Liquid biopsies come of age: towards implementation of circulating tumour DNA

Entropy driven-based catalytic biosensors for bioanalysis: From construction to application-A review

The rapid advancement of precision medicine and the continuous emergence of novel pathogens have presented new challenges for biosensors, necessitating higher requirements. Target amplification technology serves as the core component in biosensor construction. Enzyme-based amplification methods are often sensitive and selective but involve relatively complex operational steps, whereas enzyme-free amplification methods offer simplicity but frequently fail to meet both sensitivity and selectivity simultaneously. Existing research has confirmed that entropy-driven catalyst (EDC) biosensors not only fulfills the demands for sensitivity and selectivity concurrently but also offers ease of operation and flexibility in construction. In this review, we summarize the key advantages of EDC, explore how to construct DNA nanomachines based on these advantages to achieve intracellular detection and simultaneous detection of multiple targets, as well as point-of-care testing (POCT) to address practical issues in clinical diagnosis and treatment. We also anticipate potential challenges, propose corresponding solutions, and outline future development directions for EDC-based biosensors in practical clinical applications. We firmly believe that EDC sensors will emerge as a crucial branch within the realm of biosensor development.

Immune checkpoint inhibitors for glioblastoma: emerging science, clinical advances, and future directions

Glioblastoma (GBM), the most common and aggressive primary central nervous system (CNS) tumor in adults, continues to have a dismal prognosis. Across hundreds of clinical trials, few novel approaches have translated to clinical practice while survival has improved by only a few months over the past three decades. Randomized controlled trials of immune checkpoint inhibitors (ICIs), which have seen impressive success for advanced or metastatic extracranial solid tumors, have so far failed to demonstrate a clinical benefit for patients with GBM. This has been secondary to GBM heterogeneity, the unique immunosuppressive CNS microenvironment, immune-evasive strategies by cancer cells, and the rapid evolution of tumor on therapy. This review aims to summarize findings from major clinical trials of ICIs for GBM, review historic failures, and describe currently promising avenues of investigation. We explore the biological mechanisms driving ICI responses, focusing on the role of the tumor microenvironment, immune evasion, and molecular biomarkers. Beyond conventional monotherapy approaches targeting PD-1, PD-L1, CTLA-4, we describe emerging approaches for GBM, such as dual-agent ICIs, and combination of ICIs with oncolytic virotherapy, antigenic peptide vaccines, chimeric antigenic receptor (CAR) T-cell therapy, along with nanoparticle-based delivery systems to enhance ICI efficacy. We highlight potential strategies for improving patient selection and treatment personalization, along with real-time, longitudinal monitoring of therapeutic responses through advanced imaging and liquid biopsy techniques. Integrated radiomics, tissue, and plasma-based analyses, may potentially uncover immunotherapeutic response signatures, enabling early, adaptive therapeutic adjustments. By specifically targeting current therapeutic challenges, outcomes for GBM patients may potentially be improved.

Evaluation of circulating tumor DNA as a prognostic and predictive biomarker in BRAF V600E mutated colorectal cancer-results from the FIRE-4.5 study

The randomized FIRE-4.5 (AIO KRK0116) trial compared first-line therapy with FOLFOXIRI (folinic acid, fluorouracil, oxaliplatin, and irinotecan) plus either cetuximab or bevacizumab in B-Raf proto-oncogene, serine/threonine kinase (BRAF) V600E-mutant metastatic colorectal cancer (mCRC) patients. This study was accompanied by a prospective translational project analyzing cell-free circulating tumor DNA (ctDNA) in plasma to test whether ctDNA analysis may help to guide clinical treatment decision making. FIRE-4.5 included mCRC patients with BRAF V600E mutation detected by tissue-based analyses. Liquid biopsies (LBs) were collected at baseline (pre-treatment) and during therapy. Digital droplet PCR (ddPCR) technology was applied for determination of BRAF mutations and the in vitro diagnostics (IVD)-certified ONCOBEAM RAS procedure for analysis of RAS mutations. The BRAF V600E variants in ctDNA were analyzable in 66 patients at start of the therapy, at baseline. No BRAF V600E mutations were detected in 26% (17/66) of patients and was associated with a significantly longer progression-free survival (PFS: 13.2 vs 6.5 months; HR 0.47; P = 0.014) and overall survival (OS: 36.8 vs 13.2 months; HR 0.35; P = 0.02) as compared to ctDNA mutant patients. Patients with detectable BRAF mutations showed a clear superiority of FOLFOXIRI plus bevacizumab with regard to PFS (10.4 vs 5.7 months; HR 0.4; P = 0.009) and OS (16.6 vs 11.6 months; HR 0.5; P = 0.15), while this was not the case for BRAF wild-type patients. Follow-up LBs were obtained from 51 patients. Patients converting from BRAF V600E mutant to a BRAF V600 wild-type status (36%, N = 18) had a superior PFS (8.6 vs 2.3 months; P = 0.0002) and OS (17.4 vs 5.1 months; P < 0.0001) compared to patients with stable or increased mutational allele frequency (12%, N = 6). Those patients also achieved a significantly greater disease control rate (89% vs 20%; P = 0.008). In conclusion, LB evaluating ctDNA is informative and may help to guide treatment in patients with BRAF V600E-mutated mCRC.

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

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

Potentialities and critical issues of liquid biopsy in clinical practice: An umbrella review

BACKGROUND

Liquid biopsy (LB) is a laboratory test performed on a fluid sample aiming at analyzing molecular data derived from circulating cells and related entities, or from nucleic acids. This umbrella review aims to map and evaluate the evidence supporting the use of LB in medicine across different medical specialities and conditions.

METHODS

We searched three repositories from database inception up to October 1, 2023 and we included meta-analyses of observational studies reporting data on the use of LB, compared to gold standard, and its accuracy (area under the curve, AUC).

RESULTS

Among 726 articles initially screened, 42 systematic reviews were included. Most of the outcomes explored (202/211) were related to cancer. We found that 75/211 had an excellent accuracy (AUC >0.90), with one comparison with an AUC equal to 1, i.e., Cell-Free Human Papillomavirus DNA (cfHPV-DNA) for HPV-positive oropharyngeal squamous cell carcinoma. However, considering published meta-analyses, all the outcomes were graded as very low on the GRADE criteria, and the heterogeneity was never reported.

DISCUSSION

The literature about LB is rapidly increasing and some promising data about precision oncology are now available. However, this umbrella review on existing meta-analyses highlighted some critical issues for providing quantitative estimations on the different roles of LB.

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

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

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.

Whole-genome sequencing of cell-free DNA reveals DNA of tumor origin in plasma from patients with colorectal adenomas

The presence of circulating tumor DNA (ctDNA) in patients with colorectal adenomas remains uncertain. Studies using tumor-agnostic approaches report ctDNA in 10-15% of patients, though with uncertainty as to whether the signal originates from the adenoma. To obtain an accurate estimate of the proportion of patients with ctDNA, a sensitive tumor-informed strategy is preferred, as it ensures the detected signal originates from the adenoma. Here, tumor-informed whole-genome sequencing-based ctDNA analysis (MRD-EDGESNV) was applied to two independent cohorts. Cohort 1, comprising 93 patients with stage III colorectal cancer (CRC) and 40 healthy individuals, was used to establish the signal threshold at 95% specificity. This threshold was then applied to Cohort 2, consisting of 22 patients with symptomatic and 20 with asymptomatic adenomas. In stage III, MRD-EDGESNV had an area under the curve of 0.98. ctDNA was detected in 50% and 25% of patients with symptomatic and asymptomatic adenomas, respectively. The median adenoma plasma tumor fraction was 5.9 × 10-5. These finding not only demonstrate the feasibility of ctDNA detection in patients with colorectal adenomas, but also provides an estimate of the necessary sensitivity required to detect these lesions, paving the way for future ctDNA-based screening strategies.

