Unintrusive multi-cancer detection by circulating cell-free DNA methylation sequencing (THUNDER): development and independent validation studies

Early detection of multiple cancer types using multidimensional cell-free DNA fragmentomics

The multicancer early detection (MCED) test has the potential to enhance current cancer-screening methods. We evaluated a new MCED test that analyzes plasma cell-free DNA using genetic- and fragmentomics-based features from whole-genome sequencing. The present study included an internal validation cohort of 3,021 patients with cancer and 3,370 noncancer controls, and an independent cohort of 677 patients with cancer and 687 noncancer individuals. The results demonstrated an overall sensitivity of 87.4%, specificity of 97.8% and tissue-of-origin prediction accuracy of 82.4% in the independent validation cohort. Preliminary results from a prospective study of 3,724 asymptomatic participants showed a sensitivity of 53.5% (predominantly early stage cancers) and specificity of 98.1%. These findings indicate that the MCED test has strong potential to improve early cancer detection and support clinical decision-making.

ZC3H12D gene expression exhibits dual effects on the development and progression of lung adenocarcinoma

While precision oncology requires robust biomarkers, current predictors for lung adenocarcinoma (LUAD) often show limited clinical utility. This study investigates the multifaceted roles of ZC3H12D, a novel immunomodulatory molecule, in LUAD progression and tumor microenvironment regulation. Multi-omics analyses integrated ZC3H12D transcriptomic (511 tumors vs 59 normals), proteomic (74 tumors vs 69 normals), and single-cell RNA-seq data (15 tumors vs 11 normals). Immunohistochemistry validated ZC3H12D expression in 51 matched pairs. Computational biology approaches assessed immune infiltration, genomic instability (TMB/MSI/HRD), and pathway enrichment. Functional validation employed ZC3H12D knockdown in PC9 cells with colony formation and transwell assays. Multi-omics verification confirmed ZC3H12D upregulation in LUAD at both mRNA and protein levels (p < 0.001), with single-cell resolution revealing predominant localization in tumor-infiltrating immune cells. Moreover, ZC3H12D expression positively correlated with immune regulatory genes while inversely associating with genes involved in cellular respiration. Its expression was also linked to clinical markers such as TMB, MSI, HRD, tumor purity, and ploidy. Notably, high ZC3H12D expression revealed Immune-infiltrated microenvironment and favorable prognosis, despite silencing ZC3H12D resulted in significant inhibition of tumor cell proliferation and invasion in vitro (p < 0.001). Our findings demonstrate that high ZC3H12D expression in immune cells appears to enhance antitumor immune activity, whereas lower expression in malignant cells contributes to reduced cellular proliferation and migration. This spatial duality challenges conventional biomarker paradigms and provides mechanistic insights for developing cell type-targeted therapies.

Liquid biopsy in gynecological cancers: a translational framework from molecular insights to precision oncology and clinical practice

Liquid biopsy offers a noninvasive method to identify and monitor tumor-derived biomarkers, including circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), exosomes, microRNAs, and tumor-educated platelets, that provide real-time insights into the biological behavior of gynecological cancers. The detection of these markers has the potential to revolutionize cancer management by enabling earlier detection, providing novel data to personalize treatments, and predicting disease recurrence before clinical imaging and predicting disease recurrence before clinical imaging can confirm progression, thereby also guiding complex clinical decision-making. However, because this new "omics" layer introduces additional complexity, it must be fully understood, from its biological rationale to technical development and clinical integration, to prevent confusion or misapplication. That is why, focusing on 14 critical fields of inquiry, our goal is to map the current state of liquid biopsy from bench to bedside while highlighting practical considerations for clinical integration. Each topic integrates recent advances in assay sensitivity, biomarker variability, and data interpretation, underscoring how standardized protocols and robust analytical methods are pivotal for reliable results. We then translate these findings into disease-specific insights, examining how liquid biopsy could refine early detection, minimal residual disease assessment, and therapy guidance in endometrial, cervical, and ovarian cancers. Although several FDA-approved assays and promising commercial tests illustrate the field's rapid evolution, many translational hurdles remain, including the need for harmonized protocols, larger prospective clinical trials, and cost-effectiveness analyses. Crucially, our synthesis clarifies the pivotal role of interdisciplinary collaboration. Oncologists, laboratory scientists, and industry partners must align on standardized procedures and clinically relevant endpoints. Without such coordination, promising biomarkers may remain confined to research settings, limiting their practical benefit. Taken together, our review offers a translational view designed to contextualize liquid biopsy in gynecological oncology.

Multi-cancer early detection via a DNA methylation multiplex ddPCR-based blood test

Early cancer detection through minimally invasive methods is key for improving patient outcomes. We aimed to assess the performance of a novel blood-based test leveraging DNA methylation patterns for simultaneous detection of lung (LC), breast (BrC), colorectal (CRC), and prostate (PCa) cancer. Using The Cancer Genome Atlas (TCGA) methylation data, we identified shared hypermethylated gene promoters (ADCY4, MIR129-2, NID2, and MAGI2) among those four cancers. Validation was performed using online datasets, an in-house tissue set (N = 179), and plasma samples (N = 485) using droplet digital PCR (ddPCR). The test showed sensitivities of 81.82% (lung), 45% (breast), 69.23% (colorectal), and 44.14% (prostate), with 91.04% specificity. Overall, the PanCancer panel achieved 60.1% sensitivity and 87.4% specificity in detecting these four cancers. In early-stage cancers, sensitivities were slightly lower but followed a similar trend. Additionally, the test detected nine other cancer types in plasma. This proof-of-concept study demonstrates the feasibility of a single methylation-targeted blood test for multi-cancer detection, offering potential as an affordable and scalable screening tool for early cancer detection.

Cost-Effective Identification of Hepatocellular Carcinoma from Cirrhosis or Chronic Hepatitis Virus Infection Using Eight Methylated Plasma DNA Markers

Early detection of hepatocellular carcinoma (HCC) in patients with liver cirrhosis (LC) and/or hepatitis virus B/C infection (HVI) improves survival, highlighting the need for accurate, affordable diagnostic tools. Here, 11 methylated DNA markers (MDMs) are identified during marker discovery. In phase I, each selected MDM is validated in 175 plasma samples (HCC, n = 85; LC/HVI, n = 72) by the CO-methylation aMplification rEal-Time PCR (COMET) assay. Of these, 8 MDMs are qualified for phase II study, where a logistic regression model (COMET-LR) is trained and validated with 336 plasma samples (HCC, n = 211; LC/HVI, n = 113; training vs validation, 2:1). In the validation, the COMET-LR achieved 90.0% sensitivity at 97.4% specificity. Notably, sensitivity in patients with TNM stage I, diameter<3 cm, AFP-negative (<20 ng mL-1), PIVKA-II-negative (<40 mAU mL-1) is 82.4%, 77.8%, 88.6%, and 85.7%, respectively. The COMET-LR outperformed multiple protein markers (AFP, AFP-L3, and PIVKA-II) and published scores for HCC screening (GALAD, Doylestown, and ASAP), in terms of both sensitivity and specificity. The assay represents a significant advancement in addressing the unmet need for accurate, non-invasive, accessible, and cost-effective early detection tools for LC/HVI individuals. Further validation in a prospective cohort is warranted.

Performance of Liquid Biopsy-Based Multi-Omics Biomarkers for Early Detection of Gynecological Malignancies: A Prospective Study (PERCEIVE-I)

Liquid biopsy is a promising approach for early detection of gynecological malignancies. In the PERCEIVE-I study, gynecological Cancer cases (n = 249) and age-matched non-cancer controls (n = 249) are randomly divided into training and test sets at a 1:1 ratio. Data derived from multi-omics assays are obtained including a cell-free DNA methylation panel targeting ≈490 000 CpG sites, a mutation panel comprising 168 genes, and eight tumor protein markers. The results showed that the methylation model outperformed the protein and mutation models, demonstrating higher sensitivity (77.2%) while maintaining similar specificity. The multi-omics model combining methylation and protein markers achieved improved sensitivity (81.9%) with a good specificity (96.9%). The sensitivity varied across different stages, ranging from 66.7% to 100%. The model accurately identified the tissue of origin in 72.1% of cases. The superior performance of the methylation model highlights the potential of integrating multi-omics for non-invasive early detection of gynecological malignancies.

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.

