinical thinking training, and comprehensive literacy", and the satisfaction gradually increased with the growth of students' performance, exceeding 80% and 90% in the second and third stages, respectively. This fully demonstrates that the iCBL model can construct students' clinical thinking system and provide an important attempt for "early clinical practice". In addition, the constructive comments from the students made us realize the shortcomings of the method, and we will continue to improve it in the future teaching of biochemistry courses. In conclusion, the integration of interdisciplinary knowledge helps students to synthesize and apply multiple aspects of knowledge to analyze and deal with complex clinical problems.

Recurrence prediction using circulating tumor DNA in patients with early-stage non-small cell lung cancer after treatment with curative intent: A retrospective validation study

BACKGROUND

Despite treatment with curative intent, many patients with localized non-small cell lung cancer (NSCLC) develop recurrence. The current challenge is to identify high-risk patients to guide adjuvant treatment. Identification of residual disease by detection of circulating tumor DNA (ctDNA) may allow more accurate clinical decision-making, but its reliability in NSCLC is not established. We aimed to build on previous data to validate a tissue-informed personalized ctDNA assay, to predict recurrence in patients with early-stage disease.

METHODS AND FINDINGS

Tumor tissue and plasma was collected from patients with stage 0-III NSCLC enrolled to LEMA (Lung cancer Early Molecular Assessment trial, NCT02894853). Serial plasma was collected before and after definitive treatment, with the latter including key timeframes of interest (1-3 days post-treatment, between 14 and 122 days after treatment end, and ≥14 days after treatment end). Somatic mutations identified by tumor exome sequencing were used to design patient-specific assays, to analyze ctDNA. Results were compared and combined with an independent dataset (LUCID; LUng Cancer CIrculating Tumour Dna study, NCT04153526). In LEMA, 130 patients (57% male; median age 66 years (range 44-82); 69% adenocarcinoma, 22% squamous cell carcinoma (SCC); 3%/49%/19%/29% with stage 0/I/II/III) were treated with curative intent. Tumor tissue originated from surgical resection or diagnostic biopsy in 118 and 12 patients respectively. LUCID included 88 patients (51% male; median age 72 years (range 44-88); 63% adenocarcinoma, 31% SCC; 49%/28%/23% with stage I/II/III). Before treatment, ctDNA was detected in 48% LEMA and 51% LUCID patients. Sensitivity, specificity, positive and negative predictive value of ctDNA detection post-treatment (≥1 positive sample ≥14 days after treatment end) to predict recurrence were 61%, 97%, 92% and 84% for LEMA and 64%, 96%, 90% and 83% for LUCID. In the combined cohort, ctDNA detection after treatment was associated with shorter recurrence-free survival (hazard ratio (HR) 11.4 (95% confidence interval (CI) [7.0,18.7]; p < 0.001)) and overall survival (HR 8.1 (95% CI [4.6,14.2]; p < 0.001)), accounting for guarantee-time bias. Of note, a key limitation of this work was the irregular sample collection schedules, during routine follow-up visits, of both studies.

CONCLUSIONS

ctDNA detection predicted recurrence in independent retrospective cohorts with notable reproducibility, including near-identical detection rates and predictive values, confirming its ability to differentiate patients at high- versus low risk of recurrence. Our results support the potential of tissue-informed ctDNA analysis as a decision-support tool for adjuvant therapy in NSCLC.

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

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

Liquid Biopsy in Solid Tumours: An Overview

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

Engineering Dual-Responsive Nanoplatform Achieves Copper Metabolism Disruption and Glutathione Consumption to Provoke Cuproptosis/Ferroptosis/Apoptosis for Cancer Therapy

Cuproptosis is a new copper-dependent form of regulated cell death and shows enormous promise in cancer therapy. However, its therapeutic performance is compromised by the strictly regulated copper metabolism and highly expressed intracellular glutathione (GSH). Herein, an intelligent nanoplatform (NSeMON-P@CuT/LipD) is rationally developed as a copper metabolic disrupter, GSH consumer, and Fenton-like reaction trigger for cancer cuproptosis/ferroptosis/apoptosis therapy. NSeMON-P@CuT/LipD is constructed from the preparation of diselenide-bridged mesoporous organosilica nanoparticles, and then pemetrexed (Pem) is loaded followed by surface deposition with a Cu2+-3,3'-dithiobis(propionohydrazide) (TPH) coordinated network and coating with a diclofenac (DC)-encapsulated liposome. In response to the specific tumor microenvironment, the obtained NSeMON-P@CuT/LipD can release DC, Cu2+, and Pem and simultaneously amplify cellular oxidative stress by consuming GSH and catalyzing endogenous H2O2 into hydroxyl radicals (•OH). Both liberated DC and augmented oxidative stress can inhibit glycolysis, reduce ATP level, and then block copper transporter ATP7B, resulting in metabolic disorders and the high retention of copper in cells for •OH generation. Moreover, the overloaded copper can promote dihydrolipoamide S-acetyltransferase oligomerization and Fe-S cluster protein loss, thus evoking cuproptosis. Collectively, the augmented oxidative stress activates prominent ferroptosis, which cooperates with cuproptosis and Pem-mediated apoptosis to significantly inhibit the tumor growth of 4T1 tumor-bearing mice. This study demonstrates feasible strategies to enhance tumor cuproptosis using a single nanoplatform and may also inspire the design of advanced cuproptosis-related therapies.

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.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSION

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

ctDNA can detect minimal residual disease in curative treated non-small cell lung cancer patients using a tumor agnostic approach

BACKGROUND

Circulating tumor DNA (ctDNA) has the potential to become a reliable biomarker for identifying minimal residual disease (MRD) and predicting recurrence in patients with non-small cell lung cancer (NSCLC) following curative treatment. However, there is a lack of studies that investigate the clinical validity of ctDNA using a tumor-agnostic approach, which can provide significant clinical benefits.

METHODS

We analyzed samples from 45 NSCLC patients recruited in a prospective national multicenter study, all of whom had undergone curative treatment. A total of 38 pre-treatment plasma samples and 76 post-treatment plasma samples were examined using a commercially available cancer personalized profiling by deep sequencing (CAPP-seq) strategy, and a tumor-agnostic approach. Post-treatment samples were collected at two distinct landmark time points: Follow-up 1 (0.5-4.5 months post-treatment) and Follow-up 2 (4.5-7.5 months post-treatment).

RESULTS

Detectable ctDNA post-treatment was significantly associated with increased risk of tumor recurrence and shorter recurrence-free survival (RFS). Using only a single blood sample taken from Follow-up 2, we correctly identified MRD in 50% of the patients who later experienced recurrence. However, subgroup analysis further revealed that in patients treated with radiotherapy or chemoradiotherapy (CRT), ctDNA detection was significantly linked to shorter RFS in the MRD analysis from Follow-up 2, but not in the MRD analysis from Follow-up 1.

CONCLUSION

These findings suggest that post-treatment ctDNA, detected using a tumor-agnostic approach, is a reliable biomarker for predicting recurrence in NSCLC patients following curative treatment. However, the optimal timing for blood sampling to detect MRD appears to depend on the type of curative treatment received.

Lines of Therapy for Locally Advanced/Metastatic Urothelial Carcinoma: The New Paradigm

Urothelial carcinoma (UC) is the most common malignancy of the urinary tract, with urothelial bladder cancer accounting for approximately 90% of cases. Metastatic UC (mUC) is a particularly aggressive subset that presents significant treatment challenges, especially in patients who are often older than 70 years and have multiple comorbidities. For several decades, cisplatin-based chemotherapy has been the standard first-line treatment for locally advanced (LA) mUC. However, its utility has been limited as many patients are ineligible owing to their health status, and overall survival rates remain suboptimal. Recent advancements, including antibody-drug conjugates and immunotherapies, have begun to reshape the treatment landscape for LA/mUC. The combination of enfortumab vedotin and pembrolizumab has shown promising clinical outcomes. The approval of multiple novel drugs and combination therapies not only provides new opportunities for patient care but also creates the need for physicians to adapt to this evolving therapeutic paradigm. This review explores the latest clinical data on the management of LA/mUC and offers insights into sequencing therapies for patients with LA/mUC.