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

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

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.

Highly specific multiplex DNA methylation detection for liquid biopsy of colorectal cancer

BACKGROUND

Circulating tumor DNA (ctDNA) has emerged as a useful biomarker for cancer detection and prognosis. In this study, we developed a strategy for developing a highly specific multiplex qPCR assay to detect methylated ctDNA in the blood of colorectal cancer (CRC) patients and investigated the potential use for the detection and prognosis of CRC.

METHODS

Bisulfite conversion and amplicon sequencing were used to confirm potential CRC-specific DNA methylation markers. The selected DNA methylation candidates were validated by qMSP. The six best-performing markers were used to develop a new single-tube multiplex quantitative methylation-specific PCR assay (mqMSP). The mqMSP assay was applied to analyze plasma samples from 114 CRC patients, 47 patients with advanced adenoma, 45 patients with benign polyps, and 57 healthy controls. The clinical performance of the assay and associations with clinical outcomes were assessed.

RESULTS

Six DNA methylation biomarkers were confirmed to be specifically hypermethylated in CRC tumor tissues. The newly developed mqMSP assay detected CRC with extremely high specificity (specificity of 98.2 %, with sensitivity of 67.5 %). The detection rate of ctDNA was significantly correlated with tumor size and clinical stage, with ctDNA methylation levels in the blood markedly increased with larger tumor size, poor differentiation, and advanced stage. Moreover, high preoperative methylated ctDNA level was associated with worse recurrence-free survival and overall survival.

CONCLUSION

We provided a strategy for identification of multiple highly-specific DNA methylation markers for designing multiplex DNA methylation assays for liquid biopsies of CRC. The newly developed assay has potential for CRC early detection, and prognosis.

Early detection of canine hemangiosarcoma via cfDNA fragmentation and copy number alterations in liquid biopsies using machine learning

Hemangiosarcoma is a highly malignant tumor commonly affecting canines, originating from endothelial cells that line blood vessels, underscoring the importance of early detection. This canine cancer is analogous to human angiosarcoma, and the development of liquid biopsies leveraging cell-free DNA (cfDNA) represents a promising step forward in early cancer diagnosis. In this study, we utilized Whole Genome Sequencing (WGS) to analyze fragment sizes and copy number alterations (CNAs) in cfDNA from 21 hemangiosarcoma-affected and 36 healthy dogs, aiming to enhance early cancer detection accuracy through machine learning models. Our findings reveal that similar to trends in human oncology, hemangiosarcoma samples exhibited shorter DNA fragment sizes compared to healthy controls, with a notable leftward shift in the primary peak. Interestingly, canine hemangiosarcoma DNA fragment sizes demonstrated eight distinct periodic patterns diverging from those typically observed in human angiosarcoma. Additionally, we identified seven novel genomic gains and nine losses in the hemangiosarcoma samples. Applying machine learning to the cfDNA fragment size distribution, we achieved an impressive average Area Under the Curve (AUC) of 0.93 in 10-fold cross-validation, underscoring the potential of this approach for precise early-stage cancer classification. This study confirms distinctive cfDNA fragment size and CNA patterns in hemangiosarcoma-affected vs. healthy dogs and demonstrates the promise of these biomarkers in canine cancer screening, early detection, and monitoring via liquid biopsies. These findings establish a foundation for broader research on cfDNA analysis in various canine cancers, integrating methodologies from human oncology to enhance early detection and diagnostic precision in veterinary medicine.

Dynamics and Half-Life of Cell-Free DNA After Exercise: Insights from a Fragment Size-Specific Measurement Approach

Background: Cell-free DNA (cfDNA) is present in healthy individuals but is elevated in those undergoing physical exertion, trauma, sepsis, and certain cancers. Maintaining cfDNA concentrations is vital for immune homeostasis and preventing inflammatory responses. Understanding cfDNA release and clearance is essential for using cfDNA as a biomarker in clinical diagnostics. We focused on the fragment size of cfDNA and investigated cfDNA dynamics and half-life, particularly the 100-250 base pair fragments. Methods: Healthy, adult men (n = 5; age 40 ± 4.1 years) were subjected to a 30 min treadmill exercise. Blood samples were collected at 0, 5, 10, 15, 30, and 60 min post-exercise using PAXgene® Blood ccfDNA tubes to stabilize and prevent nuclease-mediated cfDNA degradation and minimize genomic DNA contamination risk. The cfDNA concentration was measured using an electrophoresis-based technique (4150 TapeStation system) to quantify the concentration based on cfDNA fragment size. Results: The results showed a cfDNA half-life of 24.2 min, with a transient increase in 100-250 base pair cfDNA fragments post-exercise, likely due to nuclease activity. These levels rapidly reverted to the baseline within an hour. Conclusions: The rapid clearance of cfDNA underscores its potential as a biomarker for real-time disease monitoring and the evaluation of treatment efficacy. This study is expected to standardize cfDNA investigations, enhancing diagnosis and treatment monitoring across various disease conditions.

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.

Glioblastoma, IDH-wildtype manifesting as intracranial hemorrhage: A case report highlighting the clinical utility of digital polymerase chain reaction in integrated diagnoses

The manifestation of glioblastoma, IDH-wildtype (GB) as intracranial hemorrhage (ICH) presents diagnostic and therapeutic challenges. Molecular characteristics, including TERT promoter mutation, EGFR amplification, and chromosome 7 gain/10 loss, were incorporated to diagnose GB in the fifth edition of the World Health Organization Classification of Tumors of the Central Nervous System. When molecular analyses fail to detect low fractions of these genetic alterations, the integrated diagnosis of GB can be enigmatic. This case report describes a 58-year-old man presenting with ICH, masking an underlying GB. Initial histopathology of the evacuated hematoma revealed a small number of atypical glial cells, but a definitive diagnosis was deferred. Subsequent surgery and molecular analysis, including digital polymerase chain reaction (dPCR), confirmed the presence of a TERT C228T mutation in the promoter area, leading to an integrated diagnosis of GB. The patient experienced a favorable clinical outcome following surgery, radiation, temozolomide, and tumor-treating field therapy, without recurrence after 50 months. This case underscores the importance of meticulous histological examination of ICH and exemplifies the clinical utility of dPCR as a complementary diagnostic tool. The effectiveness of dPCR is particularly noteworthy, even in scenarios with minimal tumor cell content, reinforcing its value in the integrated diagnosis of GB.

