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

Histine, carbohydrates/polysaccharides, and proteins with β-sheet conformation as promising staging markers for oral squamous cell carcinoma

Cancers of the oral cavity and lip ranks 15th cancer mortality being oral squamous cell carcinoma (OSCC) the predominant malignant neoplasm in the head and neck region. Liquid optical biopsy using infrared absorption spectroscopy offers rapid and accurate diagnosis of several diseases, including oral cancer. Here we investigated saliva samples from patients with OSCC and healthy individuals using micro-reflectance Fourier-transform infrared absorption spectroscopy. Partial least squares discriminant (PLSDA) and support vector machine (SVM) analysis were employed to mining the set of data. SVM analysis validated the PLSDA findings and presented excellent results with sensitivity of 98.6%, specificity of 97.3%, and area under ROC curve of 0.965. Interestingly we found that bands assigned to histidine, carbohydrates/polysaccharides, and content of proteins with β-sheet conformation contributed to discrimination among groups. Moreover we found that specific changes in these bands could be related to OSCC staging being promising disease gravity markers.

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

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

Bridging laboratory innovation to translational research and commercialization of extracellular vesicle isolation and detection

Extracellular vesicles (EVs) have emerged as promising biomarkers for various diseases. Encapsulating biomolecules reflective of their parental cells, EVs are readily accessible in bodily fluids. The prospect for minimally invasive, repeatable molecular testing has stimulated significant research; however, challenges persist in isolating EVs from complex biological matrices and characterizing their limited molecular cargo. Technical advances have been pursued to address these challenges, producing innovative EV-specific platforms. This review highlights recent technological developments, focusing on EV isolation and molecular detection methodologies. Furthermore, it explores the translation of these laboratory innovations to clinical applications through the analysis of patient samples, providing insights into the potential diagnostic and prognostic utility of EV-based technologies.

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

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

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.

Application of liquid biopsy in differentiating lung cancer from benign pulmonary nodules (Review)

The diagnosis of malignant and benign pulmonary nodules has always been a prominent research topic. Accurately distinguishing between these types of lesions, particularly small or ground glass nodules, is crucial for the early detection and proactive treatment of lung cancer, ultimately leading to improved patient survival. Although various imaging methods and tissue biopsies have advanced the diagnostic efficacy of pulmonary nodules, each approach possesses inherent limitations. In recent years, there has been a growing interest in liquid biopsy as a non‑invasive and easily obtainable alternative. Furthermore, in‑depth investigations into the mechanisms underlying tumor initiation and progression have contributed to the development of circulating biomarkers for monitoring treatment response and efficacy in lung cancer. This review provides a comprehensive overview of the current landscape of pulmonary nodule diagnosis while highlighting the latest advancements in liquid biopsy techniques, such as extracellular vesicles, tumor‑educated platelets, non‑coding RNA, circulating tumor DNA and circulating antibodies.

Early ctDNA and Survival in Metastatic Colorectal Cancer Treated With Immune Checkpoint Inhibitors: A Secondary Analysis of the SAMCO-PRODIGE 54 Randomized Clinical Trial

Importance

Immune checkpoint inhibitors (ICIs) have dramatically transformed the therapeutic landscape of deficient mismatch repair/microsatellite unstable-high (dMMR/MSI-H) metastatic colorectal cancer (mCRC); however, ICI use is challenged by primary resistance and timing of discontinuation. Whether circulating tumor DNA (ctDNA) may be predictive of progression-free survival (PFS) and overall survival (OS) in this treatment context remains unknown.

Objective

To assess the prognostic and predictive role of ctDNA, detected by tumor-specific methylation markers, in patients with dMMR/MSI-H mCRC treated with ICIs.

Design, Setting, and Participants

This prespecified secondary analysis of the SAMCO-PRODIGE 54 randomized clinical trial evaluated ctDNA in patients with dMMR/MSI-H mCRC treated with avelumab or standard chemotherapy, with or without a targeted agent in the second-line setting, to assess its prognostic role. Plasma samples were obtained prospectively for ctDNA analysis, and digital droplet polymerase chain reaction amplification of bisulfite-converted cell-free DNA (cfDNA) for WIF1 and NPY genes was used to quantify ctDNA levels. These samples were collected from April 2018 to April 2021 at 49 sites in France at baseline (V1) and 1-month posttreatment initiation (V2) during. Data analyses were performed from October 1 to November 1, 2024.

Intervention

Avelumab or standard chemotherapy with or without targeted agents.

Main Outcomes and Measures

PFS and OS according to baseline ctDNA positivity or concentration, and early ctDNA variation (ΔctDNA = [V1-V2] ÷ V1).

Results

The predictive analysis included 99 patients (mean [SD] age, 66 [13] years; 51 female [51.5%]) with plasma samples available for ctDNA assessment at V1, of which 74 had samples available also at V2 for Change in ctDNA assessment. In the 99 patients with available V1 plasma samples, baseline ctDNA positivity or concentration were not associated with clinical outcomes. Change in ctDNA (cutoff at median value) was significantly associated with both PFS (hazard ratio [HR], 2.98; 95% CI, 1.77-5.01; P < .001) and OS (HR, 3.61; 95% CI, 1.81-7.17; P < .001). This association was evident in patients treated with avelumab (PFS HR, 4.22; 95% CI, 1.77-10.1; P = .001; OS HR, 17.40; 95% CI, 3.82-79.70; P < .001) than in those receiving chemotherapy (PFS HR, 2.09; 95% CI, 1.03-4.21; P = .04; OS HR, 1.51; 95% CI, 0.61-3.72; P = .38). Avelumab (vs chemotherapy) improved PFS in favorable ctDNA responders (HR, 0.33; 95% CI, 0.14-0.77; log-rank P = .008) but not in poor responders (HR, 1.32; 95% CI, 0.67-2.62; log-rank P = .42) Combined ctDNA response and RECIST, version 1.1, assessment accurately predicted long-term OS. In the multivariable analysis, lack of ctDNA response was associated with an increased risk of disease progression and death in the avelumab group (HR, 7.27; 95% CI, 2.23-23.7; P = .001) but not in the chemotherapy group (HR, 1.61; 95% CI, 0.66-3.93; P = .30).

