Kinetics of circulating cell-free DNA for biomedical applications: critical appraisal of the literature

Assessment of plasma derived microbiome profiles in lung cancer using targeted and whole exome sequencing

Microbial infections contribute to ~20% of malignancy. Plasma-derived cell-free DNA presents a promising avenue for non-invasive cancer diagnostics, capturing microbial signatures. We analyzed 261 plasma from 50 patients with lung adenocarcinoma by targeted and whole exome sequencing at 10,000 × and 340 × depth, respectively. Comparative analyses of Kraken 2 and IPD2 reveal substantial discrepancies, highlighting challenges in microbial DNA quantification and the need for stringent bioinformatics approaches to ensure accurate cancer microbiome profiling.

Liquid Biopsy in B and T Cell Lymphomas: From Bench to Bedside

Liquid biopsy through the analysis of circulating tumor DNA (ctDNA) is emerging as a powerful and non-invasive tool complementing tissue biopsy in lymphoma management. Whilst tissue biopsy remains the diagnostic gold standard, it fails to detect the molecular heterogeneity of the tumor's multiple compartments and poses challenges for sequential disease monitoring. In diffuse large-B-cell lymphoma (DLBCL), ctDNA facilitates non-invasive genotyping by identifying hallmark mutations (e.g., MYD88, CD79B, EZH2), enabling molecular cluster classification. Dynamic changes in ctDNA levels during DLBCL treatment correlate strongly with progression-free survival and overall survival, underscoring its value as a predictive and prognostic biomarker. In Hodgkin's lymphoma, characterized by a scarcity of malignant cells in tissue biopsies, ctDNA provides reliable molecular insights into tumor biology, response to therapy, and relapse risk. In primary central nervous system lymphoma, the detection of MYD88 L265P in ctDNA offers a highly sensitive, specific, and minimally invasive diagnostic option. Likewise, in aggressive T-cell lymphomas, ctDNA supports molecular profiling, aligns with tumor burden, and shows high concordance with tissue-based results. Ongoing and future clinical trials will be critical for validating and standardizing ctDNA applications, ultimately integrating liquid biopsy into routine clinical practice and enabling more personalized and dynamic lymphoma care.

Liquid Biopsy in Neuropsychiatric Disorders: A Step Closer to Precision Medicine

Psychiatric disorders are among the leading causes of disease burden worldwide. Despite their significant impact, their diagnosis remains challenging due to symptom heterogeneity, psychiatric comorbidity, and the lack of objective diagnostic tests and well-defined biomarkers. Leveraging genomic, epigenomic, and fragmentomic technologies, circulating cell-free DNA (ccfDNA)-based liquid biopsies have emerged as a potential non-invasive diagnosis and disease-monitoring tool. ccfDNA is a DNA species released into circulation from all types of cells through passive and active mechanisms and can serve as a biomarker for various diseases, namely, cancer. Despite their potential, the application of ccfDNA in neuropsychiatry remains underdeveloped. In this review, we provide an overview of liquid biopsies and their components, with a particular focus on ccfDNA. With a summary of pre-analytical practices and current ccfDNA technologies, we highlight the current state of research regarding the use of ccfDNA as a biomarker for neuropsychiatric disorders. Finally, we discuss future steps to unlock ccfDNA's potential in clinical practice.

Computational Modeling for Circulating Cell-Free DNA in Clinical Oncology

PURPOSE

Liquid biopsy, specifically circulating cell-free DNA (cfDNA), has emerged as a powerful tool for cancer early diagnosis, prognosis, and treatment monitoring over a wide range of cancer types. Computational modeling (CM) of cfDNA data is essential to harness its full potential for real-time, noninvasive insights into tumor biology, enhancing clinical decision making.

DESIGN

This work reviews CM-cfDNA methods applied to clinical oncology, emphasizing both machine learning (ML) techniques and mechanistic approaches. The latter integrate biological principles, enabling a deeper understanding of cfDNA dynamics and its relationship with tumor evolution.

RESULTS

Key findings highlight the effectiveness of CM-cfDNA approaches in improving diagnostic accuracy, identifying prognostic markers, and predicting therapeutic outcomes. ML models integrating cfDNA concentration, fragmentation patterns, and mutation detection achieve high sensitivity and specificity for early cancer detection. Mechanistic models describe cfDNA kinetics, linking them to tumor growth and response to treatment, for example, immune checkpoint inhibitors. Longitudinal data and advanced statistical constructs further refine these models for quantification of interindividual and intraindividual variability.

CONCLUSION

CM-cfDNA represents a pivotal advancement in precision oncology. It bridges the gap between extensive cfDNA data and actionable clinical insights, supporting its integration into routine cancer care. Future efforts should focus on standardizing protocols, validating models across populations, and exploring hybrid approaches combining ML with mechanistic modeling to improve biological understanding.

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

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

Detection of Circulating Tumor DNA in Liquid Biopsy: Current Techniques and Potential Applications in Melanoma

The treatment landscape for advanced melanoma has transformed significantly with the advent of BRAF and MEK inhibitors (BRAF/MEKi) targeting BRAFV600 mutations, as well as immune checkpoint inhibitors (ICI) like anti-PD-1 monotherapy or its combinations with anti-CTLA-4 or anti-LAG-3. Despite that, many patients still do not benefit from these treatments at all or develop resistance mechanisms. Therefore, prognostic and predictive biomarkers are needed to identify patients who should switch or escalate their treatment strategies or initiate an intensive follow-up. In melanoma, liquid biopsy has shown promising results, with a potential role in predicting relapse in resected high-risk patients or in disease monitoring during the treatment of advanced disease. Several components in peripheral blood have been analyzed, such as circulating tumor cells (CTCs), cell-free DNA (cfDNA), and circulant tumoral DNA (ctDNA), which have turned out to be particularly promising. To analyze ctDNA in blood, different techniques have proven to be useful, including digital droplet polymerase chain reaction (ddPCR) to detect specific mutations and, more recently, next-generation sequencing (NGS) techniques, which allow analyzing a broader repertoire of the mutation landscape of each patient. In this review, our goal is to update the current understanding of liquid biopsy, focusing on the use of ctDNA as a biological material in the daily clinical management of melanoma patients, in particular those with advanced disease treated with ICI.

Evaluation of a biomarker for amyotrophic lateral sclerosis derived from a hypomethylated DNA signature of human motor neurons

Amyotrophic lateral sclerosis (ALS) lacks a specific biomarker, but is defined by relatively selective toxicity to motor neurons (MN). As others have highlighted, this offers an opportunity to develop a sensitive and specific biomarker based on detection of DNA released from dying MN within accessible biofluids. Here we have performed whole genome bisulfite sequencing (WGBS) of iPSC-derived MN from neurologically normal individuals. By comparing MN methylation with an atlas of tissue methylation we have derived a MN-specific signature of hypomethylated genomic regions, which accords with genes important for MN function. Through simulation we have optimised the selection of regions for biomarker detection in plasma and CSF cell-free DNA (cfDNA). However, we show that MN-derived DNA is not detectable via WGBS in plasma cfDNA. In support of our experimental finding, we show theoretically that the relative sparsity of lower MN sets a limit on the proportion of plasma cfDNA derived from MN which is below the threshold for detection via WGBS. Our findings are important for the ongoing development of ALS biomarkers. The MN-specific hypomethylated genomic regions we have derived could be usefully combined with more sensitive detection methods and perhaps with study of CSF instead of plasma. Indeed we demonstrate that neuronal-derived DNA is detectable in CSF. Our work is relevant for all diseases featuring death of rare cell-types.

Evaluating diagnostic performance: A comparative analysis of cell-free DNA and serological test in hepatic cystic Echinococcosis

Cystic Echinococcosis (CE) is a zoonotic disease caused by Echinococcus granulosus sensu lato. Diagnosing CE primarily relies on imaging techniques, and there is a crucial need for an objective laboratory test to enhance the diagnostic process. Today, cell-free DNAs (cfDNAs) have gained importance regarding their biomarker potential. This study aims to investigate the diagnostic capabilities of different cfDNA targets (Echinococcus-specific repeat sequences (mgs-4 and mgs-12) and partial fragment of repetitive sequence (EG1 Hae III)) and evaluate their diagnostic effectiveness when compared to a frequently used commercial E.granulosus-specific IgG ELISA. Seventy-six confirmed hepatic CE patients and healthy controls were included in the study. The EG1 Hae III region was assessed using nested PCR, whereas real-time PCR was employed to investigate other cfDNA targets. Analysis of the cfDNA-targeted tests indicated that mgs-4 demonstrated the highest diagnostic efficacy in distinguishing CE patients from healthy controls, achieving a sensitivity of 60.5% (p = 0.002). Combining ELISA with the mgs-4 target led to an increased sensitivity of 72.4% for distinguishing between CE patients and the control group. The sensitivity rates for ELISA and the three cfDNA targets varied among the groups. Active CE patients showed sensitivity rates of 52.9%, 52.9%, 23.5%, and 52.9% for ELISA, mgs-4, mgs-12, and EG1 Hae III assays, respectively. In contrast, inactive cyst patients displayed sensitivity rates of 21.4%, 66.7%, 19%, and 42.9% for the corresponding assays. The mgs-4, either alone or in combination with ELISA, demonstrated notably higher sensitivity values for CE diagnosis in all group comparisons compared to serology.