Value of ctDNA in surveillance of adjuvant chemosensitivity and regimen adjustment in stage III colon cancer: a protocol for phase II multicentre randomised controlled trial (REVISE trial)

INTRODUCTION

The standard of care for stage III colon cancer is 3 or 6 months of double-drug regimen chemotherapy following radical surgery. However, patients with positive circulating tumour DNA (ctDNA) exhibit a high risk of recurrence risk even if they receive standard adjuvant chemotherapy. The potential benefit of intensified adjuvant chemotherapy, oxaliplatin, irinotecan, leucovorin and fluoropyrimidine (FOLFOXIRI), for ctDNA-positive patients remains to be elucidated.

METHODS AND ANALYSIS

This multicentre phase II randomised controlled trial aims to investigate the utility of ctDNA in monitoring chemosensitivity and to preliminarily assess whether intensified chemotherapy with FOLFOXIRI can increase ctDNA clearance and improve survival outcomes. A total of 60 eligible patients with stage III colon cancer exhibiting postoperatively positive ctDNA before and after two cycles of oxaliplatin and capecitabine (XELOX) will be randomly assigned to continue five additional cycles of XELOX (control arm) or switch to eight cycles of FOLFOXIRI (experimental arm). This sequential approach is designed to escalate treatment for patients with persistent ctDNA positivity while avoiding overtreatment in those who may respond well to standard chemotherapy. The primary endpoint is the change in ctDNA concentration, defined as the difference between the ctDNA concentration measured after two cycles of XELOX and after the completion or termination of chemotherapy. Secondary endpoints include the ctDNA clearance rate, 2-year disease-free survival, distant metastasis-free survival, chemotherapy-related side effects and quality of life.

ETHICS AND DISSEMINATION

This trial has been approved by the Ethics Committee of the West China Hospital, Sichuan University (approval number: 20231998). The findings will be disseminated through peer-reviewed publications and presentations at scientific conferences.

TRIAL REGISTRATION NUMBER

ClinicalTrials.gov (NCT06242418, registered on 27 January 2024).

Ultrasensitive detection of cancer-associated nucleic acids and mutations by primer exchange reaction-based signal amplification and flow cytometry

The detection of cancer-associated nucleic acids and mutations through liquid biopsy has emerged as a highly promising non-invasive approach for early cancer detection and monitoring. In this study, we report the development of primer exchange reaction (PER) based signal amplification strategy that enables the rapid, sensitive and specific detection of nucleic acids bearing cancer specific single nucleotide mutations using flow cytometry. Using micrometer size beads as support for immobilizing oligonucleotides and programmable PER assembly for target oligonucleotide recognition and fluorescence signal amplification, we demonstrated the versatile detection of target nucleic acids including KRAS oligonucleotide, fragmented mRNAs, and miR-21. Moreover, our detection system can discriminate single base mutations frequently occurred in cancer-associated genes including KRAS, PIK3CA and P53 from cell extracts and circulating tumor DNAs (ctDNAs). The detection is highly sensitive, with a limit of detection down to 27 fM without pre-amplification. In view of a clinical application, we demonstrate the detection of single mutations after extraction and pre-amplification of ctDNAs from the plasma of breast cancer patients. Importantly, our detection strategy enabled the detection of single KRAS mutation even in the presence of 1000-fold excess of wild type (WT) DNA using multi-color flow cytometry detection approach. Overall, our strategy holds immense potential for clinical applications, offering significant improvements for early cancer detection and monitoring.

Perspectives for the clinical application of ctDNA analysis to breast cancer drug therapy

Circulating tumor DNA (ctDNA) consists of DNA fragments released from cancer cells into the blood circulation with quick clearance. Analysis of ctDNA can enable real-time assessment of the presence of cancer cells and their genomic characteristics. Therefore, ctDNA is expected to be one of the most useful biomarkers for cancer. In recent years, several ultra-sensitive assays for ctDNA analysis have been developed, and many clinical trials are using these assays to investigate the efficacy of ctDNA-based therapeutic strategies. In the perioperative phase, real-time identification of minimal residual disease at the molecular level with ctDNA analysis can help evaluate the risk of recurrence to inform escalation or de-escalation of perioperative drug therapy. Many trials have examined whether therapeutic strategies using ctDNA analysis to predict treatment efficacy or resistance to molecular targeted agents can improve prognosis in metastatic breast cancer. In this review, we discuss the most recent ctDNA assays, the significance of introducing ctDNA assays to clinical practice, and the research on their application in perioperative and metastatic phases.

Possibility of determining high quantitative fecal occult blood on stool surface using hyperspectral imaging

BACKGROUND

Fecal immunochemical tests are commonly performed for colorectal cancer screening. Instant fecal occult blood measurement in toilet bowel movements would improve convenience. Hyperspectral imaging (HSI) enables the nondestructive evaluation of materials that are difficult to assess visually. This study aimed to determine whether HSI could be used to identify fecal occult blood on stool surfaces.

METHODS

The study included 100 patients who underwent colonoscopy, divided into groups A and B (50 patients, each) for creating a discriminant algorithm and validating the accuracy of the algorithm, respectively. In group A, 100 areas were randomly selected from the stool surface, and the fecal occult blood quantitative values were measured and photographed using a hyperspectral camera (cutoff: > 400 ng/mL). A discriminant algorithm image was created to extract spectral feature differences obtained from HSI via machine learning. In group B, 250 random areas were evaluated and compared to fecal occult blood quantitative values, measuring sensitivity, specificity, accuracy, positive predictive value (PPV), and negative predictive value (NPV).

RESULTS

Groups A and B comprised 28 and 26 patients with cancer, respectively. Cancer detection sensitivity at the 400 ng/mL cutoff was 67.9% and 42.3% in groups A and B, respectively. The discriminant algorithm image exhibited high accuracy in group A (sensitivity; 77.1%, specificity; 96.9%, accuracy; 90.0%, PPV; 93.1%, NPV; 88.7%). In group B, the sensitivity, specificity, accuracy, PPV, and NPV were 83.3, 92.9, 90.8, 76.3, and 95.3%, respectively.

CONCLUSION

HSI can effectively discriminate high quantitative fecal occult blood, highlighting its potential for improved colorectal cancer screening.

Integrating multi-omics features enables non-invasive early diagnosis and treatment response prediction of diffuse large B-cell lymphoma

BACKGROUND

Multi-omics features of cell-free DNA (cfDNA) can effectively improve the performance of non-invasive early diagnosis and prognosis of cancer. However, multimodal characterization of cfDNA remains technically challenging.

METHODS

We developed a comprehensive multi-omics solution (COMOS) to specifically obtain an extensive fragmentomics landscape, presented by breakpoint characteristics of nucleosomes, CpG islands, DNase clusters and enhancers, besides typical methylation, copy number alteration of cfDNA. The COMOS was tested on 214 plasma samples of diffuse large B-cell lymphoma (DLBCL) and matched healthy controls.

RESULTS

For early diagnosis, COMOS improved the area under the curve (AUC) value to .993 compared with the individual omics model, with a sensitivity of 95% at 98% specificity. Detection sensitivity achieved 91% at 99% specificity in early-stage patients, while the AUC values of the individual omics model were 0.942, 0.968, 0.989, 0.935, 0.921, 0.781 and 0.917, respectively, with lower sensitivity and specificity. In the treatment response cohort, COMOS yielded a superior sensitivity of 88% at 86% specificity (AUC, 0.903). COMOS has achieved excellent performance in early diagnosis and treatment response prediction.