DNA methylation in breast cancer: early detection and biomarker discovery through current and emerging approaches

Breast cancer remains one of the most common cancers in women worldwide. Early detection is critical for improving patient outcomes, yet current screening methods have limitations. Therefore, there is a pressing need for more sensitive and specific approaches to detect breast cancer in its earliest stages. Liquid biopsy has emerged as a promising non-invasive method for early cancer detection and management. DNA methylation, an epigenetic alteration that often precedes genetic changes, has been observed in precancerous or early cancer stages, making it a valuable biomarker. This review explores the role of DNA methylation in breast cancer and its potential for developing blood-based tests. We discuss advancements in DNA methylation detection methods, recent discoveries of potential DNA methylation biomarkers from both single-omics and multi-omics integration studies, and the role of machine learning in enhancing diagnostic accuracy. Challenges and future directions are also addressed. Although challenges remain, advances in multi-omics integration and machine learning continue to enhance the clinical potential of methylation-based biomarkers. Ongoing research is crucial to further refine these approaches and improve early detection and patient outcomes.

Effects of Ionizing Radiation on DNA Methylation Patterns and Their Potential as Biomarkers

DNA methylation is a common endogenous chemical modification in eukaryotic DNA, primarily involving the covalent attachment of a methyl group to the fifth carbon of cytosine residues, leading to the formation of 5-methylcytosine (5mC). This epigenetic modification plays a crucial role in gene expression regulation and genomic stability maintenance in eukaryotic systems. Ionizing radiation (IR) has been shown to induce changes in global DNA methylation patterns, which exhibit significant temporal stability. This stability makes DNA methylation profiles promising candidates for radiation-specific biomarkers. This review systematically examines the impact of IR on genome-wide DNA methylation landscapes and evaluates their potential as molecular indicators of radiation exposure. Advancing the knowledge of radiation-induced epigenetic modifications in radiobiology contributes to a deeper understanding of IR-driven epigenetic reprogramming and facilitates the development of novel molecular tools for the early detection and quantitative risk assessment of radiation exposure.

Plasma methylated HIST1H3G as a non-invasive biomarker for diagnostic modeling of hepatocellular carcinoma

Background

DNA methylation carrying epigenetic aberrations could potentially serve as a non-invasive tool for revolutionizing cancer diagnosis and monitoring. Here, we comprehensively evaluated the diagnostic value of plasma methylated HIST1H3G, and constructed diagnostic and prognostic models aimed at facilitating early detection and improving the prognosis of hepatocellular carcinoma (HCC).

Methods

The level of HIST1H3G promoter methylation in HCC tissues was evaluated based on the UALCAN database, followed by validation through serum samples collected from HCC patients. We recruited 205 participants, encompassing 70 HCC patients, 79 liver cirrhosis (LC) patients, 46 hepatitis patients and 10 HCC patients before and after treatment with either transarterial chemoembolization (TACE) or radiofrequency ablation (RFA). Analysis of plasma HIST1H3G was performed using methylation-specific quantitative polymerase chain reaction (qPCR). Diagnostic and prognostic prediction models were formulated using the random forest algorithm, and the performance of these models was rigorously evaluated through receiver operating characteristics curve (ROC) analysis.

Results

The methylation level of HIST1H3G was markedly elevated in both HCC tissues and plasma samples derived from HCC patients. HIST1H3G, PIVKA-II, total bilirubin (TBIL) and age were selected as the optimal markers and were included in the development of a diagnostic model. This model demonstrated superior accuracy in distinguishing HCC from high-risk populations, outperforming alpha-fetoprotein (AFP) in both the training cohort consisting of LC patients and the validation cohort comprising hepatitis patients. Additionally, HIST1H3G and albumin (Alb) were chosen to establish a prediction model for early HCC diagnosis, and this model exhibited a remarkable ability to identify early HCC. Furthermore, our prognostic prediction model proved effective in predicting the prognosis and survival outcomes of HCC patients.

Conclusion

Together, we identified and validated a diagnostic model that incorporated methylated HIST1H3G and clinically applicable serological indicators in HCC. The findings of our study established a pivotal foundation for the development of a non-invasive approach to identification and management in HCC.

AI-Derived Blood Biomarkers for Ovarian Cancer Diagnosis: Systematic Review and Meta-Analysis

BACKGROUND

Emerging evidence underscores the potential application of artificial intelligence (AI) in discovering noninvasive blood biomarkers. However, the diagnostic value of AI-derived blood biomarkers for ovarian cancer (OC) remains inconsistent.

OBJECTIVE

We aimed to evaluate the research quality and the validity of AI-based blood biomarkers in OC diagnosis.

METHODS

A systematic search was performed in the MEDLINE, Embase, IEEE Xplore, PubMed, Web of Science, and the Cochrane Library databases. Studies examining the diagnostic accuracy of AI in discovering OC blood biomarkers were identified. The risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy Studies-AI tool. Pooled sensitivity, specificity, and area under the curve (AUC) were estimated using a bivariate model for the diagnostic meta-analysis.

RESULTS

A total of 40 studies were ultimately included. Most (n=31, 78%) included studies were evaluated as low risk of bias. Overall, the pooled sensitivity, specificity, and AUC were 85% (95% CI 83%-87%), 91% (95% CI 90%-92%), and 0.95 (95% CI 0.92-0.96), respectively. For contingency tables with the highest accuracy, the pooled sensitivity, specificity, and AUC were 95% (95% CI 90%-97%), 97% (95% CI 95%-98%), and 0.99 (95% CI 0.98-1.00), respectively. Stratification by AI algorithms revealed higher sensitivity and specificity in studies using machine learning (sensitivity=85% and specificity=92%) compared to those using deep learning (sensitivity=77% and specificity=85%). In addition, studies using serum reported substantially higher sensitivity (94%) and specificity (96%) than those using plasma (sensitivity=83% and specificity=91%). Stratification by external validation demonstrated significantly higher specificity in studies with external validation (specificity=94%) compared to those without external validation (specificity=89%), while the reverse was observed for sensitivity (74% vs 90%). No publication bias was detected in this meta-analysis.

CONCLUSIONS

AI algorithms demonstrate satisfactory performance in the diagnosis of OC using blood biomarkers and are anticipated to become an effective diagnostic modality in the future, potentially avoiding unnecessary surgeries. Future research is warranted to incorporate external validation into AI diagnostic models, as well as to prioritize the adoption of deep learning methodologies.

TRIAL REGISTRATION

PROSPERO CRD42023481232; https://www.crd.york.ac.uk/PROSPERO/view/CRD42023481232.

Liquid Biopsy in HPV-Associated Head and Neck Cancer: A Comprehensive Review

Objectives: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer globally, with HPV-positive cases emerging as a distinct subtype with unique clinical and molecular characteristics. Current diagnostic methods, including tissue biopsy and imaging, face limitations in terms of invasiveness, static disease assessment, and difficulty in distinguishing recurrence from treatment-related changes. This review aimed to assess the potential of liquid biopsy as a minimally invasive tool for the diagnosis, treatment monitoring, and surveillance of HPV-associated HNSCC. Methods: This systematic review analyzed literature from PubMed/MEDLINE, Embase, and Web of Science, focusing on original research and reviews related to liquid biopsy applications in HPV-positive HNSCC. Included studies were evaluated based on the robustness of the study design, clinical relevance, and analytical performance of liquid biopsy technologies. Biomarker types, detection methods, and implementation strategies were assessed to identify advancements and challenges in this field. Results: Liquid biopsy technologies, including circulating HPV DNA, ctDNA, and extracellular vesicles, demonstrated high sensitivity (90-95%) and specificity (>98%) in detecting HPV-positive HNSCC. These methods enabled real-time monitoring of tumor dynamics, early detection of recurrence, and insights into treatment resistance. Longitudinal analysis revealed that biomarker clearance during treatment correlates strongly with patient outcomes. Conclusions: Liquid biopsy is a transformative diagnostic and monitoring tool for HPV-associated HNSCC, offering minimally invasive, real-time insights into tumor biology. While challenges remain in standardization and clinical implementation, ongoing research and technological innovations hold promise for integrating liquid biopsy into personalized cancer care, ultimately improving patient outcomes.

Circulating cell-free DNA methylation analysis of pancreatic cancer patients for early noninvasive diagnosis

Background

Aberrant hypermethylation of genomic DNA CpG islands (CGIs) is frequently observed in human pancreatic cancer (PAC). A plasma cell-free DNA (cfDNA) methylation analysis method can be utilized for the early and noninvasive detection of PAC. This study also aimed to differentiate PAC from other cancer types.