Conclusions

The findings of this secondary analysis of an RCT found that change in ctDNA at 1-month posttreatment can predict long-term outcomes in patients with dMMR/MSI-H mCRC treated with ICIs.

Trial Registration

ClinicalTrials.gov Identifier: NCT03186326.

Discovery and validation of cell-free DNA methylation markers for specific diagnosis, differentiation from benign tumors, and prognosis of breast cancer

BACKGROUND

Plasma cell-free DNA (cfDNA) methylation is emerging as a non-invasive marker for various cancers. We aimed to identify specific methylation markers for diagnosis, differentiation from benign tumors, and prognosis of breast cancer (BC), which are essential for clinical decision-making yet seldom examined together.

METHODS

BC-specific methylation markers were identified using an in-house 850K dataset combined with large-scale publicly available 450 or 850K datasets. Multiplex digital droplet PCR (mddPCR) assays were developed to detect methylation in cfDNA from 201 BC patients, 83 healthy donors, and 71 individuals harboring benign tumors. Diagnostic and prognostic performance were evaluated using logistic and Cox regression models, respectively. The basic mechanism of a selected gene was explored through in vitro experiments.

RESULTS

We identified 21 BC-specific methylated CpG sites that distinguished BC from tumor-adjacent tissues with high diagnostic accuracy. In the cfDNA cohort, three mddPCR assays targeting eight markers achieved an area under the curve (AUC) of 0.856 (95% CI = 0.814-0.898) for distinguishing BC from healthy controls, and 0.742 (95% CI = 0.684-0.801) for differentiating BC from benign tumors. Notably, combining these methylation markers with mammography and ultrasound improved diagnostic performance, resulting in an AUC of 0.898 (95% CI = 0.858-0.938) for differentiating BC from benign tumors. In the TCGA-BC dataset, prognostic model based on six sites was associated with poor overall survival prognosis (hazard ratio = 2.826, 95%CI: 1.841-4.338, p < 0.0001). In vitro experiments elucidated that FAM126A overexpression regulates BC cells malignant phenotypes.

CONCLUSIONS

Our study demonstrated potential values of methylation-based markers in the detection and prognosis of BC.

Advancements in liquid biopsy for breast Cancer: Molecular biomarkers and clinical applications

Breast cancer is characterized by significant molecular heterogeneity; therefore, there are distinct clinical features, treatment modalities, and prognostic outcomes across its various molecular subtypes. In the era of precision medicine, liquid biopsy has emerged as a convenient and minimally invasive technique capable of dynamically representing the comprehensive tumor gene spectrum. This review systematically elaborates the clinical value of liquid biopsy as a breakthrough tool for precision diagnosis and treatment in breast cancer through dynamic detection of key biomarkers, including circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), exosomes, and non-coding RNA (ncRNA). Specific genetic mutations and methylation signatures in ctDNA can be applied to early breast cancer screening, minimal residual disease monitoring, and tracking drug resistance mechanisms. CTCs enumeration (≥1/7.5 mL in early-stage cancer or ≥ 5/7.5 mL in metastatic cancer) and PD-L1 expression levels demonstrate direct correlations with prognostic stratification and the efficacy of immunotherapy. As the specificity and sensitivity of liquid biopsy continue to improve, personalized treatment strategies, informed by biomarker analysis and targeted precision therapies, have unveiled new avenues of hope for patients with breast cancer. However, several challenges persist in the practical application of liquid biopsy. Despite persistent challenges, such as insufficient standardization and difficulties in resolving low-abundance variants, future advancements should focus on multi-omics integration and AI-driven technological breakthroughs to overcome bottlenecks in clinical translation. This review summarizes cutting-edge liquid biopsy technologies for identifying clinically significant molecular biomarkers, focusing on discussing critical challenges in the strategies to advance precision oncology applications for optimized treatment guidance and disease surveillance in breast cancer.

Time Dependency for Human Papillomavirus Circulating Tumor DNA Detection after Chemoradiation as a Prognostic Biomarker for Localized Anal Cancer

PURPOSE

Although detection of ctDNA weeks after surgery is linked to recurrence for other solid tumors, the optimal time point for ctDNA assessment as a prognostic biomarker following chemoradiation for anal cancer is undefined.

EXPERIMENTAL DESIGN

Patients with stages I to III anal cancer treated with chemoradiation between December 2020 and March 2024 were evaluated for human papillomavirus (HPV) ctDNA status at baseline, at the end of chemoradiation, and during surveillance using a droplet digital HPV ctDNA PCR assay, targeting HPV E6 and E7 oncogenes for 13 oncogenic HPV types. Median recurrence-free survival (RFS) according to HPV ctDNA status was estimated via Kaplan-Meier and compared using a log-rank test.

RESULTS

Detection of HPV ctDNA at ≥3 months after chemoradiation was associated with recurrence (80% vs. 2%; OR, 168; 95% confidence interval (CI), 13.6-2,080; P < 0.0001) and inferior RFS [4.9 months vs. not reached; HR, 39.2; 95% CI, 4.6-330; P < 0.0001] relative to HPV ctDNA-negative status. Sensitivity and specificity for recurrence according to HPV ctDNA detection were 89% and 95%, respectively, with positive and negative predictive values of 80% and 98%, respectively. Differences in RFS according to HPV ctDNA status were not observed at the end of treatment (median RFS, not reached for both; HR, 1.6; 95% CI, 0.35-7.4; P = 0.48).

CONCLUSIONS

With a novel, highly sensitive assay, detection of HPV ctDNA at least 3 months after chemoradiation was associated with unfavorable survival. Future clinical trials should incorporate this 3-month post-treatment time point to identify patients with HPV-positive anal cancer at elevated recurrence risk according to HPV ctDNA status. See related commentary by Bercz et al., p. 2261.