CONCLUSIONS

Our study provides an effectively improved approach with high accuracy for the diagnosis and prognosis of DLBCL, showing great potential for future clinical application.

KEY POINTS

A comprehensive multi-omics solution to specifically obtain an extensive fragmentomics landscape, presented by breakpoint characteristics of nucleosomes, CpG islands, DNase clusters and enhancers, besides typical methylation, copy number alteration of cfDNA. Integrated model of cfDNA multi-omics could be used for non-invasive early diagnosis of DLBCL. Integrated model of cfDNA multi-omics could effectively evaluate the efficacy of R-CHOP before DLBCL treatment.

Liquid biopsy for breast cancer and other solid tumors: a review of recent advances

Liquid biopsy using circulating tumor DNA (ctDNA) has been reported to be less invasive and effective for comprehensive genetic analysis of heterogeneous solid tumors, including decision-making for therapeutic strategies, predicting recurrence, and detecting genetic factors related to treatment resistance in various types of cancers. Breast cancer, colorectal cancer, and lung cancer are among the most prevalent malignancies worldwide, and clinical studies of liquid biopsy for these cancers are ongoing. Liquid biopsy has been used as a companion diagnostic tool in clinical settings, and research findings have accumulated, especially in cases of colorectal cancer after curative resection and non-small cell lung cancer (NSCLC) after curative chemoradiotherapy, in which ctDNA detection helps predict eligibility for adjuvant chemotherapy. Liquid biopsy using ctDNA shows promise across a wide range of cancer types, including breast cancer, and its clinical applications are expected to expand further through ongoing research. In this article, studies on liquid biopsy in breast cancer, colorectal cancer, and NSCLC are compared focusing on ctDNA.

Circulating tumor DNA predicts recurrence and survival in patients with resectable gastric and gastroesophageal junction cancer

BACKGROUND

Gastric and gastroesophageal junction (GEJ) cancer represents a significant global health challenge, with high recurrence rates and poor survival outcomes. This study investigates circulating tumor DNA (ctDNA) as a biomarker for assessing recurrence risk in patients with resectable gastric and GEJ adenocarcinomas (AC).

METHODS

Patients with resectable gastric and GEJ AC, undergoing perioperative chemotherapy and surgery, were prospectively enrolled. Serial plasma samples were collected at baseline, after one cycle of chemotherapy, after preoperative chemotherapy, and after surgery. ctDNA was assessed by a ddPCR test (TriMeth), which targets the gastrointestinal cancer-specific methylation patterns of the genes C9orf50, KCNQ5, and CLIP4.

RESULTS

ctDNA analysis was performed on 229 plasma samples from 86 patients. At baseline, ctDNA was detected in 56% of patients, which decreased to 37% following one cycle of chemotherapy, 25% after preoperative chemotherapy and 15% after surgical resection. The presence of ctDNA after one cycle of chemotherapy was associated with reduced recurrence-free survival (RFS) (HR = 2.54, 95% confidence interval (CI) 1.33-4.85, p = 0.005) and overall survival (OS) (HR = 2.23, 95% CI 1.07-4.62, p = 0.032). Similarly, ctDNA after surgery was associated with significantly shorter RFS (HR = 6.22, 95% CI 2.39-16.2, p < 0.001) and OS (HR = 6.37, 95% CI 2.10-19.3, p = 0.001). Multivariable regression analysis confirmed ctDNA after surgery as an independent prognostic factor (p < 0.001).

CONCLUSION

ctDNA analysis has the potential to identify patients at elevated risk of recurrence, thus providing personalized treatment strategies for patients with resectable gastric and GEJ cancer. Further validation in larger cohorts and ctDNA-guided interventions are needed for future clinical use.

DNA Methylation-Based Diagnosis and Treatment of Breast Cancer

DNA methylation is a key epigenetic modifier involved in tumor formation, invasion, and metastasis. The development of breast cancer is a complex process, and many studies have now confirmed the involvement of DNA methylation in breast cancer. Moreover, the number of genes identified as aberrantly methylated in breast cancer is rapidly increasing, and the accumulation of epigenetic alterations becomes a chronic factor in the development of breast cancer. The combined effects of external environmental factors and the internal tumor microenvironment promote epigenetic alterations that drive tumorigenesis. This article focuses on the relevance of DNA methylation to breast cancer, describing the role of detecting DNA methylation in the early diagnosis, prediction, progression, metastasis, treatment, and prognosis of breast cancer, as well as recent advances. The reversibility of DNA methylation is utilized to target specific methylation aberrant promoters as well as related enzymes, from early prevention to late targeted therapy, to understand the journey of DNA methylation in breast cancer with a more comprehensive perspective. Meanwhile, methylation inhibitors in combination with other therapies have a wide range of prospects, providing hope to drug-resistant breast cancer patients.

Recent progress in prompt molecular detection of liquid biopsy using Cas enzymes: innovative approaches for cancer diagnosis and analysis

Creating fast, non-invasive, precise, and specific diagnostic tests is crucial for enhancing cancer treatment outcomes. Among diagnostic methods, those relying on nucleic acid detection are highly sensitive and specific. Recent developments in diagnostic technologies, particularly those leveraging Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are revolutionizing cancer detection, providing accurate and timely results. In clinical oncology, liquid biopsy has become a noninvasive and early-detectable alternative to traditional biopsies over the last two decades. Analyzing the nucleic acid content of liquid biopsy samples, which include Circulating Tumor Cells (CTCs), Circulating Tumor DNA (ctDNA), Circulating Cell-Free RNA (cfRNA), and tumor extracellular vesicles, provides a noninvasive method for cancer detection and monitoring. In this review, we explore how the characteristics of various Cas (CRISPR-associated) enzymes have been utilized in diagnostic assays for cancer liquid biopsy and highlight their main applications of innovative approaches in monitoring, as well as early and rapid detection of cancers.

Integrating traditional biomarkers and emerging predictors to assess neoadjuvant chemotherapy efficacy in breast cancer: a multifactorial analysis of Ki-67, CDK4, EGFR, TILs and ctDNA

OBJECTIVE

This study aimed to analyse the correlation between the expression of cell proliferation-associated antigen (Ki-67), cell cycle protein-dependent kinase 4 (CDK4), epidermal growth factor receptor (EGFR), tumour-infiltrating lymphocytes (TILs) and circulating tumour DNA (ctDNA) with the outcome and prognosis of patients with breast cancer (BC) undergoing neoadjuvant chemotherapy (NACT).

METHODS

We retrospectively analysed the clinicopathological data of 231 patients with BC who underwent preoperative NACT at XX Hospital between 1 January 2018 and 31 December 2021. Logistic regression models were used to analyse factors influencing NACT efficacy. The Cox risk regression model was used to analyse prognostic factors. The TILs were assessed on pre-treatment biopsies, and ctDNA levels were monitored during NACT. Propensity score matching and subgroup analyses were performed.

RESULTS

After 4-6 cycles of chemotherapy, the response rate was 77.92% (180/231), with 58.87% (136/231) achieving pathological complete response (pCR). Multifactorial analysis showed that tumour, node and metastasis (TNM) stage II, EGFR positivity, low Ki-67 expression, CDK4 negativity, non-triple-negative subtypes and effective NACT results were associated with higher pCR rates. Higher TIL levels correlated with increased pCR rates (72.4% for high TILs vs 39.1% for low TILs, p < 0.001). The ctDNA levels decreased significantly in patients with pCR compared with patients without pCR during NACT (p < 0.001). After propensity score matching, the 3-year disease-free survival rate was significantly higher in the pCR group (88.9% vs 71.1%, p = 0.003). Subgroup analysis revealed varying pCR rates and predictive biomarkers across BC subtypes.