Melanoma's New Frontier: Exploring the Latest Advances in Blood-Based Biomarkers for Melanoma

Melanoma is one of the most malignant cancers, and the global incidence of cutaneous melanoma is increasing. While melanomas are highly prone to metastasize if diagnosed late, early detection and treatment significantly reduce the risk of mortality. Identifying patients at higher risk of metastasis, who might benefit from early adjuvant therapies, is particularly important, especially with the advent of new melanoma treatments. Therefore, there is a pressing need to develop additional prognostic biomarkers for melanoma to improve early stratification of patients and accurately identify high-risk subgroups, ultimately enabling more effective personalized treatments. Recent advances in melanoma therapy, including targeted treatments and immunotherapy, have underscored the importance of biomarkers in determining prognosis and predicting treatment response. The clinical application of these markers holds the potential for significant advancements in melanoma management. Various tumor-derived genetic, proteomic, and cellular components are continuously released into the bloodstream of cancer patients. These molecules, including circulating tumor DNA and RNA, proteins, tumor cells, and immune cells, are emerging as practical and precise liquid biomarkers for cancer. In the current era of effective molecular-targeted therapies and immunotherapies, there is an urgent need to integrate these circulating biomarkers into clinical practice to facilitate personalized treatment. This review highlights recent discoveries in circulating melanoma biomarkers, explores the challenges and potentials of emerging technologies for liquid biomarker discovery, and discusses future directions in melanoma biomarker research.

An Investigation into Cell-Free DNA in Different Common Cancers

Diagnosis is the most important step in different diseases, especially in cancers and blood malignancies. There are different methods in order to better diagnose of cancer, but many of them are invasive and also, some of them are not useful for immediate diagnosis. Cell-free DNA (cfDNA) or liquid biopsy easily accessible in peripheral blood is one of the non-invasive prognostic biomarkers in various areas of cancer management. In fact, amounts of cfDNA in serum or plasma can be used for diagnosis. In this review, we have considered some cancers such as hepatocellular carcinoma, lung cancer, breast cancer, and hematologic malignancies to compare the various methods of cfDNA diagnosis.

Evaluation of a biomarker for amyotrophic lateral sclerosis derived from a hypomethylated DNA signature of human motor neurons

Amyotrophic lateral sclerosis (ALS) lacks a specific biomarker, but is defined by relatively selective toxicity to motor neurons (MN). As others have highlighted, this offers an opportunity to develop a sensitive and specific biomarker based on detection of DNA released from dying MN within accessible biofluids. Here we have performed whole genome bisulfite sequencing (WGBS) of iPSC-derived MN from neurologically normal individuals. By comparing MN methylation with an atlas of tissue methylation we have derived a MN-specific signature of hypomethylated genomic regions, which accords with genes important for MN function. Through simulation we have optimised the selection of regions for biomarker detection in plasma and CSF cell-free DNA (cfDNA). However, we show that MN-derived DNA is not detectable via WGBS in plasma cfDNA. In support of our experimental finding, we show theoretically that the relative sparsity of lower MN sets a limit on the proportion of plasma cfDNA derived from MN which is below the threshold for detection of WGBS. Our findings are important for the ongoing development of ALS biomarkers. The MN-specific hypomethylated genomic regions we have derived could be usefully combined with more sensitive detection methods and perhaps with study of CSF instead of plasma. Indeed we demonstrate that neuronal-derived DNA is detectable in CSF. Our work is relevant for all diseases featuring death of rare cell-types.

Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges

Circulating tumor DNA (ctDNA) methylation, an innovative liquid biopsy biomarker, has emerged as a promising tool in early cancer diagnosis, monitoring, and prognosis prediction. As a noninvasive approach, liquid biopsy overcomes the limitations of traditional tissue biopsy. Among various biomarkers, ctDNA methylation has garnered significant attention due to its high specificity and early detection capability across diverse cancer types. Despite its immense potential, the clinical application of ctDNA methylation faces substantial challenges pertaining to sensitivity, specificity, and standardization. In this review, we begin by introducing the basic biology and common detection techniques of ctDNA methylation. We then explore recent advancements and the challenges faced in the clinical application of ctDNA methylation in liquid biopsies. This includes progress in early screening and diagnosis, identification of clinical molecular subtypes, monitoring of recurrence and minimal residual disease (MRD), prediction of treatment response and prognosis, assessment of tumor burden, and determination of tissue origin. Finally, we discuss the future perspectives and challenges of ctDNA methylation detection in clinical applications. This comprehensive overview underscores the vital role of ctDNA methylation in enhancing cancer diagnostic accuracy, personalizing treatments, and effectively monitoring disease progression, providing valuable insights for future research and clinical practice.

Donor-derived cell-free DNA is a valuable monitoring tool after single lung transplantation: Multicenter analysis

Background

Donor-derived cell-free DNA (dd-cfDNA) is a nonspecific plasma biomarker for tissue injury that has been validated for monitoring acute rejection (AR) after lung transplantation (LT). However, no studies to date have focused specifically on single lung transplantation (SLT). Herein, we report the performance of dd-cfDNA in detecting AR in SLT from 6 academic centers that implemented this biomarker surveillance in their standard of practice (SOP).

Methods

dd-cfDNA test results were corrected for SLT by an algorithm in the Clinical Laboratory Improvement Amendments (CLIA) laboratory to permit comparison against the same 1.0% threshold used in double-lung transplant. Investigators reviewed patient SOP electronic medical record clinical data to assign test results into cohorts based on clinical allograft health status. To avoid ambiguity in interpretation, samples drawn after a prior AR or infection event or without histopathologic confirmation of AR were excluded from further analysis. Diagnostic cohorts included AR (N=25 samples), healthy (STABLE, N=137), allograft infection (INFXN, N=41), chronic lung allograft dysfunction (CLAD, N=7), and "OTHER" types of graft injury (N=12).

Results

The study included a total of 257 dd-cfDNA results from 103 SLT patients with one patient excluded due to active cancer. Samples were drawn a median of 233 days (interquartile range: 96-489) after SLT. Laterality for SLT (R vs L) and median dd-cfDNA fraction in AR and STABLE cohort were not statistically different. The median dd-cfDNA fraction was elevated with AR (1.8%) and INFXN (1.1%) vs STABLE (0.46%; p < 0.0001). dd-cfDNA with CLAD was also significantly higher than STABLE cohort (p = 0.0155). The area under receiver operator characteristics curve was 0.850 (95% confidence interval: 0.72-0.95, p < 0.0001) for AR vs STABLE cohort. Applying the dd-cfDNA threshold ≥1.0% for detection of AR yielded a sensitivity = 77.8%, specificity = 84.6%, positive predictive value = 38.31%, and negative predictive value = 96.83%.

Conclusions

These multicenter data, incorporating real-world experiences, support the clinical validity and utility of dd-cfDNA monitoring of SLT recipients. Additional studies of the impact of biomarker surveillance on clinically meaningful outcomes should be forthcoming from robust, prospective, and clinical trials already in progress.

First-in-human clinical outcomes with NG-350A, an anti-CD40 expressing tumor-selective vector designed to remodel immunosuppressive tumor microenvironments

BACKGROUND

Tumor-selective oncolytic viral vectors are promising anticancer therapeutics; however, challenges with dosing and potency in advanced/metastatic cancers have limited efficacy and usage. NG-350A is a next-generation blood-stable adenoviral vector engineered to express an agonist anti-cluster of differentiation (CD)40 antibody without affecting tumor-selectivity and oncolytic potency.

METHODS

Intravenous and intratumoral (IT) administration of NG-350A was assessed in a phase Ia/Ib study in patients with metastatic/advanced epithelial tumors (NCT03852511). Dose-escalation was performed separately for intravenous (four dose levels available, each with infusions on Days 1, 3 and 5 of a 57-day treatment period) and IT (single injection on D1 only or injections on Days 1, 8, 15 and 22) administration. The primary objective was safety and tolerability; secondary objectives included determining a recommended dose, pharmacokinetics, and immunogenicity.