LIBELULE: A Randomized Phase III Study to Evaluate the Clinical Relevance of Early Liquid Biopsy in Patients With Suspicious Metastatic Lung Cancer

OBJECTIVES

Genomic profiling is a major component for first-line treatment decisions in patients with NSCLC and the timeliness of biomarker testing is essential to improve time to treatment initiation (TTI) or avoid inappropriate treatment.

METHODS

The phase III LIquid Biopsy for the Early detection of LUng cancer Lesion trial (NCT03721120) included patients with radiological suspicion of advanced lung cancer. They were randomized (1:1), the control arm receiving diagnostic procedures according to each center's practice, and the liquid biopsy arm with additional testing performed at the first visit using the InVisionFirst-Lung assay. Treatment initiation and type were defined according to the European Society for Medical Oncology guidelines. Primary endpoint was the time from randomization to initiation of appropriate treatment on the basis of informative genomic and pathological results in the intention-to-treat population.

RESULTS

A total of 319 patients were enrolled (liquid biopsy [LB]: 161; control: 158). The median age was 68 years, 28.8% were non-smokers, 18.1% had a performance status of 2 or higher, and 56.7% had adenocarcinoma. In the LB arm, 81% of patients had circulating tumor DNA findings. The mean TTI was not significantly reduced (LB: 29.0 d; control 34 d (p = 0.26)). Sensitivity analyses found a shorter TTI in patients from the LB arm who received systemic treatment (LB: 29.1 d; control: 38.9 d, p = 0.01), in patients with advanced non-squamous NSCLC (LB: 29.5 d; control: 40.3 d, p = 0.01), and in patients with first-line targetable alterations (LB: 21d; control 37.4 d) (p = 0.004). Time to contributory genomic results was significantly reduced (LB: 17.9 d; control: 25.6 d, p < 0.001).

CONCLUSION

Early liquid biopsy testing did not significantly shorten the TTI in unselected patients referred for suspected advanced lung cancer. Nevertheless, it could reduce the TTI in patients eligible for systemic treatment, particularly for those with actionable alterations.

Computed Tomography-Based Radiomics and Genomics Analyses for Survival Prediction of Stage III Unresectable Non-Small Cell Lung Cancer Treated With Definitive Chemoradiotherapy and Immunotherapy

The standard therapy for locally unresectable advanced non-small cell lung cancer (NSCLC) is comprised of chemoradiotherapy (CRT) before immunotherapy (IO) consolidation. However, how to predict treatment outcomes and recognize patients that will benefit from IO remain unclear. This study aimed to identify prognostic biomarkers by integrating computed tomography (CT)-based radiomics and genomics. Specifically, our research involved 165 patients suffering from unresectable Stage III NSCLC. Cohort 1 (IO following CRT) was divided into D1 (n = 74), D2 (n = 32), and D3 (n = 26) sets, and the remaining 33 patients treated with CRT alone were grouped in D4. According to the CT images of primary tumor regions, radiomic features were analyzed through the least absolute shrinkage and selection operator (LASSO) regression. The Rad-score was figured out to forecast the progression-free survival (PFS). According to the Rad-score, patients were divided into high and low risk groups. Next-generation sequencing was implemented on peripheral blood and tumor tissue samples in the D3 and D4 cohorts. The maximum somatic allele frequency (MSAF) about circulating tumor DNA levels was assessed. Mismatch repair and switching/sucrose non-fermenting signaling pathways were significantly enriched in the low-risk group compared to the high-risk group (p < 0.05). Moreover, patients with MSAF ≥ 1% and those showing a decrease in MSAF after treatment significantly benefited from IO. This study developed a radiomics model predicting PFS after CRT and IO in Stage III NSCLC and constructed a radio-genomic map to identify underlying biomarkers, supplying valuable insights for cancer biology.

Emergence of Circulating Tumor DNA as a Precision Biomarker in Lung Cancer Radiation Oncology and Beyond

Circulating tumor DNA (ctDNA) is emerging as a transformative biomarker in the management of non-small cell lung cancer (NSCLC). This review focuses on its role in detecting minimal residual disease (MRD), predicting treatment response, and guiding therapeutic decision-making in radiation oncology and immunotherapy. Key studies demonstrate ctDNA's prognostic value, particularly in identifying relapse risk and refining patient stratification for curative-intent and consolidative treatments. Future research is essential to standardize ctDNA assays, optimize integration into clinical workflows, and expand its clinical utility. This biomarker holds substantial promise by enabling non-invasive, real-time monitoring and improving outcomes for patients with NSCLC and beyond.

The Role of ctDNA for Diagnosis and Histological Prediction in Early Stage Non-Small-Cell Lung Cancer: A Narrative Review

Background: Circulating tumor DNA (ctDNA) may be released from neoplastic cells into biological fluids through apoptosis, necrosis, or active release. In patients with non-small-cell lung cancer (NSCLC), ctDNA analysis is being introduced in clinical practice only for advanced disease management. Nevertheless, an interesting and promising field of application is the analysis of ctDNA in the management of early stage non-small-cell lung cancer, both for evaluation before treatment, such as diagnosis and screening, and for prediction of histology or pathological features. Methods: A thorough review of the literature published between 2000 and 2024 was performed on PubMed, utilizing the advanced search feature to narrow down titles and abstracts containing the following keywords: ctDNA, early stage, and NSCLC. A total of 20 studies that met all inclusion criteria were chosen for this review. Results: In this review, we summarize the increasing evidence suggesting that ctDNA has potential clinical applications in the management of patients with early stage NSCLC. ctDNA levels in early stage cancers are very low, posing many technical challenges in improving the detection rate and sensitivity, especially in clinical practice, if it is to be implemented for early detection. Presently, the main limitation of ctDNA experimental and clinical studies, especially in early stage settings, is the lack of definitive standardization and consensus regarding methodology, the absence of systematically validated analyses, and the lack of adoption of sensitive approaches. Conclusions: Possible applications of this analyte open up new fields of diagnosis, treatment, and follow up, which are less invasive and more precise than other approaches currently in use, especially in early stage NSCLC patients.

Marker selection strategies for circulating tumor DNA guided by phylogenetic inference

MOTIVATION

Blood-based profiling of tumor DNA ("liquid biopsy") offers great prospects for non-invasive early cancer diagnosis and clinical guidance, but requires further computational advances to become a robust quantitative assay of tumor clonal evolution. We propose new methods to better characterize tumor clonal dynamics from circulating tumor DNA (ctDNA), through application to two specific tasks: (i) applying longitudinal ctDNA data to refine phylogeny models of clonal evolution, and (ii) quantifying changes in clonal frequencies that may be indicative of treatment response or tumor progression. We pose these through a probabilistic framework for optimally identifying markers and using them to characterize clonal evolution.

RESULTS

We first estimate a density over clonal tree models using bootstrap samples over pre-treatment tissue-based sequence data. We then refine these models over successive longitudinal samples. We use the resulting framework for modeling and refining tree densities to pose a set of optimization problems for selecting ctDNA markers to maximize measures of utility for reducing uncertainty in phylogeny models and quantifying clonal frequencies given the models. We tested our methods on synthetic data and showed them to be effective at refining tree densities and inferring clonal frequencies. Application to real tumor data further demonstrated the methods' effectiveness in refining a lineage model and assessing its clonal frequencies. The work shows the power of computational methods to improve marker selection, clonal lineage reconstruction, and clonal dynamics profiling for more precise and quantitative assays of somatic evolution and tumor progression.

AVAILABILITY AND IMPLEMENTATION

https://github.com/CMUSchwartzLab/Mase-phi.git. (DOI: 10.5281/zenodo.14776163).