The Society for Immunotherapy of Cancer Perspective on Liquid Biopsy- and Radiomics-Based Technologies for Immuno-oncology Biomarker Discovery and Application

Immuno-oncology is increasingly becoming the standard of care for cancers, with the identification of biomarkers that reliably classify immune checkpoint inhibitor response, resistance, and toxicity becoming the next frontier toward improvements in immunomodulatory treatment regimens. Recent advances in multiparametric, multiomics, and computational data platforms generating an unprecedented depth of data may assist in the discovery of increasingly robust biomarkers for enhanced patient selection and more personalized or longitudinal treatment approaches. Which emerging technologies to implement in future research and clinical settings, used alone or in combination, relies on weighing the pros and cons that aid in maximizing data outputs while minimizing patient sampling, with high reproducibility and representativeness, and minimal turnaround time and data fragmentation toward later private and public dataset harmonization strategies. The Society for Immunotherapy of Cancer Biomarkers Committee convened to identify important advances in biomarker technologies and highlight advances in biomarker discovery using liquid biopsy and in vivo imaging technologies. We address advances in liquid biopsy technologies monitoring cells, proteins, nucleic acids, antibodies, and drugs or analytes and radiomics technologies monitoring whole host-level imaging methods, including immuno-PET and MRI technologies, which are able to couple biomarkers with physical location. We include a summary of key metrics obtained by these technologies and their ease of interpretation, limitations and dependencies, technical improvements, and outward comparisons. By highlighting some of the most interesting recent examples contributed by these technologies and providing examples of improved outputs, we hope to guide correlative research directions and assist in their becoming clinically useful in immuno-oncology.

Liquid Biopsy Approaches for Cancer Characterization, Residual Disease Detection, and Therapy Monitoring

Liquid biopsy encompasses a variety of molecular approaches to detect circulating tumor DNA (ctDNA) and has become a powerful tool in the diagnosis and treatment of solid tumors. Current applications include comprehensive genomic profiling for identifying targetable mutations and therapeutic resistance mechanisms, with emerging applications in minimal residual disease detection and treatment response monitoring. Increasingly, the potential for liquid biopsy in guiding treatment decisions is under active investigation through prospective clinical trials using ctDNA-adaptive interventions in patients with early-stage and metastatic cancers. Limitations arise on the basis of the sensitivity and feasibility of individual liquid biopsy assays; nonetheless, emerging technologies set the stage for improving these shortcomings. As the global oncology community continues to ascertain the clinical value of liquid biopsy across the continuum of patient care, this minimally invasive approach heralds a significant advancement in the promise of precision oncology.

Expression characteristics and biological functions of CGB5 gene in gastric cancer

OBJECTIVE

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

METHODS

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

RESULTS

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

[Molecular testing and liquid biopsies in colorectal cancer]

BACKGROUND

The introduction of new DNA sequencing technologies has led to the discovery of many prognostically and predictively relevant biomarkers in tumor tissue and blood from patients with colorectal cancer.

OBJECTIVES

Presentation of meaningful tissue-based molecular pathological diagnostics and discussion of the clinical application of circulating tumor DNA (ctDNA) from liquid biopsies in colorectal cancer.

MATERIALS AND METHODS

Evaluation of existing literature and congress publications, discussion of post hoc analyses of clinical studies and expert recommendations.

RESULTS

In Union for International Cancer Control (UICC) stages II/III, the tissue-based evaluation of microsatellite instability (MSI-H) contributes to individual therapy optimization through advice on adjuvant chemotherapy (colon cancer, UICC II) or, if necessary, individual neo-adjuvant therapy concepts via the use of immunotherapy (colon, rectal cancer, UICC II/III). From liquid biopsies, ctDNA was associated with minimal residual disease, which influences disease-free survival. In the metastatic stage (UICC IV), tissue-based determination of RAS and BRAF V600E mutations, MSI‑H and in the near future also HER2/neu overexpression should be performed. Broader molecular diagnostics to optimize first-line therapy (molecular hyperselection) shows little additional benefit. ctDNA can be used for longitudinal monitoring of clonal tumor evolution or as an alternative to invasive diagnostics in patients.

CONCLUSIONS

Molecular pathological diagnostics from tissue and blood complement each other and should be used in a targeted and meaningful way according to the underlying question.

Targeting and engineering biomarkers for prostate cancer therapy

Prostate cancer (PCa) is the second most commonly occurring cancer among men worldwide. Although the clinical management of PCa has significantly improved, a number of limitations have been identified in both early diagnosis and therapeutic treatment. Because multiple studies show that prostate-specific antigen (PSA) screening frequently results in overdiagnosis and overtreatment, the use of PSA alone as a diagnostic marker for PCa screening has been controversial. For individuals with locally advanced or metastatic PCa, androgen deprivation therapy (ADT) is the standard initially successful treatment; nonetheless, the majority of patients will eventually develop lethal metastatic castration-resistant prostate cancer (CRPC). Alternative treatment options, including chemo-, immuno-,or radio-therapy, can only prolong the survival of CRPC patients for several months with the most developing resistance. Considering this background, there is an urgent need to discuss about selective prostate-specific biomarkers that can predict clinically relevant PCa diagnosis and to develop biomarker-driven treatments to counteract CRPC. This review addresses several PCa-specific biomarkers that will assist physicians in determining which patients are at risk of having high-grade PCa, focusing on the clinical relevance of these biomarker-based tests among PCa patients. Secondly, this review highlights the effective use of these markers as drug targets to develop precision medicine or targeted therapies to counteract CRPC. Altogether, translating this biomarker-based research into the clinic will pave the way for the effective execution of personalized therapies for the benefit of healthcare providers, the biopharmaceutical industry, and patients.

The impact of liquid biopsy in breast cancer: Redefining the landscape of non-invasive precision oncology

Breast cancer (BC) remains a leading cause of morbidity and mortality among women worldwide, necessitating the development of innovative diagnostic and monitoring strategies. Liquid biopsy (LB), a minimally invasive approach that analyzes circulating tumor cells (CTCs), cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), extracellular vesicles (EVs), and other tumor-derived biomarkers in body fluids, has emerged as a transformative tool in BC management. This review comprehensively explores the role of LB in early detection, disease monitoring, treatment stratification, and resistance surveillance in BC. We discuss the latest advancements in LB technologies, including next-generation sequencing (NGS), digital PCR, and single-cell analysis, highlighting their sensitivity and specificity. Additionally, we examine the clinical utility of LB in guiding personalized therapy, particularly in the context of hormone receptor-positive, HER2positive, and triple-negative BC subtypes. Despite its promise, several challenges, including standardization, validation, and integration into clinical practice, remain to be addressed. By summarizing current evidence and future directions, this review underscores the potential of LB to revolutionize BC diagnosis and treatment, paving the way for a more precise and dynamic approach to disease management.