Methods

We employed the methylated CpG tandem amplification and sequencing (MCTA-Seq) method, which targets approximately one-third of CGIs, on plasma samples from PAC patients (n = 50) and healthy controls (n = 52), as well as from cancerous and adjacent noncancerous tissue samples (n = 66). The method's efficacy in detecting PAC and distinguishing it from hepatocellular carcinoma (HCC), colorectal cancer (CRC), and gastric cancer (GC) was evaluated. Additionally, a methylation score and typing system for PAC was also established.

Results

We identified a total of 120 cfDNA methylation biomarkers, including IRX4, KCNS2, and RIMS4, for the detection of PAC in blood. A panel comprising these biomarkers achieved a sensitivity of 97% and 86% for patients in the discovery and validation cohorts, respectively, with a specificity of 100% in both cohorts. The methylation scoring and typing systems were clinically applicable. Furthermore, we identified hundreds of differentially methylated cfDNA biomarkers between PAC and HCC, CRC, and GC. Certain combinations of these markers can be used in a highly specific (approximately 100%) algorithm to differentiate PAC from HCC, CRC, and GC in blood.

Conclusions

Our study identified cfDNA methylation markers for PAC, offering a novel approach for the early, noninvasive diagnosis of PAC.

Multicancer Detection (MCD) Testing in Gastrointestinal Cancers: An Evolving Tool for Early Diagnosis

PURPOSE OF REVIEW

The current review aims to summarize the benefits and limitations of the novel multicancer detection tests (MCD) for diagnosing gastrointestinal (GI) malignancies.

RECENT FINDINGS

Traditional cancer screening methods can reduce deaths in malignancies involving the GI tract. For GI cancers, screening options vary by type and often involve invasive techniques with limited sensitivity. MCDs offer a promising, non-invasive (simple blood draw) alternative by analyzing biomarkers such as cell-free DNA and RNA using advanced techniques and machine learning to detect cancers across multiple organ sites. Large studies like the PATHFINDER trial and THUNDER study have demonstrated the feasibility and accuracy of MCD assays in identifying cancer signals, with high sensitivity and specificity in some GI organs that lack routine screening tests (e.g., liver, pancreas, and stomach). Despite these advancements, MCD testing faces challenges, including high costs, lack of FDA approval, false positives, and limited data on clinical utility in reducing cancer-specific mortality. MCD should not be a substitute for age-appropriate cancer screenings but may complement existing methods, particularly for cancers with no current screening tools, such as cholangiocarcinoma and pancreatic cancer. Clinicians need to discuss the limitations of MCDs, including the potential for overdiagnosis, patient anxiety, and financial burden due to insurance coverage gaps. MCD is a promising, non-invasive test that can augment traditional cancer screening. As the role of MCD in cancer detection evolves, further research is essential to establish how it will be integrated into clinical practice, ensuring informed, shared decision-making with patients.

Epigenetic modifications in early stage lung cancer: pathogenesis, biomarkers, and early diagnosis

The integration of liquid biopsy with epigenetic markers offers significant potential for early lung cancer detection and personalized treatment. Epigenetic alterations, including DNA methylation, histone modifications, and noncoding RNA changes, often precede genetic mutations and are critical in cancer progression. In this study, we explore how liquid biopsy, combined with epigenetic markers, can provide early detection of lung cancer, potentially predicting onset up to 4 years before clinical diagnosis. We discuss the challenges of targeting epigenetic regulators, which could disrupt cellular balance if overexploited, and the need for maintaining key gene expressions in therapeutic applications. This review highlights the promise and challenges of using liquid biopsy and epigenetic markers for early-stage lung cancer diagnosis, with a focus on optimizing treatment strategies for personalized and precision medicine.

Liquid biopsy entering clinical practice: Past discoveries, current insights, and future innovations

In recent years, liquid biopsy has gained prominence as an emerging biomarker in cancer research, providing critical insights into tumor biology and metastasis. Technological advancements have enabled its integration into clinical practice, with ongoing trials demonstrating encouraging outcomes. Key applications of liquid biopsy include early cancer detection, cancer staging, prognosis evaluation, and real-time monitoring of tumor progression to optimize treatment decisions. In this review, we present a comprehensive conceptual framework for liquid biopsy, discuss the challenges in its research and clinical application, and highlight its significant potential in identifying therapeutic targets and resistance mechanisms across various cancer types. Furthermore, we explore the emerging role of liquid biopsy-based multicancer screening, which has shown promising advancements. Looking ahead, standardization, multi-omics coanalysis, and the advancement of precision medicine and personalized treatments are expected to drive the future development and integration of liquid biopsy into routine clinical workflows, enhancing cancer diagnosis and treatment management.

Multi-cancer early detection tests: Attributes for clinical implementation

Guideline-recommended screening programs exist for only a few single-cancer types, and these cancers represent less than one-half of all new cancer cases diagnosed each year in the U.S. In addition, these "single-cancer" standard of care (SoC) screening tests vary in accuracy, adherence, and effectiveness, though all are generally understood to lead to reductions in cancer-related mortality. Recent advances in high-throughput technologies and machine learning have facilitated the development of blood-based multi-cancer early detection (MCED) tests. The opportunity for early detection of multiple cancers with a single blood test holds promise in addressing the current unmet need in cancer screening. By complementing existing SoC screening, MCED tests have the potential to detect a wide range of cancers at earlier stages when patients are asymptomatic, enabling more effective treatment options and improved cancer outcomes. MCED tests are positioned to be utilized as a complementary screening tool to improve screening adherence at the population level, to broaden screening availability for individuals who are not adherent with SoC screening programs, as well as for those who may harbor cancers that do not have SoC testing available. Published work to date has primarily focused on test performance relating to sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). MCED tests will require approval through the pre-market approval pathway from the United States Food and Drug Administration. Additional studies will be needed to demonstrate clinical utility (i.e., improvements in health outcomes) and establish optimal implementation strategies, (i.e., testing intervals), follow-up and logistics of shared decision making. Here, we propose core attributes of MCED testing for which clinical data are needed to ideally position MCED testing for widespread use in clinical practice.

Bile-Derived cfDNA of Syncytin-1 and SLC7A11 as a Potential Molecular Marker for Early Diagnosis of Cholangiocarcinoma

PURPOSE

Liquid biopsy technology has received widespread attention in the early diagnosis of cholangiocarcinoma (CCA).

METHODS

We collected bile samples from 48 patients with CCA and 48 patients with gallstones at Shandong Provincial third Hospital. We quantified bile circulating free DNA (cfDNA) of syncytin-1 and SLC7A11, calculated the correlation between syncytin-1 and SLC7A11 expression and clinical parameters by Spearman rank correlation, plotted Receiver Operating Characteristic (ROC) curves, and compared the Area Under Curve (AUC) values to explored early diagnostic utility in patients.

RESULTS

We first found the bile cfDNA of syncytin-1 and SLC7A11 levels in CCA were higher than in gallstones (3.06 vs. 1.32, p < 0.001; 2.39 vs. 1.30, p < 0.001). And there was significant correlation between syncytin-1 and SLC7A11 expression (p = 0.025). Additionally, bile cfDNA of syncytin-1 or SLC7A11 was differentially expressed in gallstones, cholangiocarcinoma stage I-II, and cholangiocarcinoma stage III-IV (p < 0.001; p < 0.001). The AUC of bile cfDNA of syncytin-1 was 0.805 (p < 0.001, specificity of 87.0%), the AUC of bile cfDNA of SLC7A11 was 0.755 (p < 0.001, specificity of 80.4%), and combination of bile cDNA of syncytin-1/SLC7A11/CA19-9 markers improved diagnostic efficiency in CCA patients (AUC: 0.927, p < 0.001).

CONCLUSION

The bile cfDNA of syncytin-1 and SLC7A11 was high expression in cholangiocarcinoma, which may be used as a novel biomarker for early diagnosis.