RESULTS

In total, 25 heavily pretreated patients received NG-350A (16 with intravenous and 9 with IT administration). Intravenous and IT dosing were both well tolerated, with no evidence of transgene-related or off-target viral toxicity. Intravenous and IT dosing resulted in dose-dependent increases in systemic NG-350A Cmax. Despite both routes of administration inducing anti-virus antibodies, sustained persistence of NG-350A in blood samples was observed up to 7 weeks after the last dose, particularly with higher intravenous dose levels. Delivery of NG-350A to tumors was demonstrated in biopsy samples following both routes of administration; a dose-dependent pattern was seen with intravenous infusion, with four patients remaining positive for vector DNA in biopsies at Day 57. Transgene messenger RNA from replicating NG-350A was detected in 5/12 patients with intravenous treatment and 1/9 patients with IT injection, and sustained increases in inflammatory cytokines were observed following dosing, particularly with higher intravenous dose levels.

CONCLUSIONS

This phase 1a study provided initial proof-of-mechanism for NG-350A, with strong evidence of tumor delivery, viral replication and transgene expression-particularly after intravenous dosing. The lack of transgene-related or off-target viral toxicity was consistent with the highly selective delivery and replication of NG-350A, even after systemic delivery. The efficacy of intravenous-dosed NG-350A will now be evaluated in combination with pembrolizumab (NCT05165433), as well as with chemoradiotherapy (NCT06459869).

TRIAL REGISTRATION NUMBER

NCT05165433, NCT06459869.

Systematically Evaluating Cell-Free DNA Fragmentation Patterns for Cancer Diagnosis and Enhanced Cancer Detection via Integrating Multiple Fragmentation Patterns

Cell-free DNA (cfDNA) fragmentation patterns have immense potential for early cancer detection. However, the definition of fragmentation varies, ranging from the entire genome to specific genomic regions. These patterns have not been systematically compared, impeding broader research and practical implementation. Here, 1382 plasma cfDNA sequencing samples from 8 cancer types are collected. Considering that cfDNA within open chromatin regions is more susceptible to fragmentation, 10 fragmentation patterns within open chromatin regions as features and employed machine learning techniques to evaluate their performance are examined. All fragmentation patterns demonstrated discernible classification capabilities, with the end motif showing the highest diagnostic value for cross-validation. Combining cross and independent validation results revealed that fragmentation patterns that incorporated both fragment length and coverage information exhibited robust predictive capacities. Despite their diagnostic potential, the predictive power of these fragmentation patterns is unstable. To address this limitation, an ensemble classifier via integrating all fragmentation patterns is developed, which demonstrated notable improvements in cancer detection and tissue-of-origin determination. Further functional bioinformatics investigations on significant feature intervals in the model revealed its impressive ability to identify critical regulatory regions involved in cancer pathogenesis.

Photodynamic Diagnosis and Therapy in Non-Muscle-Invasive Bladder Cancer

Bladder cancer (BC) possesses distinct molecular profiles that influence progression depending on its biological nature and delivered treatment intensity. Muscle-invasive BC (MIBC) and non-MIBC (NMIBC) demonstrate great intrinsic heterogeneity regarding different prognoses, survival, progression, and treatment outcomes. Transurethral resection of bladder tumor (TURBT) is the standard of care in treating NMIBC and serves both diagnostic and therapeutic purposes despite the prevalent recurrence and progression among many patients. In particular, flat urothelial carcinoma in situ and urothelial carcinoma with lamina propria invasion are the major precursors of MIBC. A new-generation photosensitizer, 5-Aminolevulinic acid (5-ALA), demonstrates high tumor specificity by illuminating the tumor lesion with a specific wavelength of light to produce fluorescence and has been studied for photodynamic diagnosis to detect precise tumor areas by TURBT. Additionally, it has been applied for treatment by producing its cytotoxic reactive oxygen species, as well as screening for urological carcinomas by excreting porphyrin in the blood and urine. Moreover, 5-ALA may contribute to screening before and after TURBT in NMIBC. Here, we summarize the updated evidence and ongoing research on photodynamic technology for NMIBC, providing insight into the potential for improving patient outcomes.

Clinical evaluation of droplet digital PCR in the early identification of suspected sepsis patients in the emergency department: a prospective observational study

Background

Rapid and accurate diagnosis of the causative agents is essential for clinical management of bloodstream infections (BSIs) that might induce sepsis/septic shock. A considerable number of suspected sepsis patients initially enter the health-care system through an emergency department (ED), hence it is vital to establish an early strategy to recognize sepsis and initiate prompt care in ED. This study aimed to evaluate the diagnostic performance and clinical value of droplet digital PCR (ddPCR) assay in suspected sepsis patients in the ED.

Methods

This was a prospective single-centered observational study including patients admitted to the ED from 25 October 2022 to 3 June 2023 with suspected BSIs screened by Modified Shapiro Score (MSS) score. The comparison between ddPCR and blood culture (BC) was performed to evaluate the diagnostic performance of ddPCR for BSIs. Meanwhile, correlative analysis between ddPCR and the inflammatory and prognostic-related biomarkers were conducted to explore the relevance. Further, the health economic evaluation of the ddPCR was analyzed.

Results

258 samples from 228 patients, with BC and ddPCR performed simultaneously, were included in this study. We found that ddPCR results were positive in 48.13% (103 of 214) of episodes, with identification of 132 pathogens. In contrast, BC only detected 18 positives, 88.89% of which were identified by ddPCR. When considering culture-proven BSIs, ddPCR shows an overall sensitivity of 88.89% and specificity of 55.61%, the optimal diagnostic power for quantifying BSI through ddPCR is achieved with a copy cutoff of 155.5. We further found that ddPCR exhibited a high accuracy especially in liver abscess patients. Among all the identified virus by ddPCR, EBV has a substantially higher positive rate with a link to immunosuppression. Moreover, the copies of pathogens in ddPCR were positively correlated with various markers of inflammation, coagulation, immunity as well as prognosis. With high sensitivity and specificity, ddPCR facilitates precision antimicrobial stewardship and reduces health care costs.

Conclusions

The multiplexed ddPCR delivers precise and quantitative load data on the causal pathogen, offers the ability to monitor the patient's condition and may serve as early warning of sepsis in time-urgent clinical situations as ED.

Importance

Early detection and effective administration of antibiotics are essential to improve clinical outcomes for those with life-threatening infection in the emergency department. ddPCR, an emerging tool for rapid and sensitive pathogen identification used as a precise bedside test, has developed to address the current challenges of BSI diagnosis and precise treatment. It characterizes sensitivity, specificity, reproducibility, and absolute quantifications without a standard curve. ddPCR can detect causative pathogens and related resistance genes in patients with suspected BSIs within a span of three hours. In addition, it can identify polymicrobial BSIs and dynamically monitor changes in pathogenic microorganisms in the blood and can be used to evaluate antibiotic efficacy and survival prognosis. Moreover, the copies of pathogens in ddPCR were positively correlated with various markers of inflammation, coagulation, immunity. With high sensitivity and specificity, ddPCR facilitates precision antimicrobial stewardship and reduces health care costs.

Plasma cfDNA abundance as a prognostic biomarker for higher risk of death in geriatric cardiovascular patients

The management of geriatric cardiovascular disease (CVD) patients with multimorbidity remains challenging and could potentially be improved by integrating clinical data with innovative prognostic biomarkers. In this context, the analysis of circulating analytes, including cell-free DNA (cfDNA), appears particularly promising. Here, we investigated circulating cfDNA (measured through the quantification of 247 bp and 115 bp Alu genomic fragments) in a cohort of 244 geriatric CVD patients with multimorbidity hospitalised for acute CVD or non-CVD events. Survival analysis showed a direct association between Alu 247 cfDNA abundance and risk of death, particularly evident in the first six months after admission for acute CVD events. Higher plasma cfDNA concentration was associated with mortality in the same period of time. The cfDNA integrity (Alu 247/115), although not associated with outcome, appeared to be useful in discriminating patients in whom Alu 247 cfDNA abundance is most effective as a prognostic biomarker. The cfDNA parameters were associated with several biochemical markers of inflammation and myocardial damage. In conclusion, an increase in plasma cfDNA abundance at hospital admission is indicative of a higher risk of death in geriatric CVD patients, especially after acute CVD events, and its analysis may be potentially useful for risk stratification.