Cell competition as an emerging mechanism and therapeutic target in cancer

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

A novel KRAS exon 2 drop-off digital PCR assay for mutation detection in cell-free DNA of cancer patients

BACKGROUND

KRAS exon 2 mutations are highly prevalent in human malignancies, making them attractive targets for detection and monitoring in cell-free DNA (cfDNA) of cancer patients. Drop-off assays designed for digital polymerase chain reaction (ddPCR drop-off) span entire mutational hotspots and detect any mutated allele within the covered region, overcoming a major limitation of mutation-specific ddPCR assays. We therefore set out to develop a novel KRAS codon 12/13 ddPCR drop-off assay for the robust, highly sensitive and specific detection of KRAS exon 2 hotspot mutations in cfDNA.

METHODS

We designed, optimized and extensively validated a KRAS codon 12/13 ddPCR drop-off assay. We compared assay performance to a commercially available KRAS multiplex assay. For clinical validation, we analyzed plasma samples collected from patients with KRAS-mutated gastrointestinal malignancies.

RESULTS

Limit of detection of the newly established ddPCR drop-off assay was 0.57 copies/µL, limit of blank was 0.13 copies/µ. The inter-assay precision (r2) was 0.9096. Our newly developed KRAS ddPCR drop-off assay accurately identified single nucleotide variants in 35/36 (97.2%) of circulating tumor DNA-positive samples from the patient validation cohort. Assay cross-validation showed that the newly established KRAS codon 12/13 ddPCR drop-off assay outperformed a commercially available KRAS multiplex ddPCR assay in terms of specificity. Moreover, the newly developed assay proved to be suitable for multiplexing with mutation-specific probes.

CONCLUSION

We developed and clinically validated a highly accurate ddPCR drop-off assay for KRAS exon 2 hot-spot detection in cfDNA with broad applicability for clinic and research.

Burden and projections of malignant neoplasm of bone and articular cartilage in China: an analysis for the global burden of disease study 2021

BACKGROUND

Malignant neoplasm of bone and articular cartilage (MNBAC) represents one of the most prevalent malignant tumours among adolescents. Assessing its disease burden trends is critical for formulating prevention strategies. This study aims to evaluate the temporal trends of MNBAC burden in China, project future trajectories over the next 15 years, and compare these patterns with global benchmarks.

METHODS

Data on incidence, prevalence, deaths, and disability-adjusted life years (DALYs) were extracted from the Global Burden of Disease (GBD) database 2021. Joinpoint regression analysed temporal trends, while decomposition analysis was used to investigate the impact of aging, population growth, and epidemiological factors on the deaths and DALYs rates of MNBAC. Additionally, we conducted BPAC model to project future trends to 2036. Spearman correlation assessed associations between the burden of MNBAC and the socio-demographic Index (SDI).

RESULTS

In 2021, China's age-standardised incidence rate (ASIR), age-standardised prevalence rate (ASPR), age-standardised mortality rate (ASMR) and age-standardised DALYs rate (ASDR) for MNBAC were 1.42, 9.16, 0.93, and 29.52 per 100,000 population, respectively. Compared to 1990, these metrics increased by 118.46%, 125.62%, 60.34%, and 46.43%. Age-specific analyses revealed a bimodal burden pattern globally, peaking in adolescent and elderly populations. Joinpoint regression identified fluctuating trends in China (initial declining, subsequent rise, and then in decline), contrasting with global pattern. Decomposition analysis indicated that the increasing MNBAC burden in China was primarily driven by population aging and epidemiological changes, whereas globally, population growth played a more significant role. Projections indicated modest declines in MNBAC burden for China and globally by 2036. Spearman correlation analysis showed that the ASIR and ASPR of MNBAC in China and globally were significantly positively correlated with SDI (P < 0.05), and the ASMR and ASDR of MNBAC were also positively correlated with SDI, but not significantly.

CONCLUSIONS

This analysis underscores the substantial burden of MNBAC in China, surpassing global trends. While projections suggest gradual declines, the persistent high disability burden in youth and elderly populations necessitates strengthened screening protocols and prevention strategies. These findings provide critical epidemiological evidence for optimizing MNBAC management policies.

Diagnostic Significance in Estimating Tumor Burden Using Extracellular Salivary Biomarkers in Gastric Cancer Patients

Background: We investigated the possibility of predicting tumor burden with salivary extracellular RNA (exRNA) biomarkers in gastric cancer patients. Methods: Saliva samples were prospectively collected from 50 gastric cancer patients who underwent gastrectomy with curative intent. Approximately 5 mL of saliva was collected before surgery and on the 5th to 7th days after surgery. The expression of three mRNAs (SPINK7, PPL, and SEMA4B) and two miRNAs (miR140-5p and miR301a) that were previously validated was determined by reverse transcription quantitative real-time PCR. Results: There were significant differences in the pre-operative expression of PPL (p = 0.025), SEMA4B (p = 0.012), and miR140-5p (p = 0.036) between pathologic stage I/II and III/IV groups. The area under the curve (AUC) of each respective multivariable model in predicting stage III/IV, which was adjusted for age and sex, was 75.4% (PPL), 82.5% (SEMA4B), and 75.5% (miR140-5p). In the multivariable model, including all three biomarkers, the AUC was 89.2%. On the other hand, none of the conventional tumor markers (CEA, CA19-9, and CA72-4) could predict tumor burden before surgery. The AUC of the multivariable model, including CEA, CA19-9, and CA72-4, was 67.2%, 66.2%, and 67.4%, respectively. When all three tumor markers were included in the multivariable model, the AUC was 70.5%. Conclusions: Noninvasively detected salivary biomarkers have been shown to have higher diagnostic accuracy than conventional tumor markers detected by invasive blood tests for estimating pre-operative tumor burden. This study demonstrates the potential utility of these biomarkers in pre-operative risk assessment and monitoring surgical treatment response to gastric cancer.