Artificial intelligence and machine learning in cell-free-DNA-based diagnostics

The discovery of circulating fetal and tumor cell-free DNA (cfDNA) molecules in plasma has opened up tremendous opportunities in noninvasive diagnostics such as the detection of fetal chromosomal aneuploidies and cancers and in posttransplantation monitoring. The advent of high-throughput sequencing technologies makes it possible to scrutinize the characteristics of cfDNA molecules, opening up the fields of cfDNA genetics, epigenetics, transcriptomics, and fragmentomics, providing a plethora of biomarkers. Machine learning (ML) and/or artificial intelligence (AI) technologies that are known for their ability to integrate high-dimensional features have recently been applied to the field of liquid biopsy. In this review, we highlight various AI and ML approaches in cfDNA-based diagnostics. We first introduce the biology of cell-free DNA and basic concepts of ML and AI technologies. We then discuss selected examples of ML- or AI-based applications in noninvasive prenatal testing and cancer liquid biopsy. These applications include the deduction of fetal DNA fraction, plasma DNA tissue mapping, and cancer detection and localization. Finally, we offer perspectives on the future direction of using ML and AI technologies to leverage cfDNA fragmentation patterns in terms of methylomic and transcriptional investigations.

Unveiling DNA methylation: early diagnosis, risk assessment, and therapy for endometrial cancer

Endometrial cancer (EC), one of the most common gynecologic malignancies worldwide, poses a significant burden particularly among young women, with poor treatment outcomes and prognosis for advanced and recurrent patients. Epigenetic changes, encompassing DNA methylation, are involved in the occurrence and progression of tumors and hold promise as effective tools for screening, early diagnosis, treatment strategy, efficacy evaluation, and prognosis analysis. This review provides a comprehensive summary of DNA methylation-based early diagnostic biomarkers in EC, with a focus on recent valuable research findings published in the past two years. The discussion is organized according to sample sources, including cervical scraping, vaginal fluid, urine, blood, and tissue. Additionally, we outline the role of DNA methylation in EC risk assessment, such as carcinogenesis risk, feasibility of fertility preservation approaches, and overall prognosis, aiming to provide personalized treatment decisions for patients. Finally, we review researches on DNA methylation in resistance to first-line treatment of EC and the development of new drugs, and envision the future applications of DNA methylation in EC.

High-throughput methylation sequencing reveals novel biomarkers for the early detection of renal cell carcinoma

PURPOSE

Renal cell carcinoma (RCC) is a common malignancy, with patients frequently diagnosed at an advanced stage due to the absence of sufficiently sensitive detection technologies, significantly compromising patient survival and quality of life. Advances in cell-free DNA (cfDNA) methylation profiling using liquid biopsies offer a promising non-invasive diagnostic option, but robust biomarkers for early detection are current not available. This study aimed to identify methylation biomarkers for RCC and establish a DNA methylation signature-based prognostic model for this disease.

METHODS

High-throughput methylation sequencing was performed on peripheral blood samples obtained from 49 primarily Stage I RCC patients and 44 healthy controls. Comparative analysis and Least Absolute Shrinkage and Selection Operator (LASSO) regression methods were employed to identify RCC methylation signatures.Subsequently, methylation markers-based diagnostic and prognostic models for RCC were independently trained and validated using random forest and Cox regression methodologies, respectively.

RESULTS

Comparative analysis revealed 864 differentially methylated CpG islands (DMCGIs), 96.3% of which were hypermethylated. Using a training set from The Cancer Genome Atlas (TCGA) dataset of 443 early-stage RCC tumors and matched normal tissues, we applied LASSO regression and identified 23 methylation signatures. We then constructed a random forest-based diagnostic model for early-stage RCC and validated the model using two independent datasets: a TCGA set of 460 RCC tumors and controls, and a blood sample set from our study of 15 RCC cases and 29 healthy controls. For Stage I RCC tissue, the model showed excellent discrimination (AUC-ROC: 0.999, sensitivity: 98.5%, specificity: 100%). Blood sample validation also yielded commendable results (AUC-ROC: 0.852, sensitivity: 73.9%, specificity: 89.7%). Further analysis using Cox regression identified 7 of the 23 DMCGIs as prognostic markers for RCC, allowing the development of a prognostic model with strong predictive power for 1-, 3-, and 5-year survival (AUC-ROC > 0.7).

CONCLUSIONS

Our findings highlight the critical role of hypermethylation in RCC etiology and progression, and present these identified biomarkers as promising candidates for diagnostic and prognostic applications.

"Aging Clocks" Based on Cell-Free DNA

Aging is associated with systemic changes in the physiological and molecular parameters of the body. These changes are referred to as biomarkers of aging. Statistical models that link changes in individual biomarkers to biological age are called aging clocks. These tools facilitate a comprehensive evaluation of bodily health and permit the quantitative determination of the rate of aging. A particularly promising area for the development of aging clocks is the analysis of cell-free DNA (cfDNA), which is present in the blood and contains numerous potential biomarkers. This review explores in detail the fragmentomics, topology, and epigenetic landscape of cfDNA as possible biomarkers of aging. The review further underscores the potential of leveraging single-molecule sequencing of cfDNA in conjunction with long-read technologies to simultaneously profile multiple biomarkers, a strategy that could lead to the development of more precise aging clocks.

Multi-cancer early detection tests for general population screening: a systematic literature review

Background

General population cancer screening in the United Kingdom is limited to selected cancers. Blood-based multi-cancer early detection tests aim to detect potential cancer signals from multiple cancers in the blood. The use of a multi-cancer early detection test for population screening requires a high specificity and a reasonable sensitivity to detect early-stage disease so that the benefits of earlier diagnosis and treatment can be realised.

Objective

To undertake a systematic literature review of the clinical effectiveness evidence on blood-based multi-cancer early detection tests for screening.

Methods

Comprehensive searches of electronic databases (including MEDLINE and EMBASE) and trial registers were undertaken in September 2023 to identify published and unpublished studies of multi-cancer early detection tests. Test manufacturer websites and reference lists of included studies and pertinent reviews were checked for additional studies. The target population was individuals aged 50-79 years without clinical suspicion of cancer. Outcomes of interest included test accuracy, number and proportion of cancers detected (by site and stage), time to diagnostic resolution, mortality, potential harms, health-related quality of life, acceptability and satisfaction. The risk of bias was assessed using the quality assessment of diagnostic accuracy studies-2 checklist. Results were summarised using narrative synthesis. Stakeholders contributed to protocol development, report drafting and interpretation of review findings.

Results

Over 8000 records were identified. Thirty-six studies met the inclusion criteria: 1 ongoing randomised controlled trial, 13 completed cohort studies, 17 completed case-control studies and 5 ongoing cohort or case-control studies. Individual tests claimed to detect from 3 to over 50 different types of cancer. Diagnostic accuracy of currently available multi-cancer early detection tests varied substantially: Galleri® (GRAIL, Menlo Park, CA, USA) sensitivity 20.8-66.3%, specificity 98.4-99.5% (three studies); CancerSEEK (Exact Sciences, Madison, WI, USA) sensitivity 27.1-62.3%, specificity 98.9- 99.1% (two studies); SPOT-MAS™ (Gene Solutions, Ho Chi Minh City, Vietnam) sensitivity 72.4-100%, specificity 97.0-99.9% (two studies); Trucheck™ (Datar Cancer Genetics, Bayreuth, Germany) sensitivity 90.0%, specificity 96.4% (one study); Cancer Differentiation Analysis (AnPac Bio, Shanghai, China) sensitivity 40.0%, specificity 97.6% (one study). AICS® (AminoIndex Cancer Screening; Ajinomoto, Tokyo, Japan) screens for individual cancers separately, so no overall test performance statistics are available. Where reported, sensitivity was lower for detecting earlier-stage cancers (stages I-II) compared with later-stage cancers (stages III-IV). Studies of seven other multi-cancer early detection tests at an unclear stage of development were also summarised.

Limitations

Study selection was complex; it was often difficult to determine the stage of development of multi-cancer early detection tests. The evidence was limited; there were no completed randomised controlled trials and most included studies had a high overall risk of bias, primarily owing to limited follow-up of participants with negative test results. Only one study of Galleri recruited asymptomatic individuals aged over 50 in the United States of America; however, study results may not be representative of the United Kingdom's general screening population. No meaningful results were reported relating to patient-relevant outcomes, such as mortality, potential harms, health-related quality of life, acceptability or satisfaction.

Conclusions

All currently available multi-cancer early-detection tests reported high specificity (> 96%). Sensitivity was highly variable and influenced by study design, population, reference standard test used and length of follow-up.