Serum Cell-Free DNA-based Detection of Mycobacterium avium Complex Infection

Rationale: Mycobacterium avium complex (MAC) is the most common cause of nontuberculous mycobacterial (NTM) pulmonary disease (PD), which exhibits increasing global incidence. Current microbiologic methods routinely used in clinical practice lack sensitivity and have long latencies, leading to delays in diagnosis and treatment initiation and evaluation. A clustered regularly interspaced short palindromic repeats (CRISPR)-based assay that measures MAC cell-free DNA (cfDNA) concentrations in serum could provide a rapid means to detect MAC infection and monitor response to antimicrobial treatment. Objectives: To develop and optimize a CRISPR MAC assay for MAC infection detection and to evaluate its diagnostic and prognostic performance in two MAC disease cohorts. Methods: MAC cfDNA serum concentrations were measured in individuals with diagnoses of MAC disease or who had bronchiectasis or chronic obstructive pulmonary disease diagnoses without histories of NTM PD or NTM-positive sputum cultures. Diagnostic performance was analyzed using pretreatment serum from two cohorts. Serum MAC cfDNA changes during MAC PD treatment were evaluated in a subset of patients with MAC PD who received macrolide-based multidrug regimens. Measurements and Main Results: The CRISPR MAC assay detected MAC cfDNA in MAC PD with 97.6% (91.6-99.7%) sensitivity and 97.6% (91.5-99.7%) specificity overall. Serum MAC cfDNA concentrations markedly decreased after MAC-directed treatment initiation in patients with MAC PD who demonstrated MAC culture conversion. Conclusions: This study provides preliminary evidence for the utility of a serum-based CRISPR MAC assay to rapidly detect MAC infection and monitor the response to treatment.

Therapeutic biomarkers in metastatic castration-resistant prostate cancer: does the state matter?

The treatment of metastatic castration-resistant prostate cancer (mCRPC) has been fundamentally transformed by our greater understanding of its complex biological mechanisms and its entrance into the era of precision oncology. A broad aim is to use the extreme heterogeneity of mCRPC by matching already approved or new targeted therapies to the correct tumor genotype. To achieve this, tumor DNA must be obtained, sequenced, and correctly interpreted, with individual aberrations explored for their druggability, taking into account the hierarchy of driving molecular pathways. Although tumor tissue sequencing is the gold standard, tumor tissue can be challenging to obtain, and a biopsy from one metastatic site or primary tumor may not provide an accurate representation of the current genetic underpinning. Sequencing of circulating tumor DNA (ctDNA) might catalyze precision oncology in mCRPC, as it enables real-time observation of genomic changes in tumors and allows for monitoring of treatment response and identification of resistance mechanisms. Moreover, ctDNA can be used to identify mutations that may not be detected in solitary metastatic lesions and can provide a more in-depth understanding of inter- and intra-tumor heterogeneity. Finally, ctDNA abundance can serve as a prognostic biomarker in patients with mCRPC.The androgen receptor (AR)-axis is a well-established therapeutical target for prostate cancer, and through ctDNA sequencing, insights have been obtained in (temporal) resistance mechanisms that develop through castration resistance. New third-generation AR-axis inhibitors are being developed to overcome some of these resistance mechanisms. The druggability of defects in the DNA damage repair machinery has impacted the treatment landscape of mCRPC in recent years. For patients with deleterious gene aberrations in genes linked to homologous recombination, particularly BRCA1 or BRCA2, PARP inhibitors have shown efficacy compared to the standard of care armamentarium, but platinum-based chemotherapy may be equally effective. A hierarchy exists in genes associated with homologous recombination, where, besides the canonical genes in this pathway, not every other gene aberration predicts the same likelihood of response. Moreover, evidence is emerging on cross-resistance between therapies such as PARP inhibitors, platinum-based chemotherapy and even radioligand therapy that target this genotype. Mismatch repair-deficient patients can experience a beneficial response to immune checkpoint inhibitors. Activation of other cellular signaling pathways such as PI3K, cell cycle, and MAPK have shown limited success with monotherapy, but there is potential in co-targeting these pathways with combination therapy, either already witnessed or anticipated. This review outlines precision medicine in mCRPC, zooming in on the role of ctDNA, to identify genomic biomarkers that may be used to tailor molecularly targeted therapies. The most common druggable pathways and outcomes of therapies matched to these pathways are discussed.

Cell-Free DNA As Peripheral Biomarker of Alzheimer's Disease

Alzheimer's disease (AD) and Alzheimer's disease-related disorders (ADRD) are progressive neurodegenerative diseases without cure. Alzheimer's disease occurs in 2 forms, early-onset familial AD and late-onset sporadic AD. Early-onset AD is a rare (~1%), autosomal dominant, caused by mutations in presenilin-1, presenilin-2, and amyloid precursor protein genes and the other is a late-onset, prevalent and is evolved due to age-associated complex interactions between environmental and genetic factors, in addition to apolipoprotein E4 polymorphism. Cellular senescence, promoting the impairment of physical and mental functions is constituted to be the main cause of aging, the primary risk factor for AD, which results in progressive loss of cognitive function, memory, and visual-spatial skills for an individual to live or act independently. Despite significant progress in the understanding of the biology and pathophysiology of AD, we continue to lack definitive early detectable biomarkers and/or drug targets that can be used to delay the development of AD and ADRD in elderly populations. However, recent developments in the studies of DNA double-strand breaks result in the release of fragmented DNA into the bloodstream and contribute to higher levels of cell-free DNA (cf-DNA). This fragmented cf-DNA can be released into the bloodstream from various cell types, including normal cells and cells undergoing apoptosis or necrosis and elevated levels of cf-DNA in the blood have the potential to serve as blood blood-based biomarker for early detection of AD and ADRD. The overall goal of our study is to discuss the latest developments in circulating cell-free DNA into the blood in the progression of AD and ADRD. Our article summarized the status of research on double-strand breaks and circulating cell-free DNA in both healthy and disease states and how these recent developments can be used to develop early detectable biomarkers for AD and ADRD. Our article also discussed the impact of lifestyle and epigenetic factors that are involved in DNA double-strand breaks and circulating cell-free DNA in AD and ADRD.

Circadian rhythm and circulating cell-free DNA release on healthy subjects

In the last decade, clinical studies have investigated the clinical relevance of circulating cell-free-DNA (ccfDNA) as a diagnostic and prognosis tool in various diseases including cancers. However, limited knowledge on ccfDNA biology restrains its full development in the clinical practice. To improve our understanding, we evaluated the impact of the circadian rhythm on ccfDNA release in healthy subjects over a 24-h period. 10 healthy female subjects underwent blood sampling at 8am and 20 healthy male subjects underwent serial blood sampling (8:00 AM, 9:00 AM, 12:00 PM, 4:00 PM, 8:00 PM, 12:00 AM, 4 AM (+ 1 Day) and 8 AM (+ 1 Day)). We performed digital droplet-based PCR (ddPCR) assays to target 2 DNA fragments (69 & 243 bp) located in the KRAS gene to determine the ccfDNA concentration and fragmentation profile. As control, half of the samples were re-analyzed by capillary miniaturized electrophoresis (BIAbooster system). Overall, we did not detect any influence of the circadian rhythm on ccfDNA release. Instead, we observed a decrease in the ccfDNA concentration after meal ingestion, suggesting either a post-prandial effect or a technical detection bias due to a higher plasma load in lipids and triglycerides. We also noticed a potential effect of gender, weight and creatinine levels on ccfDNA concentration.

Bladder cancer

Bladder cancer is a global health issue with sex differences in incidence and prognosis. Bladder cancer has distinct molecular subtypes with multiple pathogenic pathways depending on whether the disease is non-muscle invasive or muscle invasive. The mutational burden is higher in muscle-invasive than in non-muscle-invasive disease. Commonly mutated genes include TERT, FGFR3, TP53, PIK3CA, STAG2 and genes involved in chromatin modification. Subtyping of both forms of bladder cancer is likely to change considerably with the advent of single-cell analysis methods. Early detection signifies a better disease prognosis; thus, minimally invasive diagnostic options are needed to improve patient outcomes. Urine-based tests are available for disease diagnosis and surveillance, and analysis of blood-based cell-free DNA is a promising tool for the detection of minimal residual disease and metastatic relapse. Transurethral resection is the cornerstone treatment for non-muscle-invasive bladder cancer and intravesical therapy can further improve oncological outcomes. For muscle-invasive bladder cancer, radical cystectomy with neoadjuvant chemotherapy is the standard of care with evidence supporting trimodality therapy. Immune-checkpoint inhibitors have demonstrated benefit in non-muscle-invasive, muscle-invasive and metastatic bladder cancer. Effective management requires a multidisciplinary approach that considers patient characteristics and molecular disease characteristics.