Investigation of Body Fluids Intervention Impact on Aptamer Screening via Capillary Electrophoresis

Aptamers have presented considerable potential for disease diagnoses but still face a great challenge from the discrepancy between their screening conditions and real application in body fluid matrices (BFMs). In this study, we investigated the impact of BFM intervention on aptamer screening based on CE efficient separation and introduced adaptive screening strategies directly under the BFM background. Five BFMs, including serum, tears, artificial cerebrospinal fluid, saliva, and embryonic fluid, demonstrated the potential differentiating effects on aptamer screening based on the characterization of their "fingerprint-like profile" and their interactions with ssDNA libraries. Besides, the matrix effects of the five BFMs were quantified by calculating kinetic parameters derived from binding investigations between disease marker protein-spiked BFMs and ssDNA libraries. Through quantitative evaluation, two tailored SELEX strategies were introduced in BFM-intervened aptamer screening: spiking foreign proteins to the BFMs, and targeting proteins naturally abundant in BFMs. As proof of concept, we completed aptamer screenings for prolactin-induced protein (serum, spiked target) and human lactoferrin (tears, natural target) via CE-SELEX that demonstrated its adaptability in "splitting" BFM interference and achieving a clear collection of target-ssDNA complex. This study highlighted the critical importance of incorporating BFMs into SELEX and provided two tailored strategies that are worthy of choice for effective aptamer discovery, advancing the practical utility of aptamers.

Coupling Immunoprecipitation with Multiplexed Digital PCR for Cell-Free DNA Methylation Detection in Small Plasma Volumes of Early-Onset Colorectal Cancer

Colorectal cancer (CRC) remains a major global health challenge, with an increasing incidence of early-onset cases among young adults. Targeted analysis of cell-free DNA (cfDNA) methylation in blood has emerged as a promising minimally invasive diagnostic approach. While digital PCR (dPCR) offers high sensitivity and low turnaround times, conventional bisulfite-based dPCR assays require large plasma volumes due to cfDNA degradation, limiting clinical feasibility. To overcome this limitation, we developed a bisulfite-free, low-plasma-volume assay by coupling cell-free methylated DNA immunoprecipitation (cfMeDIP) with multiplexed dPCR for methylation detection. Assays were designed for CRC targets based on publicly available bisulfite-based plasma data and optimized for native, bisulfite-untreated cfDNA. The cfMeDIP-dPCR assays were first developed and optimized on circulating tumor DNA surrogates derived from HCT116 cells and subsequently validated in a pilot study, including 32 early-onset CRC (EO-CRC) patients and 29 non-CRC individuals. Methylation ratios, defined as the proportion of methylated to total cfDNA copies per marker, served as a diagnostic indicator. Three out of four selected markers (SEPT9, KCNQ5, and C9orf50) were successfully adapted, with significantly higher methylation ratios (p ≤ 0.001) in the EO-CRC cohort. KCNQ5 demonstrated the highest diagnostic performance, achieving an 85% sensitivity at a 90% specificity, with methylation ratios correlating with the tumor stage. This study presents the first cfMeDIP-dPCR approach, demonstrating its potential as a sensitive liquid biopsy assay. Requiring only 0.5 mL of plasma, i.e., more than 20 times less than a sensitivity-matched bisulfite-based assay, cfMeDIP-dPCR facilitates clinical implementation for CRC and other diseases with epigenetic signatures.

Circulating exosomal miR-17-92 cluster serves as a novel noninvasive diagnostic marker for patients with gastric cancer

BACKGROUND

Gastric cancer (GC) is among the most common malignant tumors and remains a leading cause of cancer-related mortality worldwide. Furthermore, exosomal miRNAs are regarded as promising noninvasive biomarkers for diagnosing malignant tumors.

AIM

To investigate the expression of exosomal miR-17-92 clusters and develop a potential biomarker for GC diagnosis

METHODS

Exosomes were isolated from serum samples obtained from 72 GC patients and 20 healthy controls. The isolated exosomes were validated using transmission electron microscopy, nanoparticle tracking analysis, and western blotting. Exosomal RNA was then extracted, and the expression profile of the miR-17-92 cluster was analyzed using qRT-PCR. Statistical methods were employed to evaluate the relationship between the serum exosomal miR-17-92 cluster expression and the clinicopathological parameters of GC patients as well as to assess the diagnostic utility of these miRNAs.

RESULTS

The expression of four members of the exosomal miR-17-92 cluster-miR-17, miR-18, miR-19a, and miR-92-was significantly upregulated in the serum samples of patients with GC compared with those of healthy controls. The miR-17-92 cluster panel demonstrated substantially higher clinical diagnostic value for GC than any individual component or pair. Additionally, the expression of traditional tumor biomarkers-carcinoembryonic antigen and carbohydrate antigen 19-9-was significantly elevated in the serum of patients with GC compared with that of healthy controls. Each biomarker, whether alone or in combination, effectively differentiated the patients from healthy controls. Furthermore, a combined panel of the two traditional tumor biomarkers and the four miR-17-92 cluster members exhibited the highest diagnostic accuracy for GC. Elevated miR-17-92 expression was also strongly associated with tumor size, tumor depth, lymph node metastasis, distant metastasis, and tumor-node-metastasis stage.

CONCLUSION

Our findings revealed that the circulating exosomal miR-17-92 cluster may be used as a potential noninvasive biomarker to improve diagnostic efficiency for GC.

Research trends and hotspots of circulating tumor DNA in colorectal cancer: a bibliometric study

Introduction

Colorectal cancer (CRC) is the third most common cancer worldwide and the second leading cause of cancer-related deaths. The current standard of care for patients with early-stage CRC includes surgical resection and, in selected patients, adjuvant chemotherapy. Circulating tumor DNA (ctDNA) testing is an important component of liquid biopsy, and with the development of testing technology, its value for clinical application has attracted widespread attention. The aim of this study was to help researchers review what has been achieved and better understand the direction of future research through bibliometric analysis.