Circulating Tumor DNA Predicts Conversion Therapy Response and Prognosis in Initially Unresectable Colorectal Liver-Limited Metastases: A Retrospective Study

Aims/Background Effective molecular biomarkers for predicting prognosis and guiding treatment in patients with initially unresectable colorectal liver metastases (CRLMs) undergoing conversion therapy are currently lacking. This study investigated the predictive value of circulating tumor DNA (ctDNA) conversion therapy outcomes in initially unresectable CRLMs. Methods A retrospective analysis was conducted on 81 patients with CRLMs treated at the Sixth Affiliated Hospital, Sun Yat-sen University from January 2017 to April 2021. The relationships between baseline and treatment ctDNA levels and clinical responses were evaluated using group comparisons based on data type. The impact of ctDNA on survival outcomes was analyzed through Cox regression survival analysis. Results Analysis of 81 patients with ctDNA-positive at baseline showed that patients in the ctDNA low-level group had a significantly longer median progression-free survival (mPFS) (p = 0.039). Among 45 patients who underwent ctDNA testing during systemic therapy, the proportion of patients in the ctDNA-negative group receiving local ablative treatment (LAT) was significantly higher (70.0% vs 26.7%, p = 0.006). Furthermore, 50% of patients in the ctDNA-negative group achieved no evidence of disease (NED) status, compared to 6.7% in the ctDNA-positive group (p = 0.004). Both mPFS and median overall survival (mOS) were significantly longer in ctDNA-negative patients compared to ctDNA-positive patients (p < 0.05). Of the 61 patients who underwent LAT, 37 received ctDNA testing at the same time as imaging assessment for NED. The proportion of patients with ctDNA clearance who achieved NED status was markedly higher than that of patients with ctDNA non-clearance (78.6% vs 33.3%, p = 0.036). Patients with ctDNA clearance demonstrated significantly improved mOS compared to those with ctDNA non-clearance (not reached vs 30.1 months, p = 0.036). Conclusion Dynamic changes in ctDNA levels can predict both long-term survival and the effectiveness of conversion therapy in patients with initially unresectable CRLMs.

Circulating tumor DNA to monitor treatment response in solid tumors and advance precision oncology

Circulating tumor DNA (ctDNA) has emerged as a dynamic biomarker in cancer, as evidenced by its increasing integration into clinical practice. Carrying tumor specific characteristics, ctDNA can be used to inform treatment selection, monitor response, and identify drug resistance. In this review, we provide a comprehensive, up-to-date summary of ctDNA in monitoring treatment response with a focus on lung, colorectal, and breast cancers, and discuss current challenges and future directions.

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 biopsies in cancer

Cancer ranks among the most lethal diseases worldwide. Tissue biopsy is currently the primary method for the diagnosis and biological analysis of various solid tumors. However, this method has some disadvantages related to insufficient tissue specimen collection and intratumoral heterogeneity. Liquid biopsy is a noninvasive approach for identifying cancer-related biomarkers in peripheral blood, which allows for repetitive sampling across multiple time points. In the field of liquid biopsy, representative biomarkers include circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and exosomes. Many studies have evaluated the prognostic and predictive roles of CTCs and ctDNA in various solid tumors. Although these studies have limitations, the results of most studies appear to consistently demonstrate the correlations of high CTC counts and ctDNA mutations with lower survival rates in cancer patients. Similarly, a reduction in CTC counts throughout therapy may be a potential prognostic indicator related to treatment response in advanced cancer patients. Moreover, the biochemical characteristics of CTCs and ctDNA can provide information about tumor biology as well as resistance mechanisms against targeted therapy. This review discusses the current clinical applications of liquid biopsy in cancer patients, emphasizing its possible utility in outcome prediction and treatment decision-making.

Unlocking the Potential of ctDNA in Sarcomas: A Review of Recent Advances

Soft tissue sarcomas (STSs) constitute a group of tumors with heterogeneous alterations and different biological behavior. Genetic profiling techniques have immense potential to revolutionize sarcoma classification, detection, and treatment. Cell-free DNA (cfDNA) analysis offers a minimally invasive approach to profiling tumor alterations, including tracking specific mutations or targeted panels of cancer-related genes via DNA sequencing methods. Circulating tumor DNA (ctDNA) platforms have gained popularity as a noninvasive alternative to tissue biopsies, offering a less invasive approach to tumor profiling. Nonetheless, ctDNA profiling in concordance with standard solid tumor comprehensive genomic profiling (CGP) is poorly characterized for STSs. Ultra-low-pass whole-genome sequencing and whole exome sequencing of cfDNA have yet to be fully leveraged in patients with sarcomas. This comprehensive review provides an overview of the application of ctDNA in STSs.

Liquid biopsy in lung cancer

Precision medicine based on biomarkers, such as genetic abnormalities and PD-L1 expression, has been established for the treatment of nonsmall cell lung cancer. Recently, liquid biopsy has emerged as a valuable and minimally invasive alternative. This method analyzes blood and other bodily fluids to detect cancer-related genetic abnormalities and molecular residual disease (MRD). Liquid biopsy, which includes testing for circulating tumor cells, circulating tumor DNA (ctDNA), and microRNA (miRNA), offers several advantages over conventional methods. It is minimally invasive, can be performed repeatedly, and provides crucial information for early cancer diagnosis, genotyping, and treatment monitoring. Elevated ctDNA levels and miRNA markers show promise for early diagnosis. Liquid biopsy complements traditional tissue biopsy during genotyping, particularly when tumor samples are insufficient. Tests such as Cobas® EGFR Mutation Test v2 and Guardant360® CDx have been shown to be effective in detecting genetic mutations and guiding treatment decisions. Although the accuracy of liquid biopsy is still lower than that of tissue biopsy, its clinical utility continues to improve. For cancer prediction recurrence and treatment monitoring, ctDNA analysis can detect MRD earlier than conventional imaging, offering potential benefits for treatment adjustment and early relapse detection. The continuous development and validation of liquid biopsy methods are essential for improving personalized lung cancer treatment strategies.

Tumor Heterogeneity and the Immune Response in Non-Small Cell Lung Cancer: Emerging Insights and Implications for Immunotherapy

Resistance to immune checkpoint inhibitors (ICIs) represents a major challenge for the effective treatment of non-small cell lung cancer (NSCLC). Tumor heterogeneity has been identified as an important mechanism of treatment resistance in cancer and has been increasingly implicated in ICI resistance. The diversity and clonality of tumor neoantigens, which represent the target epitopes for tumor-specific immune cells, have been shown to impact the efficacy of immunotherapy. Advances in genomic techniques have further enhanced our understanding of clonal landscapes within NSCLC and their evolution in response to therapy. In this review, we examine the role of tumor heterogeneity during immune surveillance in NSCLC and highlight its spatial and temporal evolution as revealed by modern technologies. We explore additional sources of heterogeneity, including epigenetic and metabolic factors, that have come under greater scrutiny as potential mediators of the immune response. We finally discuss the implications of tumor heterogeneity on the efficacy of ICIs and highlight potential strategies for overcoming therapeutic resistance.

Molecular residual disease analysis of adjuvant osimertinib in resected EGFR-mutated stage IB-IIIA non-small-cell lung cancer

Osimertinib-a third-generation epidermal growth factor receptor-tyrosine kinase inhibitor-is recommended as adjuvant therapy for resected stage IB-IIIA epidermal growth factor receptor-mutated non-small-cell lung cancer, based on significant disease-free survival (DFS) and overall survival improvement shown in the previously reported phase 3 ADAURA trial. A trend toward an increased DFS event rate after completion of 3 years adjuvant treatment in ADAURA suggests that some patients may benefit from longer adjuvant osimertinib treatment. We therefore explored whether tumor-informed, circulating tumor DNA-based, molecular residual disease (MRD) could predict recurrence in an exploratory post hoc analysis of 220 patients (n = 112 osimertinib; n = 108 placebo) from ADAURA. MRD preceded imaging DFS events in this study by a median of 4.7 (95% confidence interval, 2.2-5.6) months. DFS and MRD event-free rate at 36 months was 86% versus 36% for patients in the osimertinib versus placebo groups (hazard ratio, 0.23 (95% confidence interval, 0.15-0.36)). In the osimertinib group, DFS or MRD events were detected in 28 (25%) patients; most events occurred following osimertinib cessation (19 of 28, 68%) and within 12 months of stopping osimertinib (11 of 19, 58%). At 24 months after osimertinib, the DFS and MRD event-free rate was 66%. In this study, MRD preceded DFS events in most patients across both arms. DFS and MRD event-free status was maintained for most patients during adjuvant osimertinib treatment and posttreatment follow-up, with most MRD or DFS events occurring after osimertinib treatment discontinuation or completion. MRD detection could potentially identify patients who may benefit from longer adjuvant osimertinib, although this requires clinical confirmation. ClinicalTrials.gov identifier: NCT02511106 .