CONCLUSION

The TNM classification, EGFR, Ki-67, CDK4 expression, BC subtype and NACT results have predictive value for pCR in patients with BC. Lower TNM classification, lower Ki-67 expression and EGFR positivity are associated with better outcomes. High TIL levels and significant decreases in ctDNA during NACT correlate with improved response and prognosis. These findings highlight the potential for integrating traditional clinicopathological factors with novel biomarkers for personalised treatment strategies in BC.

Dynamic Changes in Circulating Tumor DNA During Immunotherapy for Head and Neck Cancer: SHIZUKU-HN Study

Immune checkpoint inhibitors (ICIs) are effective in treating recurrent/metastatic head and neck squamous cell carcinoma (HNSCC), but only 20% of patients achieve durable responses. This study evaluated circulating tumor DNA (ctDNA) as a real-time biomarker for monitoring treatment response in HNSCC. The SHIZUKU-HN study prospectively collected and analyzed serial plasma samples (n = 27) from HNSCC patients undergoing ICIs, using Guardant360 to assess ctDNA variant allele frequency (VAF) and genetic mutations. Tumor volumes were quantified using 3D reconstruction of CT scans, and data from Japan's C-CAT database (n = 2255) provided insights into ctDNA testing in HNSCC. C-CAT data showed that ctDNA testing was underutilized, performed in only 7% of head and neck cancer cases. In SHIZUKU-HN, mean VAF significantly correlated with tumor volume (Spearman's ρ = 0.70, p = 0.001), often preceding radiographic progression. BRAF and APC mutations disappeared in partial responders, while GNAS mutations varied. EGFR and PIK3CA amplifications, detectable via ctDNA but missed in tissue biopsies, indicated emerging resistance mechanisms. The SHIZUKU-HN study demonstrates the potential of ctDNA as a dynamic biomarker in HNSCC, offering early insights into treatment efficacy and informing personalized ICI therapy.

Sensitive liquid biopsy monitoring correlates with outcome in the prospective international GPOH-DCOG high-risk neuroblastoma RT-qPCR validation study

BACKGROUND

Liquid biopsies offer less burdensome sensitive disease monitoring. Bone marrow (BM) metastases, common in various cancers including neuroblastoma, is associated with poor outcomes. In pediatric high-risk neuroblastoma most patients initially respond to treatment, but in the majority the disease recurs with only 40% long-term survivors, stressing the need for more sensitive detection of disseminated disease during therapy.

METHODS

To validate sensitive neuroblastoma mRNA RT-qPCR BM testing, we prospectively assessed serial BM samples from 345 international high-risk neuroblastoma patients, treated in trials NB2004 (GPOH) or NBL2009 (DCOG), using PHOX2B, TH, DDC, CHRNA3, and GAP43 RT-qPCR mRNA markers and BM GD2-immunocytology. Association between BM-infiltration levels and event-free survival (EFS) and overall survival (OS) was estimated by using Cox regression models and Kaplan-Meier's methodology.

RESULTS

BM infiltration >10% by RT-qPCR at diagnosis was prognostic for survival (adjusted hazard ratio (HR) 1.82 [95%CI 1.25-2.63] and 2.04 [1.33-3.14] for EFS and OS, respectively). Any post-induction RT-qPCR positivity correlated with poor EFS and OS, with a HR of 2.10 [1.27-3.49] and 1.76 [1.01-3.08] and 5-years EFS of 26.6% [standard error 5.2%] versus 60.4% [6.7] and OS of 43.8% [5.9] versus 65.7% [6.6] for RT-qPCR-positive patients versus RT-qPCR-negative patients. In contrast, post-induction immunocytology positivity was not associated with EFS or OS (HR 1.22 [0.68-2.19] and 1.26 [0.54-2.42]).

CONCLUSION

This study validates the association of not clearing of BM metastases by sensitive RT-qPCR detection with very poor outcome. We therefore propose implementation of RT-qPCR for minimal residual disease testing in neuroblastoma to guide therapy.

Application of Circulating Tumor DNA in the Auxiliary Diagnosis and Prognosis Prediction of Glioma

Glioma is the most common primary malignant brain tumor. Despite significant advances in the past decade in understanding the molecular pathogenesis of this tumor and exploring therapeutic strategies, the prognosis of patients with glioma remains poor. Accurate diagnosis of glioma is very important for the treatment and prognosis. Although the gold-standard method for the diagnosis and prognosis prediction of patients with glioma is tissue biopsy, it still has many limitations. Liquid biopsy can provide information on the auxiliary diagnosis and prognosis of gliomas. In this review, we summarized the application of cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA) in the auxiliary diagnosis and prognosis of glioma. The common methods used to detect ctDNA in gliomas using samples including blood and cerebrospinal fluid (CSF) and the detection techniques for ctDNA, including droplet digital PCR (ddPCR) and next-generation sequencing (NGS), were discussed. Detection of ctDNA from plasma of patients with brain tumors remains challenging because of the blood-brain barrier (BBB). CSF has been proposed as a medium for ctDNA analysis in brain tumors, and mutation detection using plasma ctDNA was less sensitive than CSF ctDNA sequencing. Moreover, ongoing relevant clinical studies were summarized. Finally, we discussed the challenges, and future directions for the studies on ctDNA in glioma.

Synthetic mismatches enable specific CRISPR-Cas12a-based detection of genome-wide SNVs tracked by ARTEMIS

Detection of pathogenic DNA variants is vital in cancer diagnostics and treatment monitoring. While CRISPR-based diagnostics (CRISPRdx) offer promising avenues for cost-effective, rapid, and point-of-care testing, achieving single-nucleotide detection fidelity remains challenging. We present an in silico pipeline that scans the human genome for targeting pathogenic mutations in the seed region (ARTEMIS), the most stringent crRNA domain. ARTEMIS identified 12% of pathogenic SNVs as Cas12a recognizable, including 928 cancer-associated variants such as BRAFV600E, BRCA2E1953∗, TP53V272M, and ALDH2E504K. Cas12a exhibited remarkable tolerance to single mismatches within the seed region. Introducing deliberate synthetic mismatches within the seed region yielded on-target activity with single-nucleotide fidelity. Both positioning and nucleobase types of mismatches influenced detection accuracy. With improved specificity, Cas12a could accurately detect and semi-quantify BRAFV600E in cfDNA from cell lines and patient liquid biopsies. These results provide insights toward rationalized crRNA design for high-fidelity CRISPRdx, supporting personalized and cost-efficient healthcare solutions in oncologic diagnostics.