Methods

We used the Web of Science Core Collection database to search for ctDNA in CRC-related articles published between 2014 - 2023. Bibliometric analyses of major keywords, authors, countries, institutions, literature and journals in the field were performed using CiteSpace and VOSviewer.

Results

The number of publications in the field has continued to increase over the last decade. The United States has the highest number of publications, and Italian research scholars have made outstanding contributions. Cancers is the journal with the highest number of publications.

Conclusion

This study systematically summarizes the research findings in the field of ctDNA in CRC from 2014 to 2023 and describes the research hotspots and trends worldwide that can guide future research.

Positive preoperative circulating tumor cells level associated with lymph node metastasis in papillary thyroid carcinoma patients with capsular invasion

OBJECTIVE

Capsular invasion in papillary thyroid cancer(PTC) refers to thyroid cancer penetrating the capsule without attaching to the surrounding tissue. Patients with and without capsular invasion may differ in the likelihood of lymph node metastasis(LNM). The purpose of this study is to study the relationship between circulating tumor cells(CTCs) and LNM in PTC with or without capsular invasion.

METHODS

The clinical records of patients (age, gender, CTCs, thyroid function, Hashimoto's thyroiditis, lesions number, lesions diameter, capsular invasion, clinical stage, and LNM) were analyzed retrospectively. The relationship between CTCs level and LNM was analyzed. Logistic regression analyses were used to evaluate the relationship between CTCs and LNM after adjusting for confounding factors.

RESULTS

A total of 746 PTC patients were included, and 320 patients with capsular invasion and 426 without. The patients with capsular invasion had higher proportions of multifocality, maximum lesion diameter > 1 cm, T3-T4 stage, and LNM than patients without (all p < 0.05). In multivariate logistic regression analyses, maximum lesion diameter > 1 cm (odds ratio(OR): 4.108, 95% confidence interval(CI): 2.459-6.862, p < 0.001) was associated with LNM in patients without capsular invasion; positive preoperative CTCs levels (OR: 1.705, 95% CI: 1.023-2.842, p = 0.041), multifocality (OR: 2.811, 95% CI: 1.669-4.736, p < 0.001), and maximum lesion diameter > 1 cm (OR: 3.233, 95% CI: 1.884-5.546, p < 0.001) were associated with LNM in patients with capsular invasion.

CONCLUSIONS

Maximum lesion diameter > 1 cm was associated with LNM in PTC patients with and without capsular invasion. Positive preoperative CTCs levels and multifocality were associated with LNM in patients with capsular invasion, but not in patients without capsular invasion.

Therapeutic potential of stem cells in colorectal cancer management: Current trends and future prospects

Colorectal cancer (CRC) ranks among the leading causes of cancer-related morbidity and mortality worldwide. Despite progress in understanding its molecular intricacies, the management of CRC, especially in advanced stages, remains a significant clinical hurdle. This review delves into the evolving landscape of stem cell-based therapeutic strategies in CRC, with a specific focus on the interplay between cancer stem cells (CSCs) and CRC pathogenesis and treatment resistance. Highlighting the pivotal roles of CSCs in tumor initiation, progression, metastasis, and recurrence, the review comprehensively examines their involvement in CRC, ranging from normal colonic tissue to cancer initiation. The potential of stem cells for medicinal purposes in CRC management is explored, encompassing diverse modalities such as transplantation, differentiation therapy, immunotherapy, and gene/cell-based approaches. Challenges and opportunities associated with these strategies are also evaluated, providing insights into their clinical potential and limitations. The review also appraises preclinical investigations contributing to the understanding of CRC and stem cells. Current clinical trials, patient stratification strategies, and regulatory considerations related to stem cell-based therapies in CRC are scrutinized. Furthermore, the review explores emerging trends and future directions, including developments in stem cell technologies and ethical considerations. It highlights the transformative potential of stem cell-based therapeutic strategies in CRC.

Accelerating Cleavage Activity of CRISPR-Cas13 System on a Microfluidic Chip for Rapid Detection of RNA

It is extremely advantageous to detect nucleic acid levels in the early phases of disease management; such early detection facilitates timely treatment, and it can prevent altogether certain cancers and infectious diseases. A simple, rapid, and versatile detection platform without enzymatic amplification for both short and long sequences would be highly desirable in this regard. Our study addresses this need by introducing IMACC, an ICP-based Microfluidic Accelerator Combined with CRISPR, for amplification-free nucleic acid detection. It exploits electrokinetically induced ion concentration polarization (ICP) to concentrate target nucleic acids and CRISPR reagents near the depletion zone boundary within a microfluidic channel. This localized accumulation accelerates the CRISPR-guided promiscuous cleavage of reporter molecules while enhancing their fluorescence signals simultaneously. Simultaneous accumulation of RNA and ribonucleoproteins (RNP) in confined spaces was validated experimentally and numerically, showing overlapping regions. IMACC enabled detection of miRNA-21 (22 bp) down to 10 pM within 2 min of ICP. IMACC ensured CRISPR specificity (single mismatch (N = 1) sensitivity) during ICP, as shown by off-target and mismatch sequence experiments. IMACC was applied to long RNA samples (i.e., SARS-CoV-2), but it statistically remained challenging at this point due to nonlinear intensity trends with copy numbers and large deviations. IMACC enabled rapid detection of short RNAs such as microRNAs using only basic CRISPR reagents in a single microfluidic channel, eliminating the need for extra enzymes or buffer sets, streamlining workflow and reducing turnaround time. IMACC has the potential to advance CRISPR diagnostics and holds promise for improved detection and future prescreening applications.