Accurate Diagnosis of High-Risk Pulmonary Nodules Using a Non-Invasive Epigenetic Biomarker Test

BACKGROUND/OBJECTIVES

Accurate non-invasive tests to improve early detection and diagnosis of lung cancer are urgently needed. However, no regulatory-approved blood tests are available for this purpose. We aimed to improve pulmonary nodule classification to identify malignant nodules in a high-prevalence patient group.

METHODS

This study involved 806 participants with undiagnosed nodules larger than 5 mm, focusing on assessing nucleosome levels and histone modifications (H3.1 and H3K27Me3) in circulating blood. Nodules were classified as malignant or benign. For model development, the data were randomly divided into training (n = 483) and validation (n = 121) datasets. The model's performance was then evaluated using a separate testing dataset (n = 202).

RESULTS

Among the patients, 755 (93.7%) had a tissue diagnosis. The overall malignancy rate was 80.4%. For all datasets, the areas under curves were as follows: training, 0.74; validation, 0.86; and test, 0.79 (accuracy range: 0.80-0.88). Sensitivity showed consistent results across all datasets (0.91, 0.95, and 0.93, respectively), whereas specificity ranged from 0.37 to 0.64. For smaller nodules (5-10 mm), the model recorded accuracy values of 0.76, 0.88, and 0.85. The sensitivity values of 0.91, 1.00, and 0.94 further highlight the robust diagnostic capability of the model. The performance of the model across the reporting and data system (RADS) categories demonstrated consistent accuracy.

CONCLUSIONS

Our epigenetic biomarker panel detected non-small-cell lung cancer early in a high-risk patient group with high sensitivity and accuracy. The epigenetic biomarker model was particularly effective in identifying high-risk lung nodules, including small, part-solid, and non-solid nodules, and provided further evidence for validation.

The prospects and limitations of liquid biopsy utilization for clinical practice in Taiwan

Objective

Liquid biopsy is a promising, non-invasive diagnostic tool for cancer, offering rapid and cost-effective genomic analysis. It provides a less invasive alternative to traditional tissue biopsies, with potential benefits in monitoring disease progression and detecting minimal residual disease (MRD). However, its clinical integration faces challenges, including utility assessment and workflow adaptation. This study evaluates the value of liquid biopsy in Taiwan from a clinical physician's perspective.

Methods

A survey was conducted with 16 physicians specializing in thoracic medicine and hematologic oncology. Participants responded to a 5-point Likert scale to evaluate the timing of liquid biopsy adoption, willingness to incorporate it into clinical practice, and agreement on its role in managing specific clinical conditions.

Results

Forty percent of physicians preferred liquid biopsy when tissue samples were unavailable. The inclusion of liquid biopsy under National Health Insurance (NHI) was a key factor in its adoption. Hematologic oncologists showed a stronger preference for liquid biopsy, particularly for MRD testing, compared to their counterparts in thoracic medicine (hematologic oncology vs. thoracic medicine: 4.2 ± 0.83 vs. 3.1 ± 0.60; p value = 0.01). Younger physicians valued turnaround time, while senior physicians prioritized test brand, with a focus on report speed.

Conclusion

Physicians are generally less inclined to replace tissue biopsies with liquid biopsy, but hematologic oncologists show more flexibility. Test brand plays a role in physician decision-making, and the inclusion of liquid biopsy under NHI coverage is vital for its broader adoption in Taiwan.

Molecular residual disease assessment based on tumor-informed assay predict disease progression and postoperative recurrence of hepatobiliary cancer: A preliminary study

BackgroundHepatobiliary cancers present a heterogeneous group of diseases, and molecular residual disease (MRD) evaluation based on circulating tumor DNA (ctDNA) is anticipated to offer greater sensitivity in monitoring disease progression than glycoprotein-based tumor markers such as alpha-fetoprotein or carbohydrate antigen 19-9 (CA199).MethodsThe panels for MRD surveillance were customized for each patient based on their specific genetic mutation characteristics. The changes in ctDNA mean variant allele frequencies (mVAF) and single nucleotide variants (SNVs) were analyzed from baseline to post-operative and between post-operative measurements.ResultsA unique tumor-informed whole-exome sequencing (WES) assay revealed significant variations in gene mutations between individuals. Among 63 cases, a total of 1952 SNVs were detected in tumor tissue from 63 patients using WES; only 6 loci (0.3%) were shared by at least 2 patients, indicating that over 95% of the 20-40 loci screened were unique to individual patients . Only 17 gene alterations were common to at least 2 patients, suggesting that alterations vary widely between individuals. The mVAF and the number of SNVs in ctDNA at baseline was dramatically higher than in first post-operative MRD (MRD1). The mVAF clearance was observed in three patients, whose ctDNA was positive at MRD1 but subsequently became negative at the second post-operative MRD (MRD2). Patients exhibiting vascular invasion demonstrated a significant increase in mVAF levels and SNV numbers. Furthermore, we revealed that mVAF levels were significantly associated with clinicopathologic characteristics, including gender, age, tumor subtype, stage, metastasis, vascular invasion, hepatitis B, liver cirrhosis, and tumor differentiation. Importantly, we have shown that the detection of an MRD-guided medication regimen modification is crucial to achieve clinical complete remission.ConclusionsThis study provided data supporting the use of a more reliable assay for MRD analysis in hepatobiliary cancers based on a tumor-informed assay. Dynamic monitoring of post-operative MRD is important for assessing disease progression, risk of recurrence, and response to treatment.

Reaction Pathway Differentiation Enabled Fingerprinting Signal for Single Nucleotide Variant Detection

Accurate identification of single-nucleotide variants (SNVs) is paramount for disease diagnosis. Despite the facile design of DNA hybridization probes, their limited specificity poses challenges in clinical applications. Here, a differential reaction pathway probe (DRPP) based on a dynamic DNA reaction network is presented. DRPP leverages differences in reaction intermediate concentrations between SNV and WT groups, directing them into distinct reaction pathways. This generates a strong pulse-like signal for SNV and a weak unidirectional increase signal for wild-type (WT). Through the application of machine learning to fluorescence kinetic data analysis, the classification of SNV and WT signals is automated with an accuracy of 99.6%, significantly exceeding the 80.7% accuracy of conventional methods. Additionally, sensitivity for variant allele frequency (VAF) is enhanced down to 0.1%, representing a ten-fold improvement over conventional approaches. DRPP accurately identified D614G and N501Y SNVs in the S gene of SARS-CoV-2 variants in patient swab samples with accuracy over 99% (n = 82). It determined the VAF of ovarian cancer-related mutations KRAS-G12R, NRAS-G12C, and BRAF-V600E in both tissue and blood samples (n = 77), discriminating cancer patients and healthy individuals with significant difference (p < 0.001). The potential integration of DRPP into clinical diagnostics, along with rapid amplification techniques, holds promise for early disease diagnostics and personalized diagnostics.

Prognostic and predictive role of circulating tumor DNA detection in patients with muscle invasive bladder cancer: a systematic review and meta-analysis

BACKGROUND

At present, there is no effective prognostic indicator for muscle invasive bladder cancer (MIBC). A liquid biopsy method, plasma circulating tumor DNA (ctDNA) detection, was evaluated for use in predicting the prognosis of different cancers. This study aims to assess the prognostic value of ctDNA state for muscle-invasive bladder cancer patients.