Release of Cell-Free Tumor DNA in the Plasma of Uveal Melanoma Patients Under Radiotherapy

Purpose

Uveal melanoma (UM) is a tumor of the eye that metastasizes in approximately half of cases. Prognostic testing requires accessibility to tumor tissue, which is usually not available with eye-preserving therapies. Noninvasive approaches to prognostic testing that provide valuable information for patient care are therefore needed. The aim of this study was to evaluate the use of circulating cell-free plasma DNA analysis in UM patients undergoing brachytherapy.

Methods

The study recruited 26 uveal melanoma patients referred to the department between February and October 2020. Blood samples were collected at various time points before, during, and after treatment, and deep amplicon sequencing was used to identify oncogenic variant alleles of the GNAQ and GNA11 genes, which serve as indicators for the presence of circulating tumor DNA (ctDNA).

Results

The results showed that all patients were ctDNA negative before brachytherapy. In 31% of patients, ctDNA was detected during therapy. The variant allele fraction of GNAQ or GNA11 alleles in ctDNA positive samples ranged from 0.24% to 2% and correlates with the largest basal diameter and thickness of the tumor.

Conclusions

The findings suggest that brachytherapy increases the presence of tumor DNA in the plasma of UM patients. Thus ctDNA analysis may offer a noninvasive approach for prognostic testing. However, efforts are still required to lower the limit of detection for tumor-specific genetic alterations.

[ctHPV-DNA based precision oncology for patients with oropharyngeal cancer - Where are we?]

Human papillomavirus (HPV) is an established etiologic factor for cancers in the head and neck region, specifically for Oropharyngeal Squamous Cell Carcinoma (OPSCC). The comparatively good overall survival justifies the current discussion regarding therapy de-escalation for patients with a low-risk profile. In addition to the immunohistochemistry-based biomarker p16INK4a, there is still a need for diagnostic and prognostic biomarkers that allow risk stratification and monitoring during therapy and follow-up of these patients. In recent years, liquid biopsy, especially in the form of plasma samples, has gained importance and is already used to monitor viral DNA in patients with Epstein-Barr virus-associated nasopharyngeal carcinoma. Circulating DNA (ctDNA) released by the tumor into the bloodstream is particularly suitable for a high specificity in detecting virus-associated tumors. Detection of viral E6 and E7 oncogenes in HPV-positive OPSCC is predominantly performed by droplet digital/quantitative PCR as well as next generation sequencing. Detection of circulating HPV-DNA derived from tumor cells (ctHPV-DNA) at diagnosis is associated with advanced tumor stage, locoregional and distant metastases. Longitudinal studies have further demonstrated that detectable and/or increasing ctHPV-DNA levels are associated with treatment failure and disease relapse. However, a standardization of the diagnostic procedure is necessary before introducing liquid biopsy into the clinical routine. In the future, this might allow a valid reflection of disease progression in HPV-positive OPSCC.

Clinical Application of a Multiplex Droplet Digital PCR in the Rapid Diagnosis of Children with Suspected Bloodstream Infections

Droplet digital PCR (ddPCR) recently has been shown to be a potential diagnostic tool for adults with bloodstream infections (BSIs); however, its application in children remains obscure. In this study, 76 blood samples of children with suspected BSIs were synchronously detected by traditional blood cultures (BCs) and ddPCRs. Our team validated the diagnostic performance of ddPCR including sensitivity, specificity, and positive and negative predictive values. The 76 pediatric patients from the hematology department (67.1%), the pediatric intensive care unit (PICU, 27.6%), and other departments (5.2%) were enrolled. The positive rate of ddPCR results was 47.9%, whereas that for BC was 6.6%. In addition, the time consumption of ddPCR was shorter, only for 4.7 ± 0.9 h, in comparison with the detection timing of BC (76.7 ± 10.4 h, p < 0.01). The levels of agreement and disagreement between BC and ddPCR were 96.1% and 4.2%, and the negative agreement reached 95.6%. The sensitivity of ddPCR was 100%, with corresponding specificities ranging from 95.3 to 100.0%. In addition, a total of nine viruses were identified by ddPCR. In China, the multiplexed ddPCR first could be a tool for the rapid and accurate diagnosis of children with suspected BSIs and can be an early indicator of the possibility of viraemia in children with immunosuppression.

Liquid biopsies and minimal residual disease in lymphoid malignancies

Minimal residual disease (MRD) assessment using peripheral blood instead of bone marrow aspirate/biopsy specimen or the biopsy of the cancerous infiltrated by lymphoid malignancies is an emerging technique with enormous interest of research and technological innovation at the current time. In some lymphoid malignancies (particularly ALL), Studies have shown that MRD monitoring of the peripheral blood may be an adequate alternative to frequent BM aspirations. However, additional studies investigating the biology of liquid biopsies in ALL and its potential as an MRD marker in larger patient cohorts in treatment protocols are warranted. Despite the promising data, there are still limitations in liquid biopsies in lymphoid malignancies, such as standardization of the sample collection and processing, determination of timing and duration for liquid biopsy analysis, and definition of the biological characteristics and specificity of the techniques evaluated such as flow cytometry, molecular techniques, and next generation sequencies. The use of liquid biopsy for detection of minimal residual disease in T-cell lymphoma is still experimental but it has made significant progress in multiple myeloma for example. Recent attempt to use artificial intelligence may help simplify the algorithm for testing and may help avoid inter-observer variation and operator dependency in these highly technically demanding testing process.

IL-6 and cfDNA monitoring throughout COVID-19 hospitalization are accurate markers of its outcomes

BACKGROUND

Severe COVID-19 entails a dysregulated immune response, most likely inflammation related to a lack of virus control. A better understanding of immune toxicity, immunosuppression balance, and COVID-19 assessments could help determine whether different clinical presentations are driven by specific types of immune responses. The progression of the immune response and tissular damage could predict outcomes and may help in the management of patients.

METHODS

We collected 201 serum samples from 93 hospitalised patients classified as moderately, severely, and critically ill. We differentiated the viral, early inflammatory, and late inflammatory phases and included 72 patients with 180 samples in separate stages for longitudinal study and 55 controls. We studied selected cytokines, P-selectin, and the tissue damage markers lactate dehydrogenase (LDH) and cell-free DNA (cfDNA).

RESULTS

TNF-α, IL-6, IL-8, and G-CSF were associated with severity and mortality, but only IL-6 increased since admission in the critical patients and non-survivors, correlating with damage markers. The lack of a significant decrease in IL-6 levels in the critical patients and non-survivors in the early inflammatory phase (a decreased presence in the other patients) suggests that these patients did not achieve viral control on days 10-16. For all patients, lactate dehydrogenase and cfDNA levels increased with severity, and cfDNA levels increased in the non-survivors from the first sample (p = 0.002) to the late inflammatory phase (p = 0.031). In the multivariate study, cfDNA was an independent risk factor for mortality and ICU admission.

CONCLUSIONS

The distinct progression of IL-6 levels in the course of the disease, especially on days 10-16, was a good marker of progression to critical status and mortality and could guide the start of IL-6 blockade. cfDNA was an accurate marker of severity and mortality from admission and throughout COVID-19 progression.

Cell-free DNA-based liquid biopsies in neurology

This article reviews recent developments in the application of cell-free DNA-based liquid biopsies to neurological diseases. Over the past few decades, an explosion of interest in the use of accessible biofluids to identify and track molecular disease has revolutionized the fields of oncology, prenatal medicine and others. More recently, technological advances in signal detection have allowed for informative analysis of biofluids that are typically sparse in cells and other circulating components, such as CSF. In parallel, advancements in epigenetic profiling have allowed for novel applications of liquid biopsies to diseases without characteristic mutational profiles, including many degenerative, autoimmune, inflammatory, ischaemic and infectious disorders. These events have paved the way for a wide array of neurological conditions to benefit from enhanced diagnostic, prognostic, and treatment abilities through the use of liquid biomarkers: a 'liquid biopsy' approach. This review includes an overview of types of liquid biopsy targets with a focus on circulating cell-free DNA, methods used to identify and probe potential liquid biomarkers, and recent applications of such biomarkers to a variety of complex neurological conditions including CNS tumours, stroke, traumatic brain injury, Alzheimer's disease, epilepsy, multiple sclerosis and neuroinfectious disease. Finally, the challenges of translating liquid biopsies to use in clinical neurology settings-and the opportunities for improvement in disease management that such translation may provide-are discussed.

Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy

Cell-free DNA (cfDNA) and extracellular vesicles (EVs) are molecular biomarkers in liquid biopsies that can be applied for cancer detection, which are known to carry information on the necessary conditions for oncogenesis and cancer cell-specific activities after oncogenesis, respectively. Analyses for both cfDNA and EVs from the same body fluid can provide insights into screening and identifying the molecular subtypes of cancer; however, a major bottleneck is the lack of efficient and standardized techniques for the isolation of cfDNA and EVs from clinical specimens. Here, we achieved catch-and-release isolation by hydrogen bond-mediated binding of cfDNA in urine to zinc oxide (ZnO) nanowires, which also capture EVs by surface charge, and subsequently we identified genetic mutations in urinary cfDNA. The binding strength of hydrogen bonds between single-crystal ZnO nanowires and DNA was found to be equal to or larger than that of conventional hydrophobic interactions, suggesting the possibility of isolating trace amounts of cfDNA. Our results demonstrated that nanowire-based cancer screening assay can screen cancer and can identify the molecular subtypes of cancer in urine from brain tumor patients through EV analysis and cfDNA mutation analysis. We anticipate our method to be a starting point for more sophisticated diagnostic models of cancer screening and identification.

Phase I Study and Cell-Free DNA Analysis of T-DM1 and Metronomic Temozolomide for Secondary Prevention of HER2-Positive Breast Cancer Brain Metastases

PURPOSE

Preclinical data showed that prophylactic, low-dose temozolomide (TMZ) significantly prevented breast cancer brain metastasis. We present results of a phase I trial combining T-DM1 with TMZ for the prevention of additional brain metastases after previous occurrence and local treatment in patients with HER2+ breast cancer.

PATIENTS AND METHODS

Eligible patients had HER2+ breast cancer with brain metastases and were within 12 weeks of whole brain radiation therapy (WBRT), stereotactic radiosurgery, and/or surgery. Standard doses of T-DM1 were administered intravenously every 21 days (3.6 mg/kg) and TMZ was given orally daily in a 3+3 phase I dose escalation design at 30, 40, or 50 mg/m2, continuously. DLT period was one 21-day cycle. Primary endpoint was safety and recommended phase II dose. Symptom questionnaires, brain MRI, and systemic CT scans were performed every 6 weeks. Cell-free DNA sequencing was performed on patients' plasma and CSF.

RESULTS

Twelve women enrolled, nine (75%) with prior SRS therapy and three (25%) with prior WBRT. Grade 3 or 4 AEs included thrombocytopenia (1/12), neutropenia (1/12), lymphopenia (6/12), and decreased CD4 (6/12), requiring pentamidine for Pneumocystis jirovecii pneumonia prophylaxis. No DLT was observed. Four patients on the highest TMZ dose underwent dose reductions. At trial entry, 6 of 12 patients had tumor mutations in CSF, indicating ongoing metastatic colonization despite a clear MRI. Median follow-up on study was 9.6 m (2.8-33.9); only 2 patients developed new parenchymal brain metastases. Tumor mutations varied with patient outcome.

CONCLUSIONS

Metronomic TMZ in combination with standard dose T-DM1 shows low-grade toxicity and potential activity in secondary prevention of HER2+ brain metastases.

Bridging biological cfDNA features and machine learning approaches

Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of cell-free DNA (cfDNA) biology, are enabling the detection of tumor-specific changes with extremely high resolution and new analysis concepts beyond genetic alterations, including methylomics, fragmentomics, and nucleosomics. The interrogation of a large number of markers and the high complexity of data render traditional correlation methods insufficient. In this regard, machine learning (ML) algorithms are increasingly being used to decipher disease- and tissue-specific signals from cfDNA. Here, we review recent insights into biological ctDNA features and how these are incorporated into sophisticated ML applications.

Liquid biopsy by analysis of circulating myeloma cells and cell-free nucleic acids: a novel noninvasive approach of disease evaluation in multiple myeloma

Multiple myeloma (MM) is an incurable hematological cancer with high spatial- and temporal-heterogeneity. Invasive single-point bone marrow sampling cannot capture the tumor heterogeneity and is difficult to repeat for serial assessments. Liquid biopsy is a technique for identifying and analyzing circulating MM cells and cell products produced by tumors and released into the circulation, allowing for the minimally invasive and comprehensive detection of disease burden and molecular alterations in MM and monitoring treatment response and disease progression. Furthermore, liquid biopsy can provide complementary information to conventional detection approaches and improve their prognostic values. This article reviewed the technologies and applications of liquid biopsy in MM.

Methylation pattern of caveolin-1 in prostate cancer as potential cfDNA biomarker

High prevalence and mortality of prostate cancer (PCa) are well known global health issues. Novel biomarkers for better identifying patients with PCa are the subject of extensive research. Prostate specific antigen (PSA) shows low specificity in screening and diagnostics, leading to unnecessary biopsies and health costs. Eighty patients with PCa and benign prostate hyperplasia (BPH) were included in the study. We analyzed CAV1 gene expression and methylation in tissue. CAV1 cfDNA methylation from blood and seminal plasma was accessed as a potential PCa biomarker. Although methylation in blood plasma did not differ between PCa and BPH patients, methylation in seminal plasma showed better PCa biomarker performances than tPSA (AUC 0.63 vs. AUC 0.52). Discrimination of BPH and Gleason grade group 1 PCa patients from patients with higher Gleason grade groups revealed very good performance as well (AUC 0.72). CAV1 methylation is useful biomarker with potential for further seminal plasma cfDNA research, but its diagnostic accuracy should be improved, as well as general knowledge about cfDNA in seminal plasma.

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

BACKGROUND

Despite advances in early detection and therapies, cancer is still one of the most common causes of death worldwide. Since each tumor is unique, there is a need to implement personalized care and develop robust tools for monitoring treatment response to assess drug efficacy and prevent disease relapse.

MAIN BODY

Recent developments in liquid biopsies have enabled real-time noninvasive monitoring of tumor burden through the detection of molecules shed by tumors in the blood. These molecules include circulating tumor nucleic acids (ctNAs), comprising cell-free DNA or RNA molecules passively and/or actively released from tumor cells. Often highlighted for their diagnostic, predictive, and prognostic potential, these biomarkers possess valuable information about tumor characteristics and evolution. While circulating tumor DNA (ctDNA) has been in the spotlight for the last decade, less is known about circulating tumor RNA (ctRNA). There are unanswered questions about why some tumors shed high amounts of ctNAs while others have undetectable levels. Also, there are gaps in our understanding of associations between tumor evolution and ctNA characteristics and shedding kinetics. In this review, we summarize current knowledge about ctNA biology and release mechanisms and put this information into the context of tumor evolution and clinical utility.

CONCLUSIONS

A deeper understanding of the biology of ctDNA and ctRNA may inform the use of liquid biopsies in personalized medicine to improve cancer patient outcomes.

Biomarkers of cell damage, neutrophil and macrophage activation associated with in-hospital mortality in geriatric COVID-19 patients

BACKGROUND

The risk for symptomatic COVID-19 requiring hospitalization is higher in the older population. The course of the disease in hospitalised older patients may show significant variation, from mild to severe illness, ultimately leading to death in the most critical cases. The analysis of circulating biomolecules involved in mechanisms of inflammation, cell damage and innate immunity could lead to identify new biomarkers of COVID-19 severity, aimed to improve the clinical management of subjects at higher risk of severe outcomes. In a cohort of COVID-19 geriatric patients (n= 156) who required hospitalization we analysed, on-admission, a series of circulating biomarkers related to neutrophil activation (neutrophil elastase, LL-37), macrophage activation (sCD163) and cell damage (nuclear cfDNA, mithocondrial cfDNA and nuclear cfDNA integrity). The above reported biomarkers were tested for their association with in-hospital mortality and with clinical, inflammatory and routine hematological parameters. Aim of the study was to unravel prognostic parameters for risk stratification of COVID-19 patients.

RESULTS

Lower n-cfDNA integrity, higher neutrophil elastase and higher sCD163 levels were significantly associated with an increased risk of in-hospital decease. Median (IQR) values observed in discharged vs. deceased patients were: 0.50 (0.30-0.72) vs. 0.33 (0.22-0.62) for n-cfDNA integrity; 94.0 (47.7-154.0) ng/ml vs. 115.7 (84.2-212.7) ng/ml for neutrophil elastase; 614.0 (370.0-821.0) ng/ml vs. 787.0 (560.0-1304.0) ng/ml for sCD163. The analysis of survival curves in patients stratified for tertiles of each biomarker showed that patients with n-cfDNA integrity < 0.32 or sCD163 in the range 492-811 ng/ml had higher risk of in-hospital decease than, respectively, patients with higher n-cfDNA integrity or lower sCD163. These associations were further confirmed in multivariate models adjusted for age, sex and outcome-related clinical variables. In these models also high levels of neutrophil elastase (>150 ng/ml) appeared to be independent predictor of in-hospital death. An additional analysis of neutrophil elastase in patients stratified for n-cfDNA integrity levels was conducted to better describe the association of the studied parameters with the outcome.