Rapid miRNA detection enhanced by exponential hybridization chain reaction in graphene field-effect transistors

Scalable electronic devices that can detect target biomarkers from clinical samples hold great promise for point-of-care nucleic acid testing, but still cannot achieve the detection of target molecules at an attomolar range within a short timeframe (<1 h). To tackle this daunting challenge, we integrate graphene field-effect transistors (GFETs) with exponential target recycling and hybridization chain reaction (TRHCR) to detect oligonucleotides (using miRNA as a model disease biomarker), achieving a detection limit of 100 aM and reducing the sensing time by 30-fold, from 15 h to 30 min. In contrast to traditional linear TRHCR, our exponential TRHCR enables the target miRNA to initiate an autocatalytic system with exponential kinetics, significantly accelerating the reaction speed. The resulting reaction products, long-necked double-stranded polymers with a negative charge, are effectively detected by the GFET through chemical gating, leading to a shift in the Dirac voltage. Therefore, by monitoring the magnitude of this voltage shift, the target miRNA is quantified with high sensitivity. Consequently, our approach successfully detects 22-mer miRNA at concentrations as low as 100 aM in human serum samples, achieving the desired short timeframe of 30 min, which is congruent with point-of-care testing, and demonstrates superior specificity against single-base mismatched interfering oligonucleotides.

Minimal residual disease in colorectal cancer. Tumor-informed versus tumor-agnostic approaches: unraveling the optimal strategy

BACKGROUND

Circulating tumor DNA (ctDNA) analysis has emerged as a minimally invasive tool for detecting minimal residual disease (MRD) in colorectal cancer (CRC) patients. This enables dynamic risk stratification, earlier recurrence detection and optimized post-surgical treatment. Two primary methodologies have been developed for ctDNA-based MRD detection: tumor-informed strategies, which identify tumor-specific mutations through initial tissue sequencing to guide ctDNA monitoring, and tumor-agnostic approaches, which utilize predefined panels to detect common cancer-associated genomic or epigenomic alterations directly from plasma without prior tissue analysis. The debate over which is superior in terms of sensitivity, specificity, cost-effectiveness and clinical feasibility remains unsolved.

DESIGN

This review summarizes studies published up to November 2024, exploring the utility and performance of tumor-informed and tumor-agnostic approaches for ctDNA analysis in CRC. We evaluate the strengths and limitations of each methodology, focusing on sensitivity, specificity and clinical outcomes.

RESULTS

Both strategies demonstrate clinical utility in post-operative risk stratification and guiding adjuvant chemotherapy decisions in CRC patients. Tumor-informed approaches generally exhibit superior sensitivity and specificity for recurrence prediction, attributed to their personalized tumor profile designs. However, these methods are limited by the need for prior tissue sequencing and higher associated costs. In contrast, tumor-agnostic approaches offer broader applicability due to their reliance on plasma-only analysis, although with relatively lower sensitivity. Technological advancements, including fragmentomics and multi-omic integrations, are expanding the capabilities of ctDNA-based MRD detection, enhancing the performance of both approaches.

CONCLUSIONS

While tumor-informed strategies currently offer higher precision in MRD detection, tumor-agnostic approaches are gaining traction due to their convenience and improving performance metrics. The integration of novel technologies in ongoing clinical trials may redefine the optimal approach for MRD detection in CRC, paving the way for more personalized and adaptive patient management strategies.

Utilizing DNA Logic Device for Precise Detection of Circulating Tumor Cells via High Catalytic Activity Au Nanoparticle Anchoring

As medical advancements turn most cancers into manageable chronic diseases, new challenges arise in cancer recurrence monitoring. Detecting circulating tumor cells (CTCs) is crucial for monitoring cancer recurrence, but the current methods are cumbersome and costly. This study developed a new CTC detection system combining DNA aptamer recognition, hybridization chain reaction (HCR) technology, and DNA logic devices, enabling the one-step recognition of CTCs by identifying multiple membrane proteins. After catalytically active Au nanoparticles were attached through reduction synthesis in situ onto the DNA hybridization strands of the CTCs surface, a 3,3',5,5'-tetramethylbenzidine (TMB) colorimetric reaction was used to detect CTCs concentration via peroxidase-like catalysis. With this CTCs detection reporting system, we achieved an LOD of 4 cells/mL using an ultraviolet-visible (UV-vis) spectrophotometer. At certain concentrations, CTCs could even be detected visually without the need for an instrument. The development of this CTCs detection reporting system provided a convenient, reliable, and cost-effective detection strategy for widespread CTCs-based cancer recurrence monitoring.

Liquid biopsy in cancer current: status, challenges and future prospects

Cancer has a high mortality rate across the globe, and tissue biopsy remains the gold standard for tumor diagnosis due to its high level of laboratory standardization, good consistency of results, relatively stable samples, and high accuracy of results. However, there are still many limitations and drawbacks in the application of tissue biopsy in tumor. The emergence of liquid biopsy provides new ideas for early diagnosis and prognosis of tumor. Compared with tissue biopsy, liquid biopsy has many advantages in the diagnosis and treatment of various types of cancer, including non-invasive, quickly and so on. Currently, the application of liquid biopsy in tumor detection has received widely attention. It is now undergoing rapid progress, and it holds significant potential for future applications. Around now, liquid biopsies encompass several components such as circulating tumor cells, circulating tumor DNA, exosomes, microRNA, circulating RNA, tumor platelets, and tumor endothelial cells. In addition, advances in the identification of liquid biopsy indicators have significantly enhanced the possibility of utilizing liquid biopsies in clinical settings. In this review, we will discuss the application, advantages and challenges of liquid biopsy in some common tumors from the perspective of diverse systems of tumors, and look forward to its future development prospects in the field of cancer diagnosis and treatment.

High Prevalence of Chromosomal Rearrangements and LINE Retrotranspositions Detected in Formalin-Fixed, Paraffin-Embedded Colorectal Cancer Tissue

Structural variants (SVs) caused by chromosomal rearrangements in common fragile sites or long interspersed nuclear element (LINE) retrotranspositions are highly prevalent in colorectal cancer. However, methodology for the targeted detection of these SVs is lacking. This article reports the use of formalin-fixed, paraffin-embedded targeted-locus capture (FFPE-TLC) sequencing as a novel technology for the targeted detection of tumor-specific SVs. Analysis of 29 FFPE colorectal tumor samples and 8 matched normal samples revealed tumor-specific SVs in 24 patients (83%), with a median of 2 SVs per patient (range, 1 to 21). A total of 104 SVs were found in the common fragile site-associated genes MACROD2, PRKN, FHIT, and WWOX in 18 patients (62%), and 39 SVs caused by three LINE transposable elements were found in 15 patients (52%). Tumor specificity of SVs was independently verified by droplet digital PCR of tumor tissue DNA, and their applicability as plasma circulating tumor DNA biomarkers was demonstrated. FFPE-TLC sequencing enabled the detection of tumor-specific SVs caused by chromosomal rearrangements and LINE retrotranspositions in FFPE tissue. Therefore, FFPE-TLC sequencing facilitates the investigation of the biological and clinical effects of SVs using FFPE material from (retrospective) cohorts of cancer patients and has potential clinical applicability in the detection of SV biomarkers in the routine molecular diagnostics setting.

Measurable Residual Disease in Mantle Cell Lymphoma: The Unbearable Lightness of Being Undetectable

PURPOSE OF REVIEW

This paper evaluates the benefits and limitations of detecting measurable residual disease (MRD) in mantle cell lymphoma (MCL) and assesses its prognostic value. It also aims to highlight the importance of detecting low MRD levels post-treatment and their application in clinical practice.