METHODS

We comprehensively searched three public databases (PubMed, EMBASE, and the Cochrane Library) in December 2023 according to the Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) statement. Studies investigating ctDNA and prognostic outcome indicators in patients with MIBC were included in our analysis. The hazard ratios (HRs) with 95% confidence intervals (CIs) were extracted to evaluate the association between ctDNA and the prognosis in patients with MIBC.

RESULTS

Eleven studies and 1,170 patients diagnosed with muscle-invasive bladder cancer, comprising a total of four retrospective cohort studies and eight prospective cohort studies, included in our meta-analysis, one of which had two different cohorts. The analysis revealed that a positive ctDNA state was associated with poor overall survival (OS), progression-free survival (PFS), and recurrence-free survival (RFS) in patients with MIBC (HR = 4.51, 95% CI: 2.64-7.69, P < 0.001; HR = 4.50, 95% CI: 2.77-7.30, P < 0.001; HR = 6.56, 95% CI: 4.18-10.30, P < 0.001), with significant prognostic effects both pre- and post-treatment. In addition, longitudinal ctDNA analysis proved to be effective in the monitoring of patients with MIBC receiving different treatments (HR = 0.24, 95% CI: 0.14-0.41, P < 0.001).

CONCLUSIONS

A positive ctDNA state was associated with poor OS, PFS, and RFS in patients with MIBC pre- and post-treatment. Meanwhile, clearance of ctDNA was associated with improved RFS in patients with MIBC. These findings suggest that the ctDNA state is a predictive and prognostic indicator for patients with MIBC, which can be used to monitor recurrence and guide treatment. Thus, ctDNA level detection shows potential for the treatment and prognosis of patients with MIBC.

Impact of Sensitive Circulating Tumor DNA Monitoring on CT Scan Intervals During Postoperative Colorectal Cancer Surveillance

Objective

This study investigated whether digital polymerase chain reaction (dPCR)-based circulating tumor DNA (ctDNA) monitoring can allow longer intervals between computed tomography (CT) scans during postoperative surveillance of colorectal cancer (CRC).

Background

Practical guidelines still recommend intensive postoperative surveillance of CRC using periodical CT scans and serum carcinoembryonic antigen testing.

Methods

The longitudinal dynamics of ctDNA for 52 patients with CRC as measured by dPCR using probes targeting 87 individual tumor-specific mutations (1-5 per patient) were compared with results from conventional (ie, clinical) surveillance using serum tumor markers and CT.

Results

A total of 382 CT procedures were carried out for the patient cohort (3.3/year per patient) and the median lead time from ctDNA relapse to clinical relapse was 182 days (range, 0-376 days). If the CT interval was annual, potential delays in the detection of clinical relapse would have occurred for 7 of the 10 patients who experienced clinical relapse (9 of 13 events), with a median delay of 164 days (range, 0-267 days). If annual CT surveillance was performed together with ctDNA monitoring, 218 (57.1%) CTs would not have been needed to detect the first clinical relapse. In addition, the ctDNA monitoring would have provided a lead time of 339 days for detection of clinical relapse (range, 42-533 days).

Conclusions

Our findings suggest that the ctDNA monitoring as part of postoperative surveillance and clinical relapse detection for patients with CRC could allow the CT interval to be lengthened.

Trial Registration

This trial was registered with University Hospital Medical Information Network Clinical Trial Registry (UMIN000045114).

Clonal driver neoantigen loss under EGFR TKI and immune selection pressures

Neoantigen vaccines are under investigation for various cancers, including epidermal growth factor receptor (EGFR)-driven lung cancers1,2. We tracked the phylogenetic history of an EGFR mutant lung cancer treated with erlotinib, osimertinib, radiotherapy and a personalized neopeptide vaccine (NPV) targeting ten somatic mutations, including EGFR exon 19 deletion (ex19del). The ex19del mutation was clonal, but is likely to have appeared after a whole-genome doubling (WGD) event. Following osimertinib and NPV treatment, loss of the ex19del mutation was identified in a progressing small-cell-transformed liver metastasis. Circulating tumour DNA analyses tracking 467 somatic variants revealed the presence of this EGFR wild-type clone before vaccination and its expansion during osimertinib/NPV therapy. Despite systemic T cell reactivity to the vaccine-targeted ex19del neoantigen, the NPV failed to halt disease progression. The liver metastasis lost vaccine-targeted neoantigens through chromosomal instability and exhibited a hostile microenvironment, characterized by limited immune infiltration, low CXCL9 and elevated M2 macrophage levels. Neoantigens arising post-WGD were more likely to be absent in the progressing liver metastasis than those occurring pre-WGD, suggesting that prioritizing pre-WGD neoantigens may improve vaccine design. Data from the TRACERx 421 cohort3 provide evidence that pre-WGD mutations better represent clonal variants, and owing to their presence at multiple copy numbers, are less likely to be lost in metastatic transition. These data highlight the power of phylogenetic disease tracking and functional T cell profiling to understand mechanisms of immune escape during combination therapies.

Early Circulating Tumor DNA Kinetics as a Dynamic Biomarker of Cancer Treatment Response

PURPOSE

Circulating tumor DNA (ctDNA) assays are promising tools for the prediction of cancer treatment response. Here, we build a framework for the design of ctDNA biomarkers of therapy response that incorporate variations in ctDNA dynamics driven by specific treatment mechanisms. These biomarkers are based on novel proposals for ctDNA sampling protocols, consisting of frequent sampling within a compact time window surrounding therapy initiation-which we hypothesize to hold valuable prognostic information on longer-term treatment response.

METHODS

We develop mathematical models of ctDNA kinetics driven by tumor response to several therapy classes and use them to simulate randomized virtual patient cohorts to test candidate biomarkers.

RESULTS

Using this approach, we propose specific biomarkers, on the basis of ctDNA longitudinal features, for targeted therapy and radiation therapy. We evaluate and demonstrate the efficacy of these biomarkers in predicting treatment response within a randomized virtual patient cohort data set.

CONCLUSION

This study highlights a need for tailoring ctDNA sampling protocols and interpretation methodology to specific biologic mechanisms of therapy response, and it provides a novel modeling and simulation framework for doing so. In addition, it highlights the potential of ctDNA assays for making early, rapid predictions of treatment response within the first days or weeks of treatment and generates hypotheses for further clinical testing.

Modulation of tumor inflammatory signaling and drug sensitivity by CMTM4

Although inflammation has been widely associated with cancer development, how it affects the outcomes of immunotherapy and chemotherapy remains incompletely understood. Here, we show that CKLF-like MARVEL transmembrane domain-containing member 4 (CMTM4) is highly expressed in multiple human and murine cancer types including Lewis lung carcinoma, triple-negative mammary cancer and melanoma. In lung carcinoma, loss of CMTM4 significantly reduces tumor growth and impairs NF-κB, mTOR, and PI3K/Akt pathway activation. Furthermore, we demonstrate that CMTM4 can regulate epidermal growth factor (EGF) signaling post-translationally by promoting EGFR recycling and preventing its Rab-dependent degradation. Consequently, CMTM4 knockout sensitizes human lung tumor cells to EGFR inhibitors. In addition, CMTM4 knockout tumors stimulated with EGF show a decreased ability to produce inflammatory cytokines including granulocyte colony-stimulating factor (G-CSF), leading to decreased recruitment of polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) and therefore establishing a less suppressive tumor immune environment in both lung and mammary cancers. We also present evidence indicating that CMTM4-targeting siRNA-loaded liposomes reduce lung tumor growth in vivo and prolong animal survival. Knockout of CMTM4 enhances immune checkpoint blockade or chemotherapy to further reduce lung tumor growth. These data suggest that CMTM4 represents a novel target for the inhibition of tumor inflammation, and improvement of the immune response and tumor drug sensitivity.