Future work

Further research should report patient-relevant outcomes and consider patient and service impacts.

Study registration

This study is registered as PROSPERO CRD42023467901.

Funding

This award was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme (NIHR award ref: NIHR161758) and is published in full in Health Technology Assessment; Vol. 29, No. 2. See the NIHR Funding and Awards website for further award information.

Multi-Cancer Early Detection Tests: State of the Art and Implications for Radiologists

Multi-cancer early detection (MCED) tests are already being marketed as noninvasive, convenient opportunities to test for multiple cancer types with a single blood sample. The technology varies-involving detection of circulating tumor DNA, fragments of DNA, RNA, or proteins unique to each targeted cancer. The priorities and tradeoffs of reaching diagnostic resolution in the setting of possible false positives and negatives remain under active study. Given the well-established role of imaging in lesion detection and characterization for most cancers, radiologists have an essential role to play in selecting diagnostic pathways, determining the validity of test results, resolving false-positive MCED test results, and evaluating tradeoffs for clinical policy. Appropriate access to and use of imaging tests will also factor into clinical guidelines. Thus, all clinicians potentially involved with MCED tests for cancer screening will need to weigh the benefits and harms of MCED testing, including consideration of how the tests will be used alongside or in place of other screening options, how diagnostic confirmation tests should be selected, and what the implications are for policy and reimbursement decisions. Further, patients will need regular support to make informed decisions about screening using MCED tests in the context of their personal cancer risks, health-related values, and access to care.

Implementation of a Multicancer Detection (MCD) Test in a Tertiary Referral Center in Asymptomatic Patients: An 18-Month Prospective Cohort Study

OBJECTIVE

Multicancer Detection (MCD) tests, such as the GRAIL Galleri, offer a novel approach to cancer screening by detecting cancer-specific methylation patterns in cell-free DNA through a single blood sample. This study evaluated an 18-month implementation of MCD testing in a tertiary ambulatory internal medicine clinic.

PATIENTS AND METHODS

Between June 2022 and November 2023, 2244 asymptomatic (without symptoms attributed to cancer) patients underwent MCD testing. The study focused on operational workflows, patient and physician education, and diagnostic follow-up of positive results. Standardized materials, including electronic health record (EHR) workflows, FAQs, and diagnostic pathways, were developed to facilitate implementation. Challenges included managing false positives, patient anxiety, costs, and ethical considerations.

RESULTS

Of the 2244 patients tested, 17 (0.76%) had positive results, and 15 underwent further diagnostic evaluation. Cancer was confirmed in 11 (73.3%) patients, including cases of breast, colon, esophageal, lymphoma, ovarian, and pancreatic cancers. Four patients had no identifiable malignancy despite comprehensive work-up.

CONCLUSIONS

MCD testing is feasible in routine clinical workflows, with 73% of positive cases yielding cancer diagnoses. While promising, further research is required to assess long-term outcomes, cost-effectiveness, and optimal implementation strategies of cancer interception in broader healthcare settings.

Early Detection, Precision Treatment, Recurrence Monitoring: Liquid Biopsy Transforms Colorectal Cancer Therapy

Colorectal cancer (CRC) is a significant global health concern. We need ways to detect it early and determine the best treatments. One promising method is liquid biopsy, which uses cancer cells and other components in the blood to help diagnose and treat the disease. Liquid biopsies focus on three key elements: circulating tumor DNA (ctDNA), circulating microRNA (miRNA), and circulating tumor cells (CTC). By analyzing these elements, we can identify CRC in its early stages, predict how well a treatment will work, and even spot signs of cancer returning. This study investigates the world of liquid biopsy, a rapidly growing field. We want to understand how it can help us better recognize the molecular aspects of cancer, improve and diagnostics, tailor treatments to individual patients, and keep track of the disease over the long-term. We explored specific components of liquid biopsy, like extracellular vesicles and cell-free DNA, and how they are used to detect CRC. This review sheds light on the current state of knowledge and the many ways a liquid biopsy can be used in treating colorectal cancer. It can transform patient care, disease management, and clinical outcomes by offering non-invasive cancer-targeting solutions.

Development of a urine-based metabolomics approach for multi-cancer screening and tumor origin prediction

Background

Cancer remains a leading cause of mortality worldwide. A non-invasive screening solution was required for early diagnosis of cancer. Multi-cancer early detection (MCED) tests have been considered to address the challenge by simultaneously identifying multiple types of cancer within a single test using minimally invasive blood samples. However, a multi-cancer screening strategy utilizing urine-based metabolomics has not yet been developed.

Methods

We enrolled 911 cancer patients with 548 lung cancer (LC), 177 with gastric cancer (GC), and 186 with colorectal cancer (CRC), alongside 563 individuals with non-cancerous benign diseases and 229 healthy controls (HC) and investigated the metabolic profiles of urine samples. Participants were randomly allocated to discovery and validation cohorts. The discovery cohort was used for identifying multi-cancer and tissue-specific signatures to build the cancer screening and tumor origin prediction models, while the validation cohort was employed for assessing the performance of these models.

Results

We identified and annotated a total of 360 metabolites from the urine samples. Using the LASSO regression algorithm, 18 metabolites were characterized as urinary metabolic biomarkers and exhibited excellent discriminative performance between cancer patients and HC with AUC of 0.96 in the validation cohort. In comparison with the performance of traditional tumor markers CEA, the screening model performed higher sensitivity across the cancer stages, with a particularly increase in sensitivity among early-stage cancer patients. Moreover, the screening model also exhibited in high classification of cancers from non-cancerous group, comprising with HC and benign disease participants. Furthermore, two non-overlapping metabolic panels were selected to differentiate LC from Non-LC and GC from CRC with the AUC values of 0.87 and 0.83 in validation cohorts, respectively. Additionally, the model accurately predicted the origin of three lethal cancers: lung, gastric, and colorectal, with an overall accuracy of 0.75. The AUC values for LC, GC, and CRC were 0.88, 0.88, and 0.80, respectively.

Discussion

Our study demonstrates the potential of urine-based metabolomics for multi-cancer early detection. The approach offers non-invasive cancer screening, promising widespread implementation in population-based programs for early detection and improved outcomes. Further validation and expansion are needed for broader clinical applicability.

Leveraging CAR macrophages targeting c-Met for precision immunotherapy in pancreatic cancer: insights from single-cell multi-omics

BACKGROUND

Pancreatic cancer is known for its poor prognosis and resistance to conventional therapies, largely due to the presence of cancer stem cells (CSCs) and aggressive angiogenesis. Effectively targeting these CSCs and associated angiogenic pathways is crucial for effective treatment. This study leverages single-cell multi-omics to explore a novel therapeutic approach involving Chimeric Antigen Receptor (CAR) macrophages engineered to target the c-Met protein on pancreatic CSCs.

METHODS

We employed single-cell RNA sequencing to analyze pancreatic cancer tissue, identifying c-Met as a key marker of CSCs. CAR macrophages were engineered using a lentiviral system to express a c-Met-specific receptor. The phagocytic efficiency of these CAR macrophages against pancreatic CSCs was assessed in vitro, along with their ability to inhibit angiogenesis. The in vivo efficacy of CAR macrophages was evaluated in a mouse model of pancreatic cancer.

RESULTS

CAR macrophages demonstrated high specificity for c-Met + CSCs, significantly enhancing phagocytosis and reducing the secretion of angiogenic factors such as VEGFA, FGF2, and ANGPT. In vivo, these macrophages significantly suppressed tumor growth and angiogenesis, prolonging survival in pancreatic cancer-bearing mice.

CONCLUSION

CAR macrophages targeting c-Met represent a promising therapeutic strategy for pancreatic cancer, offering targeted elimination of CSCs and disruption of tumor angiogenesis. This study highlights the potential of single-cell multi-omics in guiding the development of precision immunotherapies.