CONCLUSIONS

On the whole, biomarkers of cell-free DNA integrity, neutrophil and macrophage activation might provide a valuable contribution to identify geriatric patients with high risk of COVID-19 in-hospital mortality.

Nanopore sequencing of clonal IGH rearrangements in cell-free DNA as a biomarker for acute lymphoblastic leukemia

Background

Acute Lymphoblastic Leukemia (ALL) is the most common pediatric cancer, and patients with relapsed ALL have a poor prognosis. Detection of ALL blasts remaining at the end of treatment, or minimal residual disease (MRD), and spread of ALL into the central nervous system (CNS) have prognostic importance in ALL. Current methods to detect MRD and CNS disease in ALL rely on the presence of ALL blasts in patient samples. Cell-free DNA, or small fragments of DNA released by cancer cells into patient biofluids, has emerged as a robust and sensitive biomarker to assess cancer burden, although cfDNA analysis has not previously been applied to ALL.

Methods

We present a simple and rapid workflow based on NanoporeMinION sequencing of PCR amplified B cell-specific rearrangement of the (IGH) locus in cfDNA from B-ALL patient samples. A cohort of 5 pediatric B-ALL patient samples was chosen for the study based on the MRD and CNS disease status.

Results

Quantitation of IGH-variable sequences in cfDNA allowed us to detect clonal heterogeneity and track the response of individual B-ALL clones throughout treatment. cfDNA was detected in patient biofluids with clinical diagnoses of MRD and CNS disease, and leukemic clones could be detected even when diagnostic cell-count thresholds for MRD were not met. These data suggest that cfDNA assays may be useful in detecting the presence of ALL in the patient, even when blasts are not physically present in the biofluid sample.

Conclusions

The Nanopore IGH detection workflow to monitor cell-free DNA is a simple, rapid, and inexpensive assay that may ultimately serve as a valuable complement to traditional clinical diagnostic approaches for ALL.

Circulating Tumor DNA Allele Fraction: A Candidate Biological Signal for Multicancer Early Detection Tests to Assess the Clinical Significance of Cancers

Current imaging-based cancer screening approaches provide useful but limited prognostic information. Complementary to existing screening tests, cell-free DNA-based multicancer early detection (MCED) tests account for cancer biology [manifested through circulating tumor allele fraction (cTAF)], which could inform prognosis and help assess the cancer's clinical significance. This review discusses the factors affecting circulating tumor DNA (ctDNA) levels and cTAF, and their correlation with the cancer's clinical significance. Furthermore, it discusses the influence of cTAF on MCED test performance, which could help inform prognosis. Clinically significant cancers show higher ctDNA levels quantified by cTAF than indolent phenotype cancers within each stage. This is because more frequent mitosis and cell death combined with increased trafficking of cell-free DNA into circulation leads to greater vascularization and depth of tumor invasion. cTAF has been correlated with biomarkers for cancer aggressiveness and overall survival; cancers with lower cTAF had better survival when compared with cancers as determined by the higher cTAF and Surveillance, Epidemiology, and End Results-based survival for that cancer type at each stage. MCED-detected cancers in case-control studies had comparable survival to Surveillance, Epidemiology, and End Results-based survival at each stage. Because many MCED tests use ctDNA as an analyte, cTAF could provide a common metric to compare performance. The prognostic value of cTAF may allow MCED tests to preferentially detect clinically significant cancers at early stages when outcomes are favorable and this may avoid overdiagnosis.

Tumor volume as a predictor of cell free DNA mutation detection in advanced non-small cell lung cancer

Background

Cell free DNA (cfDNA) is an exciting biomarker with applications across the cancer care continuum. Determinants of cfDNA shedding dynamics remain an active research area. We performed a detailed analysis of tumor volume and factors associated with detection of cfDNA mutations.

Methods

Patients with advanced non-small cell lung cancers (NSCLCs) were prospectively enrolled on a plasma biomarker protocol. Next generation sequencing (NGS) was performed using a validated, bias-corrected, hybrid-capture panel assay of lung cancer-associated genes. Volume of tumor in different subsites and total tumor volume were determined through manual volume delineation using PET/CT and brain magnetic resonance imaging (MRI) imaging. The primary endpoint was detection of cfDNA mutation; secondary endpoints were overall survival (OS) and variant allele frequency (VAF).

Results

There were 110 patients included, 78 of whom had at least one mutation detected. Median total tumor volume for the entire cohort, patients with mutation detected, and patients with no mutation detected were 66 mL (range, 2-1,383 mL), 76 mL (range, 5-1,383 mL), and 45 mL (range, 2-460 mL), respectively (P=0.002; mutation detected vs. not). The optimal total tumor volume threshold to predict increased probability of mutation detection was 65 mL (P=0.006). Total tumor volume greater than 65 mL was a significant predictor of mutation detection on multivariate analysis (OR: 4.30, P=0.003). Significant predictors of OS were age (HR: 1.04, P=0.002), detection of cfDNA mutation (HR: 2.11, P=0.024), and presence of bone metastases (HR: 1.66, P=0.047).

Conclusions

Total tumor volume greater than 65 mL was associated with cfDNA mutation detection in patients with advanced NSCLC.

Applications of Liquid Biopsies in Non-Small-Cell Lung Cancer

The concept of liquid biopsy as an analysis tool for non-solid tissue carried out for the purpose of providing information about solid tumors was introduced approximately 20 years ago. Additional to the detection of circulating tumor cells (CTCs), the liquid biopsy approach quickly included the analysis of circulating tumor DNA (ctDNA) and other tumor-derived markers such as circulating cell-free RNA or extracellular vesicles. Liquid biopsy is a non-invasive technique for detecting multiple cancer-associated biomarkers that is easy to obtain and can reflect the characteristics of the entire tumor mass. Currently, ctDNA is the key component of the liquid biopsy approach from the point of view of the prognosis assessment, prediction, and monitoring of the treatment of non-small-cell lung cancer (NSCLC) patients. ctDNA in NSCLC patients carries variants or rearrangements that drive carcinogenesis, such as those in EGFR, KRAS, ALK, or ROS1. Due to advances in pharmacology, these variants are the subject of targeted therapy. Therefore, the detection of these variants has gained attention in clinical medicine. Recently, methods based on qPCR (ddPCR, BEAMing) and next-generation sequencing (NGS) are the most effective approaches for ctDNA analysis. This review addresses various aspects of the use of liquid biopsy with an emphasis on ctDNA as a biomarker in NSCLC patients.

Circulating Tumor DNA in Pediatric Cancer

The measurement of circulating tumor DNA (ctDNA) has gained increasing prominence as a minimally invasive tool for the detection of cancer-specific markers in plasma. In adult cancers, ctDNA detection has shown value for disease-monitoring applications including tumor mutation profiling, risk stratification, relapse prediction, and treatment response evaluation. To date, there are ctDNA tests used as companion diagnostics for adult cancers and it is not understood why the same cannot be said about childhood cancer, despite the marked differences between adult and pediatric oncology. In this review, we discuss the current understanding of ctDNA as a disease monitoring biomarker in the context of pediatric malignancies, including the challenges associated with ctDNA detection in liquid biopsies. The data and conclusions from pediatric cancer studies of ctDNA are summarized, highlighting treatment response, disease monitoring and the detection of subclonal disease as applications of ctDNA. While the data from retrospective studies highlight the potential of ctDNA, large clinical trials are required for ctDNA analysis for routine clinical use in pediatric cancers. We outline the requirements for the standardization of ctDNA detection in pediatric cancers, including sample handling and reproducibility of results. With better understanding of the advantages and limitations of ctDNA and improved detection methods, ctDNA analysis may become the standard of care for patient monitoring in childhood cancers.