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

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

Laryngeal Cancer in the Modern Era: Evolving Trends in Diagnosis, Treatment, and Survival Outcomes

Background/Objectives: Laryngeal cancer (LC), predominantly squamous cell carcinoma (SCC), represents a considerable health burden worldwide. Tumour subsite heterogeneity (supraglottic, glottic, subglottic) influences clinical behavior and outcomes. This review synthesizes current knowledge on epidemiology, risk factors, diagnostics, histological variants, biomarkers, treatment modalities, and survival. Results: This narrative review synthesizes current literature on the epidemiology, risk factors, diagnosis, histological variants, biomarkers, and prognosis of LC. The review highlights the critical influence of tumour sites (supraglottic, glottic, subglottic) on metastatic patterns and survival. Key risk factors of LC include tobacco and alcohol use, human papillomavirus (HPV) infection, and occupational exposures. The diagnostic process encompasses clinical examination, endoscopy, biopsy, and imaging. Several biomarkers that aid in diagnosis, treatment plan determination, and prognosis prediction have been established. These biomarkers include long noncoding RNAs, cell cycle regulators, apoptosis regulators, oncogenes, tumour suppressor genes, growth factor pathway components, angiogenic factors, structural proteins, sex hormone receptors, and immunological markers. Current treatment modalities range from organ-preserving surgery and radiotherapy to combined chemoradiotherapy and total laryngectomy. Finally, survival data are presented and stratified by stage and subsite. Conclusions: The review underscores the need for a multidisciplinary approach to LC management, integrating clinical, pathological, and molecular information to optimize patient outcomes.

Mechanical Conditioning (MeCo) Score Progressively Increases Through the Metastatic Cascade in Breast Cancer via Circulating Tumor Cells

BACKGROUND

The mechanical conditioning (MeCo) score is a multigene expression signature that is acquired by cancer cells in the primary breast tumor and is reflective of their responsiveness to ECM stiffness caused by tumor fibrosis. Chromatin remodeling downstream of mechanotransduction allows cancer cells to retain these acquired aggressive features even in the absence of mechanical stimulation from the primary tumor microenvironment, for instance, after dissemination through systemic circulation during metastasis. Importantly, patients who have high MeCo score tumors are at higher risk of developing metastatic breast cancer, compared to those with low MeCo scores. Moreover, circulating tumor cells (CTCs) are associated with a higher rate of metastatic dissemination, making CTC detection in the circulation of patients with breast cancer a significant prognostic biomarker for breast cancer metastasis. Beyond their enumeration per blood volume units, specific prognostic features of CTCs are not fully explored. We sought to determine whether MeCo scores increase stepwise along the metastatic cascade, from primary tumors to CTCs to distant metastatic colonization, using patient-matched biopsies.

METHODS

CTCs were isolated from the peripheral blood of two patient cohorts: patients with early-stage breast cancer using immunomagnetic enrichment/FACS methodology; and patients with late-stage breast cancer using the ANGLE Parsortix microfluidics system. Gene expression profiling using RNA-seq was performed on CTCs and matched primary tumors (PTs) in the early-stage cohort, and on CTCs and matched metastases (METs) for the late-stage cohorts. A quantile normalization approach was used to allow comparison across cohorts and MeCo scores were computed for all samples. The Wilcoxon matched-pairs signed rank test was performed for the comparison of MeCo scores from matching samples within each cohort; the Mann-Whitney unpaired test was used to compare MeCo scores of CTCs across cohorts.

RESULTS

In 12 pairs of patients with early-stage breast cancer, MeCo scores in CTCs were significantly higher than in their matched PTs (p = 0.026). Additionally, in 26 pairs of metastatic patient CTCs and METs, MeCo scores were significantly higher in METs compared to matched CTCs (p = 0.0004). MeCo scores of CTCs were similar between patients with early- and late-stage breast cancers, despite differing CTC isolation strategies (epitope-dependent and microfluidics size gradient). Notably, 98% of the genes in the MeCo score were present across evaluable CTC, MET, and PT samples.

CONCLUSIONS

Our results show that the MeCo score is higher in CTCs than in PTs, and higher in METs compared to CTCs, in early- and late-stage breast cancer, respectively (i.e., PT < CTC < MET). Therefore, the MeCo score is progressively higher throughout the metastatic cascade in breast cancer. These findings demonstrate that mechanical conditioning from primary tumors is retained during metastatic progression, after mechanical induction by ECM stiffness is lost, as cancer cells disseminate through systemic circulation. Additionally, these findings support that cancer cells with higher MeCo scores are more competent with-and potentially selected for-metastatic progression. Importantly, these findings provide a novel feature of CTCs, mechanical conditioning (MeCo), which is associated with higher capacity for metastasis. Furthermore, since the CTC MeCo score is elevated even in early-stage breast cancer, it could provide, in addition to CTC enumeration, a potential prognostic indicator to improve metastatic risk assessment in early disease.

Clinical value of circulating tumor DNA for patients with epithelial ovarian cancer

Despite progress in recent years, epithelial ovarian cancer remains a pathology with a poor prognosis, primarily because of late and invasive diagnosis. Conventional follow-up relies on imaging, CA125, and predictive tools such as KELIM-CA125 and the chemotherapy response score. However, these methods are non-specific and result in delays before obtaining results. Recently, many research teams have focused on liquid biopsies, which provide direct access to tumor material in biological fluids. This review examines the clinical potential of circulating tumor DNA (ctDNA) in epithelial ovarian cancer. A systematic search of the PubMed database was conducted. Inclusion criteria were studies published in English, original research articles, reviews, or meta-analyses focused on ctDNA and ovarian cancer. Exclusion criteria included non-peer-reviewed sources, articles with insufficient data, and studies not directly related to the topic. In epithelial ovarian cancer, ctDNA allows quantitative evaluation of tumor burden and qualitative analysis by detecting specific tumor DNA variations, such as epigenetic modifications or genetic mutations. Furthermore, its half-life is less than 2 hours, enabling dynamic monitoring of tumor evolution. This capability could facilitate earlier diagnosis, better screening, and more effective therapeutic follow-up. The qualitative approach also has the potential to predict chemoresistance. Technologies used to detect ctDNA in blood include quantitative polymerase chain reaction, digital polymerase chain reaction, and next-generation sequencing, which allow quantification and identification of DNA molecule modifications. CtDNA is a promising biomarker for epithelial ovarian cancer and could address several challenges in its management. However, further research is needed to establish its role in routine clinical practice, particularly, to identify a detection method that is highly sensitive, specific, and generalizable to a wide patient population.