Evaluation and integration of cell-free DNA signatures for detection of lung cancer

Cell-free DNA (cfDNA) analysis has shown potential in detecting early-stage lung cancer based on non-genetic features. To distinguish patients with lung cancer from healthy individuals, peripheral blood were collected from 926 lung cancer patients and 611 healthy individuals followed by cfDNA extraction. Low-pass whole genome sequencing and targeted methylation sequencing were conducted and various features of cfDNA were evaluated. With our customized algorithm using the most optimal features, the ensemble stacked model was constructed, called ESim-seq (Early Screening tech with Integrated Model). In the independent validation cohort, the ESim-seq model achieved an area under the curve (AUC) of 0.948 (95 % CI: 0.915-0.981), with a sensitivity of 79.3 % (95 % CI: 71.5-87.0 %) across all stages at a specificity of 96.0 % (95 % CI: 90.6-100.0 %). Specifically, the sensitivity of the ESim-seq model was 76.5 % (95 % CI: 67.3-85.8 %) in stage I patients, 100 % (95 % CI: 100.0-100.0 %) in stage II patients, 100 % (95 % CI: 100.0-100.0 %) in stage III patients and 87.5 % (95 % CI: 64.6%-100.0 %) in stage IV patients in the independent validation cohort. Besides, we constructed LCSC model (Lung Cancer Subtype multiple Classification), which was able to accurately distinguish patients with small cell lung cancer from those with non-small cell lung cancer, achieving an AUC of 0.961 (95 % CI: 0.949-0.957). The present study has established a framework for assessing cfDNA features and demonstrated the benefits of integrating multiple features for early detection of lung cancer.

Circulating tumour DNA and risk of recurrence in patients with asymptomatic versus symptomatic colorectal cancer

BACKGROUND

Multiple initiatives aim to develop circulating tumour DNA (ctDNA) tests for early cancer detection in asymptomatic individuals. The few studies describing ctDNA-testing in both asymptomatic and symptomatic patients report lower ctDNA detection in the asymptomatic patients. Here, we explore if asymptomatic patients differ from symptomatic patients e.g. by including a 'low-ctDNA-shedding' and 'less-aggressive' subgroup.

METHODS

ctDNA assessment was performed in two independent cohorts of consecutively recruited patients with asymptomatic colorectal cancer (CRC) (Cohort#1: n = 215, Cohort#2: n = 368) and symptomatic CRC (Cohort#1: n = 117, Cohort#2: n = 722).

RESULTS

After adjusting for tumour stage and size, the odds of ctDNA detection was significantly lower in asymptomatic patients compared to symptomatic patients (Cohort#1: OR: 0.4, 95%CI: 0.2-0.8, Cohort#2: OR: 0.7, 95%CI: 0.5-0.9). Further, the recurrence risk was lower in asymptomatic patients (Cohort#1: sHR: 0.6, 95%CI: 0.3-1.2, Cohort#2: sHR: 0.6, 95%CI: 0.4-1.0). Notably, ctDNA-negative asymptomatic patients had the lowest recurrence risk compared to the symptomatic patients (Cohort#1: sHR: 0.2, 95%CI: 0.1-0.6, Cohort#2: sHR: 0.3, 95%CI: 0.2-0.6).

CONCLUSIONS

Our study suggests that asymptomatic patients are enriched for a 'low-ctDNA-shedding-low-recurrence-risk' subgroup. Such insights are needed to guide ctDNA-based early-detection initiatives and should prompt discussions about de-escalation of therapy and follow-up for ctDNA-negative asymptomatic CRC patients.

Prevention of Ovarian Cancer: Where are We Now and Where are We Going?

PURPOSE OF REVIEW

To describe current and future strategies to reduce the burden of ovarian cancer through prevention.

RECENT FINDINGS

Current strategies in genetic testing are missing a substantial number of individuals at risk, representing a missed opportunity for ovarian cancer prevention. Past efforts at screening and early detection have thus far failed to improve ovarian cancer mortality, and novel techniques are needed. Surgical prevention is highly effective, but surgical menopause from oophorectomy has significant side effects. Novel surgical strategies aimed at reducing risk while minimizing these harms are currently being studied. To maximize ovarian cancer prevention, a multi-pronged approach is needed. We propose that more inclusive and accurate genetic testing to identify more individuals at risk, novel molecular screening and early detection, surgical prevention that maximizes quality of life while reducing risk, and broader adoption of targeted and opportunistic salpingectomy will together reduce the burden of ovarian cancer.

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

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

Multicancer Early Detection Tests: A State-of-the-Art Review for Otolaryngologists

Objective

To provide a review of the science and applicability of current multi-cancer early detection (MCED) tests for otolaryngologists.

Data Sources

PubMed, clinicaltrials.gov, company websites.

Review Methods

Using PRISMA methodology, primary literature regarding MCED tests was queried from April 26 to May 12, 2024 using MCED search terms. Ongoing clinical trials incorporating MCED screens were identified via the National Institutes of Health clinicaltrials.gov website. Company websites for available or upcoming MCED tests were reviewed.

Conclusion

Long-term robust data regarding the performance characteristics, effects on clinical outcomes, and cost-utility of MCED tests for head and neck cancer are currently lacking. Otolaryngologists should be aware of the implications of MCED tests as these assays become more widely used.

Implications for Practice

Although not FDA-approved or covered by insurances at the time of writing of this manuscript, MCED testing is rapidly gaining interest, and patients with positive tests are presenting to otolaryngologists for evaluation. While MCED technologies hold great promise for early detection of disease and potential reduction of morbidity and mortality, more study is needed about their utility for head and neck cancer and optimal diagnostic workflows.

New diagnostic and nonsurgical local treatment modalities for early stage lung cancer

This paper highlights developments in diagnostic and nonsurgical local treatment modalities that have changed the management of early-stage lung cancer. These innovations aim to enhance diagnostic accuracy, minimize invasiveness, and improve patient outcomes. Liquid biopsies are emerging as promising tools for non-invasive diagnosis and monitoring, enabling earlier intervention without being standardized yet as well as not yet anchored in the guidelines. Endobronchial navigation has emerged as an innovative tool. By combining electromagnetic or GPS-like technology with 3D imaging and a steerable catheter, it enables accurate biopsy of small, peripheral lesions that were once challenging to sample, with a very low pneumothorax rate. Regarding nonsurgical treatments, stereotactic body radiotherapy (SBRT) continues to shine as a non-invasive local treatment modality for early-stage lung cancer and is the guideline-recommended standard-of-care for inoperable patients and patients refusing the risk of surgical resection. The low toxicity and excellent local control has made it an attractive alternative to surgery even in fitter patients. Percutaneous ablative techniques utilising energies such as microwave or pulse-field electroporation are options for patients who are not candidates for surgery or SBRT. Bronchoscopic ablation delivers the same energies but with a very lower pneumothorax rate and it is therefore also open to patients with multiple and bilateral lesions.

Multibiomarker panels in liquid biopsy for early detection of pancreatic cancer - a comprehensive review

Pancreatic ductal adenocarcinoma (PDAC) is frequently detected in late stages, which leads to limited therapeutic options and a dismal overall survival rate. To date, no robust method for the detection of early-stage PDAC that can be used for targeted screening approaches is available. Liquid biopsy allows the minimally invasive collection of body fluids (typically peripheral blood) and the subsequent analysis of circulating tumor cells or tumor-associated molecules such as nucleic acids, proteins, or metabolites that may be useful for the early diagnosis of PDAC. Single biomarkers may lack sensitivity and/or specificity to reliably detect PDAC, while combinations of these circulating biomarkers in multimarker panels may improve the sensitivity and specificity of blood test-based diagnosis. In this narrative review, we present an overview of different liquid biopsy biomarkers for the early diagnosis of PDAC and discuss the validity of multimarker panels.

Advancements in precision oncology: Investigating the function of circulating DNA in the advancement of liquid biopsy technologies

While the traditional method is a biopsy of the potential tumor tissue, more non-invasive methods have been developed such as the liquid biopsy. It is an emerging, powerful cancer detection method that is used for molecular profiling of tumours apart from tissue-specific biopsy. It involves the analysis of free, circulating tumor genetic material and circulating tumor cells (CTCs) that are found in the fluids of the patient. This analysis helps to detect the abnormal genetic anomalies associated with the various forms of cancer as well as identify mutations corresponding to specific tumours. It is an upcoming method of diagnostics applied in the field of precision oncology that helps overcome the limitations of the traditional biopsy. It can interrogate and look through difficult-to-biopsy tumours and also aid in early cancer detection. Sequencing techniques help in building databases with different information on mutations in the genetic as well as epigenetic levels. In this review, we understand the role of liquid biopsy as not only a diagnostic tool but its role in therapeutics and its potential in the future.