Cell‐free DNA as a biomarker after lung transplantation: A proof‐of‐concept study

Background

Methods

Results

Conclusions

Oxidative nucleic acid damage as a biomarker for preeclampsia

Recent studies have reported that nucleic acid oxidation is elevated in preeclampsia. Furthermore, it is known that products of nucleic acid oxidation are eventually removed through the urine. The aim of this study was to check whether urine can be used as a non-invasive specimen to analyse nucleic acid oxidation in preeclampsia. We carried out a case-control study by enrolling preeclamptic pregnant (n = 31) and normotensive pregnant (n = 31) women. Urine samples from the study participants were collected and the levels of oxidised guanine species (a common product of nucleic acid oxidation) were determined by ELISA method. The urinary levels of oxidised guanine species were significantly higher in the preeclamptic pregnant group compared to the normotensive pregnant group (p = 0.001). The results were also analysed after stratifying the preeclamptic group in terms of severity and gestational age of onset. A significant difference was observed in both mild (p = 0.005) and severe preeclampsia (p = 0.01). However, a significant difference was observed only in the late onset (p = 0.001) and not in the early onset preeclampsia (p = 0.56). The results of this study show that oxidised guanine level is elevated in the urine of preeclamptic pregnant women. IMPACT STATEMENTWhat is already known on this subject? Nucleic acid oxidation is elevated in preeclampsia. However, the utility of urine (a non-invasive specimen) to analyse nucleic acid oxidation is not known.What do the results of this study add? This study shows that the levels of oxidised guanine (a marker of nucleic acid oxidation) are elevated in the urine of preeclamptic women.What are the implications of these findings for clinical practice and/or further research? Urinary levels of oxidised guanine may be developed as a non-invasive biomarker for preeclampsia.

Plasma DNA and deoxyribonuclease are associated with glucose metabolism in healthy mice

It is currently unknown why obesity leads in some patients to prediabetes and metabolic syndrome. Microinflammation potentially caused by extracellular DNA is supposed to be involved. The aim of this cross-sectional study in healthy mice was to analyze the association between plasma extracellular DNA and glucose metabolism. Fasting glycemia and insulin were measured in healthy adult female mice that subsequently underwent an oral glucose tolerance test. Indices of glucose metabolism and insulin sensitivity were calculated. DNA was isolated from plasma and quantified fluorometrically. Deoxyribonuclease (DNase) activity of plasma was measured using the single radial enzyme diffusion method. Fasting glycemia correlated negatively with both, extracellular DNA and DNase (r = -0.44 and r = -0.32, respectively). DNase was associated positively with the incremental area under curve (r = 0.35), while extracellular DNA correlated negatively with total area under curve of glycemia during oral glucose tolerance test (r = -0.34). Measures of insulin sensitivity were found to be associated with neither extracellular DNA, nor DNase. The hypothesis of an association of low DNase with increased fasting glucose was partially proved. Surprisingly, low extracellular DNA is associated with higher fasting glucose and lower glucose tolerance in mice. As novel therapeutic targets for prediabetes and metabolic syndrome are highly needed, this study provides novel unexpected associations within the limitations of the focus on physiological variability as it was conducted on healthy mice. The causality of these associations should be proved in further interventional experiments.

The Minimal Residual Disease Using Liquid Biopsies in Hematological Malignancies

The study of cell-free DNA (cfDNA) and other peripheral blood components (known as "liquid biopsies") is promising, and has been investigated especially in solid tumors. Nevertheless, it is increasingly showing a greater utility in the diagnosis, prognosis, and response to treatment of hematological malignancies; in the future, it could prevent invasive techniques, such as bone marrow (BM) biopsies. Most of the studies about this topic have focused on B-cell lymphoid malignancies; some of them have shown that cfDNA can be used as a novel way for the diagnosis and minimal residual monitoring of B-cell lymphomas, using techniques such as next-generation sequencing (NGS). In myelodysplastic syndromes, multiple myeloma, or chronic lymphocytic leukemia, liquid biopsies may allow for an interesting genomic representation of the tumor clones affecting different lesions (spatial heterogeneity). In acute leukemias, it can be helpful in the monitoring of the early treatment response and the prediction of treatment failure. In chronic lymphocytic leukemia, the evaluation of cfDNA permits the definition of clonal evolution and drug resistance in real time. However, there are limitations, such as the difficulty in obtaining sufficient circulating tumor DNA for achieving a high sensitivity to assess the minimal residual disease, or the lack of standardization of the method, and clinical studies, to confirm its prognostic impact. This review focuses on the clinical applications of cfDNA on the minimal residual disease in hematological malignancies.

Liquid Biopsy for Promising Non-invasive Diagnostic Biomarkers in Parasitic Infections

BACKGROUND

Liquid biopsy refers to the sampling and molecular analysis of body fluids such as blood, saliva, and urine in contrast to conventional tissue biopsies. Liquid biopsy approach can offer powerful non-invasive biomarkers (circulating markers) for diagnosis and monitoring treatment response of a variety of diseases, including parasitic infections.

METHODS

In this review, we concentrate on cell-free DNA (cfDNA), microRNA (miRNA), and exosomes in the published literature.

RESULTS

Considering the high prevalence and severity of parasitic infections worldwide, circulating biomarkers can provide a new insight into the diagnosis and prognosis of parasites in the near future. Moreover, identifying and characterizing parasite- or host-derived circulating markers are important for a better understanding of the pathogenesis of parasite infection and host-parasite relationship at the molecular level. Profiling of biomarkers for parasitic diseases is a promising potential field, though further studies and optimization strategies are required, both in vitro and in vivo.

CONCLUSION

In this review, we discuss three approaches in the liquid biopsy including circulating cfDNA, miRNAs, and exosomes for diagnosis and evaluation of parasites and summarize circulating biomarkers in non-invasive samples during parasitic infections.

A Review of Circulating Tumor DNA in the Diagnosis and Monitoring of Esophageal Cancer

Circulating tumor DNA (ctDNA) is a type of cell-free DNA released by tumor cells after necrosis and apoptosis, and it can be actively secreted by tumor cells. Since ctDNA is derived from various tumor sites, it can provide far more comprehensive genomic and epigenomic information than a single-site biopsy. Therefore, ctDNA can overcome tumor heterogeneity, which is the major limitation of a traditional tissue biopsy approach. Noninvasive ctDNA assays allow continuous real-time monitoring of the molecular status of cancers. Recently, ctDNA assays have been widely used in clinical practice, including cancer diagnosis, evaluation of therapeutic efficacy and prognosis, and monitoring of relapse and metastasis. Although ctDNA shows a high diagnostic performance in advanced esophageal cancer, it is far from satisfactory for early diagnosis of esophageal cancer. Monitoring the dynamic changes of ctDNA is beneficial for the evaluation of therapeutic efficacy and prediction of early recurrence in esophageal cancer. It is necessary to establish standards for individualized ctDNA detection in the evaluation of treatment response and surveillance of esophageal cancer and to develop clinical practice guideline for the systemic treatment of patients with "ctDNA recurrence." This review aims to provide an update on the role of ctDNA in the diagnosis and monitoring of esophageal cancer.

Cell-free DNA as a solid-organ transplant biomarker: technologies and approaches

High-quality biomarkers that detect emergent graft damage and/or rejection after solid-organ transplantation offer new opportunities to improve post-transplant monitoring, allow early therapeutic intervention and facilitate personalized patient management. Donor-derived cell-free DNA (DD-cfDNA) is a particularly exciting minimally invasive biomarker because it has the potential to be quantitative, time-sensitive and cost-effective. Increased DD-cfDNA has been associated with graft damage and rejection episodes. Efforts are underway to further improve sensitivity and specificity. This review summarizes the procedures used to process and detect DD-cfDNA, measurement of DD-cfDNA in clinical transplantation, approaches for improving sensitivity and specificity and long-term prospects as a transplant biomarker to supplement traditional organ monitoring and invasive biopsies.

Cell-free tumor DNA, CA125 and HE4 for the objective assessment of tumor burden in patients with advanced high-grade serous ovarian cancer

BACKGROUND

The present prospective study aimed at determining the impact of cell-free tumor DNA (ct-DNA), CA125 and HE4 from blood and ascites for quantification of tumor burden in patients with advanced high-grade serous epithelial ovarian cancer (EOC).

METHODS

Genomic DNA was extracted from tumor FFPE and ct-DNA from plasma before surgery and on subsequent post-surgical days. Extracted DNA was subjected to hybrid-capture based next generation sequencing. Blood and ascites were sampled before surgery and on subsequent post-surgical days. 20 patients (10 undergoing complete resection (TR0), 10 undergoing incomplete resection (TR>0)) were included.

RESULTS

The minor allele frequency (MAF) of TP53 mutations in ct-DNA of all patients with TR0 decreased significantly, compared to only one patient with TR>0. It was not possible to distinguish between patients with TR0 and patients with TR>0, using CA125 and HE4 from blood and ascites.

CONCLUSIONS

Based upon the present findings, ct-DNA assessment in patients with high-grade serous EOC might help to better determine disease burden compared to standard tumor markers. Further studies should prospectively evaluate whether this enhancement of accuracy can help to optimize management of patients with EOC.