RECENT FINDINGS

Recent studies show that MRD levels predict relapse and survival outcomes in hematologic neoplasms, including MCL. RT-qPCR is currently the most used method due to its high reproducibility and sensitivity. Ideal MRD detection should be highly sensitive, cost-effective, and applicable to a wide demographic of patients. This paper concludes that MRD detection has prognostic value in MCL but faces limitations in sensitivity and specificity. Further research is needed to establish the significance of low MRD levels before integrating these methods into clinical practice. Improved MRD detection technologies and understanding their impact on clinical outcomes will guide better patient management in MCL.

Liquid biopsy: paving a new avenue for cancer research

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

PD-1/PD-L1 immune checkpoint blockade in breast cancer: research insights and sensitization strategies

Immunotherapy targeting programmed cell death-1 (PD-1) and PD-L1 immune checkpoints has reshaped treatment paradigms across several cancers, including breast cancer. Combining PD-1/PD-L1 immune checkpoint blockade (ICB) with chemotherapy has shown promising efficacy in both early and metastatic triple-negative breast cancer, although only a subset of patients experiences durable responses. Identifying responders and optimizing immune drug selection are therefore critical. The effectiveness of PD-1/PD-L1 immunotherapy depends on both tumor-intrinsic factors and the extrinsic cell-cell interactions within the tumor microenvironment (TME). This review systematically summarizes the key findings from clinical trials of ICBs in breast cancer and examines the mechanisms underlying PD-L1 expression regulation. We also highlight recent advances in identifying potential biomarkers for PD-1/PD-L1 therapy and emerging evidence of TME alterations following treatment. Among these, the quantity, immunophenotype, and spatial distribution of tumor-infiltrating lymphocytes stand out as promising biomarkers. Additionally, we explore strategies to enhance the effectiveness of ICBs in breast cancer, aiming to support the development of personalized treatment approaches tailored to the unique characteristics of each patient's tumor.

Evolving landscape of detection and targeting miRNA/epigenetics for therapeutic strategies in ovarian cancer

Ovarian cancer (OC) accounts for the highest mortality rates among all gynecologic malignancies. The high mortality of OC is often associated with delayed detection, prolonged latency, enhanced metastatic potential, acquired drug resistance, and frequent recurrence. This review comprehensively explores key aspects of OC, including cancer diagnosis, mechanisms of disease resistance, and the pivotal role of epigenetic regulation, particularly by microRNAs (miRs) in cancer progression. We highlight the intricate regulatory mechanisms governing miR expression within the context of OC and the current status of epigenetic advancement in the therapeutic development and clinical trial progression. Through network analysis we elucidate the regulatory interactions between dysregulated miRs in OC and their targets which are involved in different signaling pathways. By exploring these interconnected facets and critical analysis, we endeavor to provide a nuanced understanding of the molecular dynamics underlying OC, its detection and shedding light on potential avenues for miRs and epigenetics-based therapeutic intervention and management strategies.

Patient-Specific Circulating Tumor DNA for Monitoring Response to Menin Inhibitor Treatment in Preclinical Models of Infant Leukemia

BACKGROUND

In infant KMT2A (MLL1)-rearranged (MLL-r) acute lymphoblastic leukemia (ALL), early relapse and treatment response are currently monitored through invasive repeated bone marrow (BM) biopsies. Circulating tumor DNA (ctDNA) in peripheral blood (PB) provides a minimally invasive alternative, allowing for more frequent disease monitoring. However, a poor understanding of ctDNA dynamics has hampered its clinical translation. We explored the predictive value of ctDNA for detecting minimal/measurable residual disease (MRD) and drug response in a patient-derived xenograft (PDX) model of infant MLL-r ALL.

METHODS

Immune-deficient mice engrafted with three MLL-r ALL PDXs were monitored for ctDNA levels before and after treatment with the menin inhibitor SNDX-50469.

RESULTS

The amount of ctDNA detected strongly correlated with leukemia burden during initial engraftment prior to drug treatment. However, following SNDX-50469 treatment, the leukemic burden assessed by either PB leukemia cells through flow cytometry or ctDNA levels through droplet digital polymerase chain reaction (ddPCR) was discrepant. This divergence could be attributed to the persistence of leukemia cells in the spleen and BM, highlighting the ability of ctDNA to reflect disease dynamics in key leukemia infiltration sites.

CONCLUSIONS

Notably, ctDNA analysis proved to be a superior predictor of MRD compared to PB assessment alone, especially in instances of low disease burden. These findings highlight the potential of ctDNA as a sensitive biomarker for monitoring treatment response and detecting MRD in infant MLL-r ALL.

Nano-enabled pharmacogenomics: revolutionizing personalized drug therapy

The combination of pharmacogenomics and nanotechnology science of pharmacogenomics into a highly advanced single entity has given birth to personalized medicine known as nano-enabled pharmacogenomics. This review article covers all aspects starting from pharmacogenomics to gene editing tools, how these have evolved or are likely to be evolved for pharmacogenomic application, and how these can be delivered using nanoparticle delivery systems. In this prior work, we explore the evolution of pharmacogenomics over the years, as well as new achievements in the field of genomic sciences, the challenges in drug creation, and application of the strategy of personalized medicine. Particular attention is paid to how nanotechnology helps avoid the problems that accompanied the development of pharmacogenomics earlier, for example, the question of drug resistance and targeted delivery. We also review the latest developments in nano-enabled pharmacogenomics, such as the coupling with other nanobio-technologies, artificial intelligence, and machine learning in pharmacogenomics, and the ethical and regulatory aspects of these developing technologies. The possible uses of nanotechnology in improving the chances of pated and treating drug-resistant cancers are exemplified by case studies together with the current clinical uses of nanotechnology. In the last section, we discuss the future trends and research prospects in this dynamically growing area, stressing the importance of further advancements and collaborations which will advance the nano-enabled pharmacogenomics to their maximum potential.

PROGNOSTIC MARKERS FOR THROMBOTIC EVENTS IN PATIENTS WITH GASTRIC OR COLORECTAL ADENOCARCINOMAS

BACKGROUND

The relationship between thrombosis and cancer is based on evidence that cancer promotes prothrombotic changes in the host hemostatic system. The activation of blood coagulation is closely linked to tumor growth and dissemination.

AIMS

To evaluate whether quantifications of plasma circulation tumor deoxyribonucleic acid (DNA) and thrombin-antithrombin complex could act as predictors for thrombotic events and death in patients with gastric or colorectal adenocarcinomas, while also evaluating the Karnofsky Performance Status.

METHODS

Eighty-two patients were included in the study and divided into three groups: controls (n=20), gastric adenocarcinomas (n=21), and colorectal adenocarcinomas (n=41). In order to calculate the Karnofsky index, information was collected to measure the patient's ability to perform common daily tasks. The following serum measurements were conducted: complete blood count, platelet count, extracellular deoxyribonucleic acid, and thrombin-antithrombin complex.

RESULTS

Ten patients (16%) experienced thrombosis during treatment. Patients with thrombin-antithrombin complex levels greater than 0.53 had a five-times higher risk of thrombosis. Lower Karnofsky Performance Status was also a risk factor for the event in this population. Neither thrombin-antithrombin complex nor plasma circulation tumor DNA were predictors of death after multivariate adjustment. Thus, Karnofsky index signaled a better overall survival prognosis for colorectal and gastric adenocarcinoma patients.