Liquid biopsy: An arsenal for tumour screening and early diagnosis

Cancer has become the second leading cause of death in the world, and more than 50% of cancer patients are diagnosed at an advanced stage. Early diagnosis of tumours is the key to improving patient quality of life and survival time and reducing the socioeconomic burden. However, there is still a lack of reliable early diagnosis methods in clinical practice. In recent years, liquid biopsy technology has developed rapidly. It has the advantages of noninvasiveness, easy access to sample sources, and reproducibility. It has become the main focus of research on the early diagnosis methods of tumours. This review summarises the research progress of existing liquid biopsy markers, such as circulating tumour DNA, circulating viral DNA, DNA methylation, circulating tumour cells, circulating RNA, exosomes, and tumour education platelets in early diagnosis of tumours, and analyses the current advantages and limitations of various markers, providing a direction for the application and transformation of liquid biopsy research in early diagnosis of clinical tumours.

Latest Research Progress of Liquid Biopsy in Tumor-A Narrative Review

Human life expectancy is significantly impacted by cancer, with liquid biopsy emerging as an advantageous method for cancer detection because of its noninvasive nature, high accuracy, ease of sampling, and cost-effectiveness compared with conventional tissue biopsy techniques. Liquid biopsy shows promise in early cancer detection, real-time monitoring, and personalized treatment for various cancers, including lung, cervical, and prostate cancers, and offers innovative approaches for cancer diagnosis and management. By utilizing circulating tumor DNA, circulating tumor cells, and exosomes as biomarkers, liquid biopsy enables the tracking of cancer progression. Various techniques commonly used in life sciences research, such as polymerase chain reaction (PCR), next-generation sequencing (NGS), and droplet digital PCR, are employed to assess cancer progression on the basis of different indicators. This review examines the latest advancements in liquid biopsy markers-circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and exosomes-for cancer diagnosis over the past three years, with a focus on their detection methodologies and clinical applications. It encapsulates the pivotal aims of liquid biopsy, including early detection, therapy response prediction, treatment monitoring, prognostication, and its relevance in minimal residual disease, while also addressing the challenges facing routine clinical adoption. By combining the latest research advancements and practical clinical experiences, this work focuses on discussing the clinical significance of DNA methylation biomarkers and their applications in tumor screening, auxiliary diagnosis, companion diagnosis, and recurrence monitoring. These discussions may help enhance the application of liquid biopsy throughout the entire process of tumor diagnosis and treatment, thereby providing patients with more precise and effective treatment plans.

Discovery and Validation of Methylation Signatures in Circulating Cell-Free DNA for the Detection of Colorectal Cancer

This study was conducted with the primary objective of assessing the performance of cfDNA methylation in the detection of colorectal cancer (CRC). Five tumor tissue, 20 peripheral blood leucocyte, and 169 cfDNA samples were collected for whole-genome bisulfite sequencing (WGBS) analysis. Bioinformatic analysis was conducted to identify differentially methylated regions (DMRs) and their functional characteristics. Quantitative methylation-specific PCR (qMSP) was used to validate the methylation levels of DMRs in the tissues and leucocytes. cfDNA samples from CRC patients and healthy controls were used to evaluate the performance of the DMR analysis. WGBS analysis revealed a decrease in DNA methylation levels in the CpG context in CRC tumor tissues compared with adjacent normal tissues. A total of 132 DMRs in cfDNA were identified as potential markers for diagnosing CRC. In a cohort of 95 CRC patients and 74 healthy controls, a combination of the three DMRs (DAB1, PPP2R5C, and FAM19A5) yielded an AUC of 0.763, achieving 64.21% sensitivity and 78.38% specificity in discriminating CRC patients from healthy controls. This study provides insights into DNA methylation patterns in CRC and identifies a set of DMRs in cfDNA with potential diagnostic value for CRC. These DMRs hold promise as biomarkers for CRC detection, offering promise for non-invasive CRC diagnosis. Further research is warranted to validate these findings in larger cohorts.

Multiyear Clinical Outcomes of Cancers Diagnosed Following Detection by a Blood-Based Multicancer Early Detection Test

In the US, <20% of cancers are diagnosed by standard-of-care (SoC) screening. Multicancer early detection (MCED) tests offer the opportunity to expand cancer screening. Understanding the characteristics and clinical outcomes of MCED-detected cancers is critical to clarifying MCED tests' potential impact. DETECT-A is the first prospective interventional trial of an MCED blood test (CancerSEEK). CancerSEEK, coupled with diagnostic PET-CT, identified cancers including those not detected by SoC screening, the majority of which were localized or regional. We report multiyear outcomes in patients with cancers diagnosed following a positive CancerSEEK test. Nine cancer types were diagnosed in 26 participants whose cancers were first detected by CancerSEEK. Information on cancer diagnoses, treatments, and clinical outcomes was extracted from medical records through November 2022. Data collection occurred at a median of 4.4 years (IQR: 4.1-4.6) following study enrollment. Thirteen of 26 (50%) participants were alive and cancer-free [ovarian (4), thyroid (1), uterine (2), breast (1), colorectal (2), and lung (3)]; 7/13 (54%) had cancers without recommended SoC screening modalities. All eight treated stage I or II participants (8/8, 100%) and 12/14 (86%) surgically treated participants were alive and cancer-free. Eligibility for surgical treatment was associated with favorable multiyear outcomes (P = 0.0002). Half of participants with MCED-detected cancers were alive and cancer-free after 4.4 years median follow-up. Most were diagnosed with early-stage cancers and were treated surgically. These results suggest that early cancer detection by CancerSEEK may have facilitated curative-intent treatments and associated positive clinical outcomes in some DETECT-A participants. Prevention Relevance: This study provides preliminary evidence of the potential of multicancer early detection testing as an effective screening tool for detecting cancers without standard-of-care (SoC) screening modalities and complementing SoC cancer screening.

The systematic role of pancreatic cancer exosomes: distant communication, liquid biopsy and future therapy

Pancreatic cancer remains one of the most lethal diseases worldwide. Cancer-derived exosomes, benefiting from the protective role of the lipid membrane, exhibit remarkable stability in the circulatory system. These exosomes, released by tumor microenvironment, contain various biomolecules such as proteins, RNAs, and lipids that plays a pivotal role in mediating distant communication between the local pancreatic tumor and other organs or tissues. They facilitate the transfer of oncogenic factors to distant sites, contributing to the compromised body immune system, distant metastasis, diabetes, cachexia, and promoting a microenvironment conducive to tumor growth and metastasis in pancreatic cancer patients. Beyond their intrinsic roles, circulating exosomes in peripheral blood can be detected to facilitate accurate liquid biopsy. This approach offers a novel and promising method for the diagnosis and management of pancreatic cancer. Consequently, circulating exosomes are not only crucial mediators of systemic cell-cell communication during pancreatic cancer progression but also hold great potential as precise tools for pancreatic cancer management and treatment. Exosome-based liquid biopsy and therapy represent promising advancements in the diagnosis and treatment of pancreatic cancer. Exosomes can serve as drug delivery vehicles, enhancing the targeting and efficacy of anticancer treatments, modulating the immune system, and facilitating gene editing to suppress tumor growth. Ongoing research focuses on biomarker identification, drug delivery systems, and clinical trials to validate the safety and efficacy of exosome-based therapies, offering new possibilities for early diagnosis and precision treatment in pancreatic cancer. Leveraging the therapeutic potential of exosomes, including their ability to deliver targeted drugs and modulate immune responses, opens new avenues for innovative treatment strategies.

Circulating tumor DNA (ctDNA): can it be used as a pan-cancer early detection test?

Circulating tumor DNA (ctDNA, DNA shed by cancer cells) is emerging as one of the most transformative cancer biomarkers discovered to-date. Although potentially useful at all the phases of cancer detection and patient management, one of its most exciting possibilities is as a relatively noninvasive pan-cancer screening test. Preliminary findings with ctDNA tests such as Galleri or CancerSEEK suggest that they have high specificity (> 99.0%) for malignancy. Their sensitivity varies depending on the type of cancer and stage of disease but it is generally low in patients with stage I disease. A major advantage of ctDNA over existing screening strategies is the potential ability to detect multiple cancer types in a single test. A limitation of most studies published to-date is that they are predominantly case-control investigations that were carried out in patients with a previous diagnosis of malignancy and that used apparently healthy subjects as controls. Consequently, the reported sensitivities, specificities and positive predictive values might be lower if the tests are used for screening in asymptomatic populations, that is, in the population where these tests are likely be employed. To demonstrate clinical utility in an asymptomatic population, these tests must be shown to reduce cancer mortality without causing excessive overdiagnosis in a large randomized prospective randomized trial. Such trials are currently ongoing for Galleri and CancerSEEK.