Binary classification of gynecological cancers based on ATR-FTIR spectroscopy and machine learning using urine samples

Making an early diagnosis of cancer still in the early stages, when completely asymptomatic, is the challenge modern medicine has been setting for several decades. In gynecology, no effective screening has yet been found and approved for endometrial and ovarian cancer. Mammography is an effective screening method for Breast Cancer, as well as Pap Test for Cervical Cancer, but they are underused in third world countries because of their expensive and specific instrumentation. Previous studies showed how "machine learning analysis methods" of the spectral information obtained from dried urine samples could provide good accuracy in differentiation between healthy and ovarian or endometrial cancer. In this study, we also apply ATR-FTIR spectrometry's practical, fast, and relatively inexpensive principles to liquid urine analysis from 309 patients undergoing surgical treatment for benign or malignant diseases (endometrium, breast, cervix, vulvar and ovarian cancer). The data obtained from those liquid samples were then analyzed to train a machine learning model to classify healthy VS cancer patients. We obtained an accuracy of > 91%, and we also identified discriminant wavelengths (2093, 1774 cm-1). These frequencies are close to already reported ones in other studies, indicating a possible association with tumor presence and/or progression.

A model workflow for microfluidic enrichment and genetic analysis of circulating melanoma cells

Circulating melanoma cells (CMCs) are responsible for the hematogenous spread of melanoma and, ultimately, metastasis. However, their study has been limited by the low abundance in patient blood and the heterogeneous expression of surface markers. The FDA-approved CellSearch platform enriches CD146-positive CMCs, whose number correlates with progression-free survival and overall survival. However, a single marker may not be sufficient to identify them all. The Parsortix system allows enrichment of CMCs based on their size and deformability, keeping them viable and suitable for downstream molecular analyses. In this study, we tested the strengths, weaknesses and potential convergences of both platforms to integrate the counting of CMCs with a protocol for their genetic analysis. Samples run on Parsortix were labeled with a customized melanoma antibody cocktail, which efficiently labeled and distinguished CMCs from endothelial cells/leukocytes. The capture rate of CellSearch and Parsortix was comparable for cell lines, but Parsortix had a higher capture rate in real-life samples. Moreover, double enrichment with both CellSearch and Parsortix succeeded in removing most of the leukocyte contamination, resulting in an almost pure CMC sample suitable for genetic analysis. In this regard, a proof-of-concept analysis of CMCs from a paradigmatic case of a metastatic uveal melanoma patient led to the identification of multiple genetic alterations. In particular, the GNAQ p.Q209L was identified as homozygous, while a deletion in BAP1 exon 9 was found hemizygous. Moreover, an isochromosome 8 and a homozygous deletion of the CDKN2A gene were detected. In conclusion, we have optimized an approach to successfully enrich and retrieve viable CMCs from metastatic melanoma patients. Moreover, this study provides proof-of-principle for the feasibility of a marker-agnostic CMC enrichment followed by CMC phenotypic identification and genetic analysis.Kindly check and confirm the processed contributed equally is correctly identify We confirm.

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

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

Advancing precision oncology with AI-powered genomic analysis

Multiomics data integration approaches offer a comprehensive functional understanding of biological systems, with significant applications in disease therapeutics. However, the quantitative integration of multiomics data presents a complex challenge, requiring highly specialized computational methods. By providing deep insights into disease-associated molecular mechanisms, multiomics facilitates precision medicine by accounting for individual omics profiles, enabling early disease detection and prevention, aiding biomarker discovery for diagnosis, prognosis, and treatment monitoring, and identifying molecular targets for innovative drug development or the repurposing of existing therapies. AI-driven bioinformatics plays a crucial role in multiomics by computing scores to prioritize available drugs, assisting clinicians in selecting optimal treatments. This review will explain the potential of AI and multiomics data integration for disease understanding and therapeutics. It highlight the challenges in quantitative integration of diverse omics data and clinical workflows involving AI in cancer genomics, addressing the ethical and privacy concerns related to AI-driven applications in oncology. The scope of this text is broad yet focused, providing readers with a comprehensive overview of how AI-powered bioinformatics and integrative multiomics approaches are transforming precision oncology. Understanding bioinformatics in Genomics, it explore the integrative multiomics strategies for drug selection, genome profiling and tumor clonality analysis with clinical application of drug prioritization tools, addressing the technical, ethical, and practical hurdles in deploying AI-driven genomics tools.

Identification of Driver Mutations and Risk Stratification in Lung Adenocarcinoma via Liquid Biopsy

BACKGROUND

Liquid biopsy using plasma cfDNA has been established as a tool for informing the management of advanced-stage NSCLC. However, its effectiveness in early lung cancer detection, including the identification of high-risk cases, remains to be determined.

METHODS

We analyzed plasma cfDNA and matched tumors from 117 stage I-IV lung adenocarcinoma cases and compared the variants identified across all stages using the Oncomine Precision Assay on the GenexusTM next-generation sequencing platform.

RESULTS

Cancer-specific mutations were detected in plasma from approximately 72% (84/117) of cases (all stages), with detection rates increasing by stage. Concordance between cfDNA and tumor tissue also increased with stage 0% (stage I), 19% (stage II), 45% (stage III), and 75% (stage IV). KRAS mutations were concordant in approximately 22% (6/27) of stage II and 46% (11/24) of stage III cases. Clinically important EGFR variants showed concordance in 11% (1/9) of stage II and 80% (8/10) in stage III/IV cases. Actionable mutations, targetable with FDA-approved drugs, were detected in 11% (4/37) of stage II, 27% (12/45) of stage III, and 55% (4/9) of stage IV cases, underscoring the potential of liquid biopsy for early detection of therapeutic targets. Moreover, co-occurring mutations with varying actionability were identified more frequently in plasma than in tumor tissues. Plasma detection of clinically important KRAS and EGFR variants was mostly associated with advanced-stage disease, suggesting the presence of these variants in plasma as a potential indication of disease progression.

CONCLUSIONS

Liquid biopsy holds promise for identifying high-risk lung adenocarcinoma cases and serves as a complementary diagnostic tool in advanced stages, enhancing disease management strategies.

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.

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

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

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

PURPOSE

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

EXPERIMENTAL DESIGN

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

RESULTS

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

CONCLUSIONS

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

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

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

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSION

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

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

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

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

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

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

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

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

The promising role of nanopore sequencing in cancer diagnostics and treatment

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

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

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