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.

Clinical Significance of Perioperative Minimal Residual Disease Detected by Circulating Tumor DNA in Patients With Lung Cancer With a Long Follow-up Data: An Exploratory Study

Introduction

Molecular residual disease detected by circulating tumor DNA (ctDNA) has been reported to be predictive of patients' outcomes in various types of cancers after curative intent treatment. Nevertheless, additional detailed information regarding the association of longitudinal ctDNA detection with long-term follow-up in lung cancer is needed. Here, we report on a cohort of patients with NSCLC who underwent definitive surgery and ctDNA analysis in the pre-operative, adjuvant, and surveillance settings.

Method

Plasma samples were collected from 46 patients with clinical stage II-III NSCLC before surgery (n = 46), after surgery (n = 45), and every six months until two years thereafter (n = 78). A clinically validated, personalized, tumor-informed 16-plex polymerase chain reaction-next-generation sequencing assay was used for the detection and quantification of ctDNA in retrospectively analyzed plasma samples.

Results

Circulating tumor DNA was detected in the first postoperative (within 51 days after surgery) plasma samples in 13% (6/45) of patients (landmark analysis). All of them had disease recurrence within a median of 9.1 months. These patients had shorter recurrence-free and overall survivals than those without detectable ctDNA at a landmark time point (p < 0.01) and in multivariate analyses (p < 0.03). Longitudinally (considering all postoperative follow-up time points), ctDNA was detected in 13 patients, all of whom experienced disease recurrence (positive predictive value = 100%). Three patients who had central nervous system-only metastases did not have detectable ctDNA.

Conclusions

The presence of ctDNA post-surgery or during surveillance identifies patients with NSCLC at high risk of recurrence. Serial testing is important to detect disease recurrence earlier (lead-time: 3.2 months).

Cell-free DNA as a complementary diagnostic tool for neglected tropical diseases towards achieving the WHO NTDs elimination by 2030

Neglected Tropical Diseases (NTDs) continue to ravage the poorest regions of the world, with over 600 million people being affected in Sub-Saharan Africa. The global burden of NTDs within these regions is staggering, particularly post-COVID-19 pandemic, where the emerging infection intercepted the existing eradication efforts and protocols such as the Mass Drug Administration (MDA). This further complicated the approaches laid down to achieve the endgame program of eliminating the neglect and transmission of NTDs. To compensate for the detriment of COVID-19's interruption, accurate and timely diagnoses play a vital role in attaining the objectives of the WHO's goal of NTD elimination by 2030. To this effect, alternative approaches in diagnostics are urgently needed, particularly with the inadequacy of current diagnostic strategies for NTDs. Cell-free DNA (cfDNA) has shown great promise in detecting NTDs. Several studies have demonstrated its potential for diagnosing diseases such as malaria, leishmaniasis, and schistosomiasis. However, the adoption of cfDNA in NTD research faces several challenges, including the cost of the procedure, standardization, and technical expertise. Proper capacity building and training can mitigate some of these challenges. However, despite these limitations, the affordability of cfDNA detection is improving due to increased awareness of the approach and researchers' integration considerations into current diagnostic routines. In conclusion, while there are challenges to adopting cfDNA in NTD research, it remains a promising alternative strategy to be considered in the fight against NTDs.

Current advances and future prospects of blood-based techniques for identifying benign and malignant pulmonary nodules

Lung cancer is the leading cause of cancer-related mortality worldwide, highlighting the urgent need for more accurate and minimally invasive diagnostic tools to improve early detection and patient outcomes. While low-dose computed tomography (LDCT) is effective for screening in high-risk individuals, its high false-positive rate necessitates more precise diagnostic strategies. Liquid biopsy, particularly ctDNA methylation analysis, represents a promising alternative for non-invasive classification of indeterminate pulmonary nodules (IPNs). This review highlights the progress and clinical potential of liquid biopsy technologies, including traditional proteins markers, cfDNA, exosomes, metabolomics, circulating tumor cells (CTCs) and platelets, in lung cancer diagnosis. We discuss the integration of ctDNA methylation analysis with traditional imaging and clinical data to enhance the early detection of IPNs, as well as potential solutions to address the challenges of low biomarker concentration and background noise. By advancing precision diagnostics, liquid biopsy technologies could transform lung cancer management, improve survival rates, and reduce the disease burden.

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.

Clinicopathological Predictors of the Presence of Blood Circulating Tumor DNA in Early-Stage Non-Small Cell Lung Cancers

The implementation of lung cancer screening programs across the world has drawn considerable attention to improving early-stage lung cancer detection and prognostication. Several blood-based assays detecting circulating tumor DNA (ctDNA) recently emerged as noninvasive methods to detect malignancies. However, their limited sensitivity and predictive value remain a hurdle to their clinical use. We aimed to evaluate the association between clinicopathological parameters and presurgical ctDNA detection in clinical stage I non-small cell lung cancer patients to further understand ctDNA shedding biology. The cohort included 180 adenocarcinomas (LUAD) and 80 squamous cell carcinomas (LUSC) stage I patients who underwent lung cancer resection. Patients' clinical and pathological features were collected. A multicancer early-detection test (GRAIL LLC) was used to detect ctDNA using targeted methylation patterns. The association between the cell-free DNA tumor methylated fraction (TMeF) and the clinicopathological predictors was evaluated using univariate and multivariate modeling. LUSC was associated with a higher TMeF than LUAD. Pathological stage, tumor grade, and tumor volume were key determinants of ctDNA detection in both LUSC and LUAD. In LUAD, ctDNA detection also correlated with histologic pattern composition, necrosis, acute inflammation, and, to a lesser degree, spread through alveolar spaces and lymphovascular invasion. Based on our results, we propose classification methods for both LUAD (using histologic pattern composition) and LUSC (using tumor grade and pathological stage) to identify patients likely to have high ctDNA levels. These results confirm previous findings and suggest that previously unidentified factors, including histologic pattern composition and acute inflammation, influence ctDNA levels. These results will help in understanding the ctDNA shedding process and may allow identification of patients eligible for ctDNA detection-based follow-up.

ctDNA as an Objective Marker for Postoperative Residual Disease in Primary Advanced High-Grade Serous Ovarian Cancer

BACKGROUND/OBJECTIVES

The surgeon's subjective intraoperative evaluation is the standard of care to assess postoperative residual disease (RD) in advanced epithelial ovarian cancer (EOC). We investigated the feasibility of ctDNA as an objective marker for postoperative RD.

METHODS

This prospective study included 27 patients with advanced ovarian cancer (FIGO IIIA1-IVB) who underwent primary surgery between July 2021 and July 2022. Blood samples were analyzed preoperatively and on days 2 (d2) and 10 (d10) postoperatively. Low-coverage whole genome sequencing (WGS) was used to identify structural variants (SVs) at single-base pair resolution, single nucleotide variants (SNVs), and indels in tumor tissue to develop personalized, tumor-informed digital polymerase chain reaction (dPCR) fingerprint assays for each patient.

RESULTS

dPCR fingerprint assays were successfully developed for all patients by identifying one to eight SVs/SNVs per patient. ctDNA was detected in 96% (n = 26/27) of patients preoperatively and in 81% (n = 22/27) of patients at d10. Median ctDNA levels at d10 were significantly higher in patients with postoperative RD (median 367.38 copies (cps)/mL, 2.84% variant allele frequency; VAF) than in patients without postoperative RD (median 0.92 cps/mL, 0.017% VAF, p < 0.001). In patients with postoperative RD, ctDNA levels increased from the preoperative stage to d10 in seven out of eight patients (p = 0.016). In patients with complete tumor resection, ctDNA levels decreased from the preoperative stage to d10 in 17/19 patients (p < 0.001).

CONCLUSIONS

A tumor-informed personalized ctDNA approach demonstrated feasibility, providing extremely high detection rates pre- and postoperatively. These results indicate that this approach could potentially be used for postoperative RD assessment in patients with primary advanced EOC.