CONCLUSIONS

Thrombin-antithrombin complex acts as a marker for thrombosis in patients with colorectal and gastric adenocarcinomas. We recommend prophylactic anticoagulation when the Karnofsky value is low and/or the thrombin-antithrombin complex concentration is greater than 0.53 ng/ml.

Role of Proteins in Oncology: Advances in Cancer Diagnosis, Prognosis, and Targeted Therapy-A Narrative Review

Modern oncology increasingly relies on the role of proteins as key components in cancer diagnosis, prognosis, and targeted therapy. This review examines advancements in protein biomarkers across several cancer types, including breast cancer, lung cancer, ovarian cancer, and hepatocellular carcinoma. These biomarkers have proven critical for early detection, treatment response monitoring, and tailoring personalized therapeutic strategies. The article highlights the utility of targeted therapies, such as tyrosine kinase inhibitors and monoclonal antibodies, in improving treatment efficacy while minimizing systemic toxicity. Despite these advancements, challenges like tumor resistance, variability in protein expression, and diagnostic heterogeneity persist, complicating universal application. The review underscores future directions, including the integration of artificial intelligence, advanced protein analysis technologies, and the development of combination therapies to overcome these barriers and refine personalized cancer treatment.

Cell-free DNA from clinical testing as a resource of population genetic analysis

As a noninvasive biomarker, cell-free DNA (cfDNA) has achieved remarkable success in clinical applications. Notably, cfDNA is essentially DNA, and conducting whole-genome sequencing (WGS) can yield a wealth of genetic information. These invaluable data should not be confined to one-time use; instead, they should be leveraged for more comprehensive population genetic analysis, including genetic variation spectrum, population structure and genetic selection, and genome-wide association studies (GWASs), among others. Such research findings can, in turn, facilitate clinical practice, enabling more advanced and accurate disease predictions. This review explores the advantages, challenges, and current research areas of cfDNA in population genetics. We hope that this review can serve as a new chapter in the repurposing of cfDNA sequence data generated from clinical testing in population genetics.

Stool and blood biomarkers for colorectal cancer management: an update on screening and disease monitoring

BACKGROUND

Biomarkers have revolutionized the management of colorectal cancer (CRC), facilitating early detection, prevention, personalized treatment, and minimal residual disease (MRD) monitoring. This review explores current CRC screening strategies and emerging biomarker applications.

MAIN BODY

We summarize the landscape of non-invasive CRC screening and MRD detection strategies, discuss the limitations of the current approaches, and highlight the promising potential of novel biomarker solutions. The fecal immunochemical test remained the cornerstone of CRC screening, but its sensitivity has been improved by assays that combined its performance with other stool analytes. However, their sensitivity for advanced adenomas and the patient compliance both remain suboptimal. Blood-based tests promise to increase compliance but require further refinement to compete with stool-based biomarker tests. The ideal scenario involves leveraging blood tests to increase screening participation, and simultaneously promote stool- and endoscopy-based screening among those who are compliant. Once solely reliant on upfront surgery followed by stage and pathology-driven adjuvant chemotherapy, the treatment of stage II and III colon cancer has undergone a revolutionary transformation with the advent of MRD testing after surgery. A decade ago, the concept of using a post-surgical test instead of stage and pathology to determine the need for adjuvant chemotherapy was disruptive. Today, a blood test may be more informative of the need for chemotherapy than the stage at diagnosis.

CONCLUSION

Biomarker research is not just improving, but bringing a transformative change to CRC clinical management. Early detection is not just getting better, but improving thanks to a multi-modality approach, and personalized treatment plans are not just becoming a reality, but a promising future with MRD testing.

Treatment of oligometastatic breast cancer: The role of patient selection

Up to 90 % of death from solid tumors are caused by metastases. By 2040, breast cancer (BC) is predicted to increase to over 3 million new cases. Additionally, with the personalization and intensification of BC follow-up, many patients will relapse with oligometastatic disease (OMD). Over the past decades, advances in treatment planning, image guidance, target position reproducibility, and online tracking, along with a compelling radiobiological rationale, have led to the implementation of Stereotactic Body Radiation Therapy (SBRT). This has become a valid ablative treatment option for OMD patients. However, there are still concerns about which patients benefit the most from ablative treatment. In this review, we will analyze the literature regarding SBRT for OMD in BC patients. We aim to present the current data on its effectiveness and define the optimal tailored scenarios for SBRT outcomes.

Molecular Imaging Biomarkers for Early Cancer Detection: A Systematic Review of Emerging Technologies and Clinical Applications

BACKGROUND

Early cancer detection is crucial for improving patient outcomes. Molecular imaging biomarkers offer the potential for non-invasive, early-stage cancer diagnosis.

OBJECTIVES

To evaluate the effectiveness and accuracy of molecular imaging biomarkers for early cancer detection across various imaging modalities and cancer types.

METHODS

A comprehensive search of PubMed/MEDLINE, Embase, Web of Science, Cochrane Library, and Scopus was performed, covering the period from January 2010 to December 2023. Eligibility criteria included original research articles published in English on molecular imaging biomarkers for early cancer detection in humans. The risk of bias for included studies was evaluated using the QUADAS-2 tool. The findings were synthesized through narrative synthesis, with quantitative analysis conducted where applicable.

RESULTS

In total, 50 studies were included. Positron emission tomography (PET)-based biomarkers showed the highest sensitivity (mean: 89.5%, range: 82-96%) and specificity (mean: 91.2%, range: 85-100%). Novel tracers such as [68Ga]-PSMA for prostate cancer and [18F]-FES for breast cancer demonstrated promising outcomes. Optical imaging techniques showed high specificity in intraoperative settings.

CONCLUSIONS

Molecular imaging biomarkers show significant potential for improving early cancer detection. Integration into clinical practice could lead to earlier interventions and improved outcomes. Further research is needed to address standardization and cost-effectiveness.

Clinical use of circulating tumor DNA analysis in patients with lymphoma

The analysis of circulating tumor DNA (ctDNA) in liquid biopsy specimens has an established role for the detection of predictive molecular alterations and acquired resistance mutations in several tumors. The low-invasiveness of this approach allows for repeated sampling and dynamic monitoring of disease evolution. Originating from the entire body tumor bulk, plasma-derived ctDNA reflects intra- and interlesional genetic heterogeneity. In the management of lymphoma patients, ctDNA quantification at various timepoints of the patient's clinical history is emerging as a complementary tool that may improve risk stratification, assessment of treatment response and early relapse detection during follow-up, most prominently in patients with diffuse large B-cell lymphoma or classic Hodgkin lymphoma. While liquid biopsies have not yet entered standard-of-care treatment protocols in these settings, several trials have provided evidence that at least a subset of lymphoma patients may benefit from the introduction of liquid biopsies into daily clinical care. In parallel, continuous technological developments have enabled highly sensitive ctDNA assessment methods, which span from locus-specific techniques identifying single hotspot mutations, to sequencing panels and genome-wide approaches that explore broader genetic and epigenetic alterations. Here, we provide an overview of current methods and ongoing technical developments for ctDNA evaluation. We also summarize the most important data from a selection of clinical studies that have explored the clinical use of ctDNA in several lymphoma entities.

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

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