Development of new techniques and clinical applications of liquid biopsy in lung cancer management

Lung cancer is an exceedingly malignant tumor reported as having the highest morbidity and mortality of any cancer worldwide, thus posing a great threat to global health. Despite the growing demand for precision medicine, current methods for early clinical detection, treatment and prognosis monitoring in lung cancer are hampered by certain bottlenecks. Studies have found that during the formation and development of a tumor, molecular substances carrying tumor-related genetic information can be released into body fluids. Liquid biopsy (LB), a method for detecting these tumor-related markers in body fluids, maybe a way to make progress in these bottlenecks. In recent years, LB technology has undergone rapid advancements. Therefore, this review will provide information on technical updates to LB and its potential clinical applications, evaluate its effectiveness for specific applications, discuss the existing limitations of LB, and present a look forward to possible future clinical applications. Specifically, this paper will introduce technical updates from the prospectives of engineering breakthroughs in the detection of membrane-based LB biomarkers and other improvements in sequencing technology. Additionally, it will summarize the latest applications of liquid biopsy for the early detection, diagnosis, treatment, and prognosis of lung cancer. We will present the interconnectedness of clinical and laboratory issues and the interplay of technology and application in LB today.

DNA methylation markers in esophageal cancer

Background

Esophageal cancer (EC) is a prevalent malignancy characterized by a low 5-year survival rate, primarily attributed to delayed diagnosis and limited therapeutic options. Currently, early detection of EC heavily relies on endoscopy and pathological examination, which pose challenges due to their invasiveness and high costs, leading to low patient compliance. The detection of DNA methylation offers a non-endoscopic, cost-effective, and secure approach that holds promising prospects for early EC detection.

Methods

To identify improved methylation markers for early EC detection, we conducted a comprehensive review of relevant literature, summarized the performance of DNA methylation markers based on different input samples and analytical methods in EC early detection and screening.

Findings

This review reveals that blood cell free DNA methylation-based method is an effective non-invasive method for early detection of EC, although there is still a need to improve its sensitivity and specificity. Another highly sensitive and specific non-endoscopic approach for early detection of EC is the esophageal exfoliated cells based-DNA methylation analysis. However, while there are substantial studies in esophageal adenocarcinoma, further more validation is required in esophageal squamous cell carcinoma.

Conclusion

In conclusion, DNA methylation detection holds significant potential as an early detection and screening technology for EC.

Early detection and prognosis evaluation for hepatocellular carcinoma by circulating tumour DNA methylation: A multicentre cohort study

BACKGROUND

Early diagnosis of hepatocellular carcinoma (HCC) can significantly improve patient survival. We aimed to develop a blood-based assay to aid in the diagnosis, detection and prognostic evaluation of HCC.

METHODS

A three-phase multicentre study was conducted to screen, optimise and validate HCC-specific differentially methylated regions (DMRs) using next-generation sequencing and quantitative methylation-specific PCR (qMSP).

RESULTS

Genome-wide methylation profiling was conducted to identify DMRs distinguishing HCC tumours from peritumoural tissues and healthy plasmas. The twenty most effective DMRs were verified and incorporated into a multilocus qMSP assay (HepaAiQ). The HepaAiQ model was trained to separate 293 HCC patients (Barcelona Clinic Liver Cancer (BCLC) stage 0/A, 224) from 266 controls including chronic hepatitis B (CHB) or liver cirrhosis (LC) (CHB/LC, 96), benign hepatic lesions (BHL, 23), and healthy controls (HC, 147). The model achieved an area under the curve (AUC) of 0.944 with a sensitivity of 86.0% in HCC and a specificity of 92.1% in controls. Blind validation of the HepaAiQ model in a cohort of 523 participants resulted in an AUC of 0.940 with a sensitivity of 84.4% in 205 HCC cases (BCLC stage 0/A, 167) and a specificity of 90.3% in 318 controls (CHB/LC, 100; BHL, 102; HC, 116). When evaluated in an independent test set, the HepaAiQ model exhibited a sensitivity of 70.8% in 65 HCC patients at BCLC stage 0/A and a specificity of 89.5% in 124 patients with CHB/LC. Moreover, HepaAiQ model was assessed in paired pre- and postoperative plasma samples from 103 HCC patients and correlated with 2-year patient outcomes. Patients with high postoperative HepaAiQ score showed a higher recurrence risk (Hazard ratio, 3.33, p < .001).

CONCLUSIONS

HepaAiQ, a noninvasive qMSP assay, was developed to accurately measure HCC-specific DMRs and shows great potential for the diagnosis, detection and prognosis of HCC, benefiting at-risk populations.

Circulating tumor DNA in liquid biopsy: Current diagnostic limitation

With the rapid development of science and technology, cell-free DNA (cfDNA) is rapidly becoming an important biomarker for tumor diagnosis, monitoring and prognosis, and this cfDNA-based liquid biopsy technology has great potential to become an important part of precision medicine. cfDNA is the total amount of free DNA in the systemic circulation, including DNA fragments derived from tumor cells and all other somatic cells. Tumor cells release fragments of DNA into the bloodstream, and this source of cfDNA is called circulating tumor DNA (ctDNA). cfDNA detection has become a major focus in the field of tumor research in recent years, which provides a new opportunity for non-invasive diagnosis and prognosis of cancer. In this paper, we discuss the limitations of the study on the origin and dynamics analysis of ctDNA, and how to solve these problems in the future. Although the future faces major challenges, it also contains great potential.

Circulating tumor DNA in liquid biopsy: Current diagnostic limitation

With the rapid development of science and technology, cell-free DNA (cfDNA) is rapidly becoming an important biomarker for tumor diagnosis, monitoring and prognosis, and this cfDNA-based liquid biopsy technology has great potential to become an important part of precision medicine. cfDNA is the total amount of free DNA in the systemic circulation, including DNA fragments derived from tumor cells and all other somatic cells. Tumor cells release fragments of DNA into the bloodstream, and this source of cfDNA is called circulating tumor DNA (ctDNA). cfDNA detection has become a major focus in the field of tumor research in recent years, which provides a new opportunity for non-invasive diagnosis and prognosis of cancer. In this paper, we discuss the limitations of the study on the origin and dynamics analysis of ctDNA, and how to solve these problems in the future. Although the future faces major challenges, it also contains great potential.

NMR and MS reveal characteristic metabolome atlas and optimize esophageal squamous cell carcinoma early detection

Metabolic changes precede malignant histology. However, it remains unclear whether detectable characteristic metabolome exists in esophageal squamous cell carcinoma (ESCC) tissues and biofluids for early diagnosis. Here, we conduct NMR- and MS-based metabolomics on 1,153 matched ESCC tissues, normal mucosae, pre- and one-week post-operative sera and urines from 560 participants across three hospitals, with machine learning and WGCNA. Aberrations in 'alanine, aspartate and glutamate metabolism' proved to be prevalent throughout the ESCC evolution, consistently identified by NMR and MS, and reflected in 16 serum and 10 urine metabolic signatures in both discovery and validation sets. NMR-based simplified panels of any five serum or urine metabolites outperform clinical serological tumor markers (AUC = 0.984 and 0.930, respectively), and are effective in distinguishing early-stage ESCC in test set (serum accuracy = 0.994, urine accuracy = 0.879). Collectively, NMR-based biofluid screening can reveal characteristic metabolic events of ESCC and be feasible for early detection (ChiCTR2300073613).

Cancer Screening: Present Recommendations, the Development of Multi-Cancer Early Development Tests, and the Prospect of Universal Cancer Screening

Cancer continues to pose a considerable challenge to global health. In the search for innovative strategies to combat this complex enemy, the concept of universal cancer screening has emerged as a promising avenue for early detection and prevention. In contrast to targeted approaches that focus on specific populations or high-risk individuals, universal screening seeks to cast a wide net to detect incipient malignancies in different demographic groups. This paradigm shift in cancer care underscores the importance of comprehensive screening programs that go beyond conventional boundaries. As our understanding of the complex molecular and genetic basis of cancer deepens, the need to develop comprehensive screening methods becomes increasingly apparent. In this article, we look at the rationale and potential benefits of universal cancer screening.