Challenges in blood fractionation for cancer liquid biopsy: how can microfluidics assist?

Liquid biopsy provides a minimally invasive approach to characterise the molecular and phenotypic characteristics of a patient's individual tumour by detecting evidence of cancerous change in readily available body fluids, usually the blood. When applied at multiple points during the disease journey, it can be used to monitor a patient's response to treatment and to personalise clinical management based on changes in disease burden and molecular findings. Traditional liquid biopsy approaches such as quantitative PCR, have tended to look at only a few biomarkers, and are aimed at early detection of disease or disease relapse using predefined markers. With advances in the next generation sequencing (NGS) and single-cell genomics, simultaneous analysis of both circulating tumour DNA (ctDNA) and circulating tumour cells (CTCs) is now a real possibility. To realise this, however, we need to overcome issues with current blood collection and fractionation processes. These include overcoming the need to add a preservative to the collection tube or the need to rapidly send blood tubes to a centralised processing lab with the infrastructure required to fractionate and process the blood samples. This review focuses on outlining the current state of liquid biopsy and how microfluidic blood fractionation tools can be used in cancer liquid biopsy. We describe microfluidic devices that can separate plasma for ctDNA analysis, and devices that are important in isolating the cellular component(s) in liquid biopsy, i.e., individual CTCs and CTC clusters. To facilitate a better understanding of these devices, we propose a new categorisation system based on how these devices operate. The three categories being 1) solid Interaction devices, 2) fluid Interaction devices and 3) external force/active devices. Finally, we conclude that whilst some assays and some cancers are well suited to current microfluidic techniques, new tools are necessary to support broader, clinically relevant multiomic workflows in cancer liquid biopsy.

Mismatch repair (MMR) and microsatellite instability (MSI) phenotypes across solid tumors: A comprehensive cBioPortal study on prevalence and prognostic impact

Mismatch repair deficiency (MMR-d) and microsatellite instability (MSI) are prognostic and predictive biomarkers in oncology. Current testing for MMR/MSI relies on immunohistochemistry (IHC) for MMR proteins and molecular assays for MSI detection. This combined diagnostic strategy, however, lacks tumor specificity and does not account for gene variants. This study provides an in-depth analysis of MMR mutations frequency, spectrum, and distribution in solid tumors. Data from 23,893 patients across 11 tumor types, using 66 publicly available studies, were analyzed. MMR-mutated (MMR-m) status was defined by alterations in MLH1, PMS2, MSH2, and/or MSH6; MSI was assessed by MSIsensor. Cases with indeterminate labelling were excluded. Survival was analyzed using the Kaplan-Meier method. Among 19,353 tumors, 949 MMR variants were identified, comprising 432 pathogenic and 517 variants of unknown significance (VUS), as defined by OncoKB. MSH6 mutations were the most frequent (n = 279, 29.4 %), followed by MSH2 (n = 198, 20.9 %), MLH1 (n = 187, 19.7 %), and PMS2 (n = 161, 16.9 %). MMR-m cases were more frequent in endometrial (EC, 20.5 %), colorectal (CRC, 8.2 %), bladder (BLCA, 8.7 %), and gastroesophageal cancers (GEC, 5.4 %). Pathogenic mutations were more common than non-pathogenic in EC, CRC, and GEC (p < 0.001, p = 0.01, p = 0.32, respectively). MMR-m status was not associated with MSI in 247 (48.9 %) cases, including 67 (13.2 %) with pathogenic mutations. The highest concordance between MMR-m and MSI was observed in CRC (65.7 %), EC (91.2 %), and GEC (69.6 %), while the lowest in pancreatic (0.2 %) and lung cancers (0.1 %). MMR-m GECs showed improved overall survival compared to MMR-wt (p = 0.009), a relationship not observed in other tumor types. This study demonstrates that the MMR spectrum is extremely hetoerogeneous in solid tumors, highliting the need for comprehensive and tumor-specific testing strategies.

Early circulating tumor DNA changes predict outcomes in head and neck cancer patients under re-radiotherapy

Local recurrence after radiotherapy is common in locally advanced head and neck cancer (HNC) patients. Re-irradiation can improve local disease control, but disease progression remains frequent. Hence, predictive biomarkers are needed to adapt treatment intensity to the patient's individual risk. We quantified circulating tumor DNA (ctDNA) in sequential plasma samples and correlated ctDNA levels with disease outcome. Ninety four longitudinal plasma samples from 16 locally advanced HNC patients and 57 healthy donors were collected at re-radiotherapy baseline, after 5 and 10 radiation fractions, at irradiation end, and at routine follow-up visits. Plasma DNA was subjected to low coverage whole genome sequencing for copy number variation (CNV) profiling to quantify ctDNA burden. CNV-based ctDNA burden was detected in 8/16 patients and 25/94 plasma samples. Ten additional ctDNA-positive samples were identified by tracking patient-specific CNVs found in earlier sequential plasma samples. ctDNA-positivity after 5 and 10 radiation fractions (both: log-rank, p = .050) as well as at the end of irradiation correlated with short progression-free survival (log-rank, p = .006). Moreover, a pronounced decrease of ctDNA toward re-radiotherapy termination was associated with worse treatment outcome (log-rank, p = .005). Dynamic ctDNA tracking in serial plasma beyond re-radiotherapy reflected treatment response and imminent disease progression. In five patients, molecular progression was detected prior to tumor progression based on clinical imaging. Our findings emphasize that quantifying ctDNA during re-radiotherapy may contribute to disease monitoring and personalization of adjuvant treatment, follow-up intervals, and dose prescription.

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.

Circulating tumor DNA in muscle-invasive bladder cancer: A systematic review

OBJECTIVES

To evaluate the role of circulating tumor DNA (ctDNA) as a prognostic and predictive biomarker in the perioperative management of muscle-invasive bladder cancer (MIBC).

METHODS

We conducted a systematic literature review using PubMed, MEDLINE, and Embase, following PRISMA guidelines. Studies from January 2013 to March 2024 were included if they examined ctDNA in MIBC patients undergoing radical cystectomy (RC) and perioperative chemotherapy or immunotherapy.

RESULTS

Eight studies were included. ctDNA detected before RC was associated with poor recurrence-free survival and higher risk of nodal and locally advanced disease. Postoperative ctDNA levels correlated with shorter disease-free survival and higher recurrence rates. ctDNA clearance during neoadjuvant chemotherapy was predictive of treatment response. ctDNA status post-neoadjuvant immunotherapy correlated with pathological outcomes and recurrence rates.

CONCLUSIONS

ctDNA is a promising biomarker for predicting oncological outcomes in MIBC, with potential to guide perioperative treatment decisions. Further randomized controlled trials are needed to validate these findings.

Whole genome sequencing-powered ctDNA sequencing for breast cancer detection

BACKGROUND

Circulating tumour DNA (ctDNA)-based detection of molecular residual disease (MRD) presents a strategy to identify patients at high risk of relapse. In this article, we profile early breast cancer patients with an ultrasensitive, whole genome sequencing (WGS)-based, tumour-informed ctDNA platform.

MATERIALS AND METHODS

We analysed 617 plasma samples (median 8, range 2-14) from 78 patients (23 triple-negative breast cancer, 35 human epidermal growth factor receptor 2-positive, 18 hormone receptor-positive, and 2 unknown). Samples were collected at diagnosis before therapy, cycle 2 of neoadjuvant chemotherapy, post-surgery after neoad'juvant therapy if administered, every 3 months during the first year, and every 6 months thereafter. Plasma DNA was analysed using the NeXT Personal MRD platform, a tumour-informed WGS approach to produce personalized ctDNA sequencing panels tracking a median of 1451 variants per patient. MRD detection was correlated with clinical outcomes.

RESULTS

ctDNA was detected at levels ranging from 2.19 parts per million (PPM) to 204 900 PPM (median 405 PPM), with 39% of all ctDNA detections in the ultra-low range <100 PPM. Of patients with samples at diagnosis, 98% (49/50) had ctDNA detected before treatment. At a median follow-up of 76 months (range 5-118 months), detection of ctDNA was associated with high risk of future relapse (P < 0.0001; log-rank test) and shortened overall survival (P < 0.0001) with a median lead time from ctDNA detection to clinical relapse of 15 months (range 0.9-61.5 months). MRD was identified in 100% (11/11) of patients who relapsed, with a median level of ctDNA at first MRD detection of 13.1 PPM. No ctDNA-undetected patients relapsed throughout follow-up (64/64). Comparison with exome-powered MRD detection assays showed improved sensitivity and lead time.

CONCLUSIONS

A whole genome-powered MRD assay detected breast cancer relapse with a long lead time over clinical relapse, and was strongly associated with relapse-free survival. Rates of ctDNA detection at diagnosis were higher than those reported with exome-based tumour-informed assays.

Clinical characteristics of EGFR-ctDNA shedders in EGFR-mutant NSCLC patients

BACKGROUND

Circulating tumor DNA (ctDNA) revolutionized the molecular diagnostics of lung cancer by enabling non-invasive, sensitive identification of actionable mutations. However, ctDNA analysis may be challenging due to tumor shedding variability, leading to false negative results. This study aims to understand the determinants for ctDNA shedding based on clinical characteristics of lung cancer patients, for a better interpretation of false negative results to be considered when ordering ctDNA analysis for clinical practice.

METHODS

Blood samples were collected from patients with stage IV EGFR-mutated (mEGFR) NSCLC before treatment and monitored until disease progression. EGFR was assessed on tissue by standard procedures, while EGFR status on ctDNA was tested using dPCR at baseline and at the first reassessment. NGS was used to evaluate patients mutational status at the progression of the disease.

RESULTS

A total of 40 mEGFR tissue samples were collected. Plasma samples were analyzed for mEGFR before starting the first line, 65 % of patients had detectable mEGFR in ctDNA ("shedders"). Higher ECOG PS (p = 0.04), bilateral localization of primary tumor (p = 0.04), and the presence of intrathoracic/extrathoracic disease (p = 0.05), were associated to mEGFR shedding. Shedders had shorter PFS compared to non-shedders (p = 0.03). Patients with detectable mEGFR in ctDNA at the first radiological assessment exhibited worse PFS compared to patients with ctDNA clearance (p = 0.05).

CONCLUSION

Our preliminary data demonstrate that specific clinical characteristics predict mEGFR shedding in ctDNA of NSCLC, suggesting a potential clinical applicability for understanding potential false negative results and appropriate reporting in clinical practice.

Liquid Biopsy in Progressing Prostate Cancer Patients Starting Docetaxel with or Without Enzalutamide: A Biomarker Study of the PRESIDE Phase 3b Trial

BACKGROUND AND OBJECTIVE

The PRESIDE (NCT02288247) randomized trial demonstrated prolonged progression-free survival (PFS) with continuing enzalutamide beyond progression in metastatic castration-resistant prostate cancer (mCRPC) patients starting docetaxel. This study aims to test the associations of PFS and circulating tumor DNA (ctDNA) prior to and after one cycle (cycle 2 day 1 [C2D1]) of docetaxel and with a liquid biopsy resistance biomarker (LBRB; plasma androgen receptor [AR] gain and/or circulating tumor cells [CTCs] expressing AR splice variant 7 [CTC-AR-V7]) prior to continuation of enzalutamide/placebo.

METHODS

Patients consenting to the biomarker substudy and donating blood before starting docetaxel with enzalutamide/placebo (N = 157) were included. Sequential plasma DNA samples were characterized with a prostate-cancer bespoke next-generation-sequencing capture panel (PCF_SELECT), and CTCs were assessed for AR-V7 (Epic Sciences, San Diego, CA, USA). Cox models, Kaplan-Meier, and restricted mean survival time (RMST) at 18 mo were calculated.

KEY FINDINGS AND LIMITATIONS

There was a significant association of worse PFS with pre-docetaxel ctDNA detection (N = 86 (55%), 8.1 vs 10.8 mo hazard ratio [HR] = 1.78, p = 0.004) or persistence/rise of ctDNA at C2D1 (N = 35/134, 5.5 vs 10.9 mo, HR = 1.95, 95% confidence interval [CI] = 1.15-3.30, p = 0.019). LBRB-positive patients (N = 62) had no benefit from continuing enzalutamide with docetaxel (HR = 0.78, 95% CI = 0.41-1.48, p = 0.44; RMST: 7.9 vs 7.1 mo, p = 0.50). Conversely, resistance biomarker-negative patients (N = 87) had significantly prolonged PFS (HR = 0.49, 95% CI = 0.29-0.82, p = 0.006; RMST: 11.5 vs 8.9 mo, p = 0.005). Eight patients were unevaluable. An exploratory analysis identified increased copy-number gains (CDK6/CDK4) at progression on docetaxel. Limitations included relatively low detection of CTC-AR-V7. Validation of impact on overall survival is required.

CONCLUSIONS AND CLINICAL IMPLICATIONS

Liquid biopsy gives an early indication of docetaxel futility, could guide patient selection for continuing enzalutamide, and identifies cell cycle gene alterations as a potential cause of docetaxel resistance in mCRPC.

PATIENT SUMMARY

In the PRESIDE biomarker study, we found that detecting circulating tumor DNA in plasma after starting treatment with docetaxel (chemotherapy) for metastatic prostate cancer resistant to androgen deprivation therapy can predict early how long patients will take to respond to treatment. Patients negative for a liquid biopsy resistance biomarker (based on the status of androgen receptor (AR) gene and AR splice variant 7 in circulating tumor cells) benefit from continuing enzalutamide in combination with docetaxel, while patients positive for the resistance biomarker did not. Additionally, we identified alterations in the cell cycle genes CDK6 and CDK4 as a potential genetic cause of resistance to docetaxel, which may support testing of specific drugs targeting these alterations.

Asian Thoracic Oncology Research Group expert consensus statement on the peri-operative management of non-small cell lung cancer

The peri-operative management of non-small cell lung cancer (NSCLC) in earlier stage disease has seen significant advances in recent years with the incorporation of immune checkpoint inhibitors and targeted therapy. However, many unanswered questions and challenges remain, including the application of clinical trial data to routine clinical practice. Recognising the unique demographic profile of Asian patients with NSCLC and heterogeneous healthcare systems, the Asian Thoracic Oncology Research Group (ATORG) convened a consensus meeting in Singapore on 26 April 2024 to discuss relevant issues spanning diagnostic testing to post-neoadjuvant treatment considerations and future directions. An interdisciplinary group of 19 experts comprising medical oncologists, thoracic surgeons, radiation oncologists, pulmonologists and pathologists from Singapore, Hong Kong, Mainland China, Korea, Japan, Taiwan, India, Malaysia, Thailand, Vietnam and Australia met to discuss emerging data, identify existing gaps in clinical care and develop a multidisciplinary, multinational expert consensus statement on the peri-operative management of NSCLC tailored to the Asia-Pacific region.

What the Clinician Needs to Know About Laboratory Analyses of Circulating Tumor DNA

Liquid biopsies offer the possibility to evaluate cancer patients using noninvasive approaches. Circulating cell-free DNA (ccfDNA) is 1 of the most used and promising sources. Detecting tumor DNA among ccfDNA (ctDNA) can be used for early cancer detection, treatment response assessment, prognosis, and predictive evaluations. Providing analyses that can increase the quality of patient treatment is very much a joint effort between laboratory scientists and clinicians. With its use approaching clinical practice, it is important for clinicians to be familiar with the basic concepts and analyses behind ctDNA results in a similar way as laboratory scientists should have knowledge of the clinical needs to provide relevant analyses. In this Perspective, we describe the whole process of ctDNA analyses, from the preanalytical standards to reporting/analyzing results, and highlight some important factors that need to be addressed in the process of implementing them to clinical practice.