Circulating tumor DNA for central nervous system germ cell tumor diagnosis

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• High detection rate of circulating-tumor DNA from cerebrospinal fluid of children with central nervous system germ cell tumors
• Monitoring pediatric CNS non-germinomatous germ cell tumors via cerebrospinal fluid circulating tumor DNA
• A comprehensive overview of liquid biopsy applications in pediatric solid tumors
• Circulating Liquid Biopsy Biomarkers in Glioblastoma: Advances and Challenges
• Cerebrospinal Fluid Liquid Biopsies in the Evaluation of Adult Gliomas
• Plasma ctDNA Monitoring of a PTCH1-Mutant Metastatic Adult Medulloblastoma Showing a Durable Benefit With Vismodegib

Circulating tumor DNA in cerebrospinal fluid (CSF) has emerged as a promising non-invasive biomarker for diagnosing and monitoring central nervous system germ cell tumors (CNS-GCTs). These tumors, particularly in children and adolescents, are challenging to diagnose and manage due to their location, potential marker negativity, and risks associated with invasive biopsy procedures. The analysis of ctDNA offers an alternative method to assess the tumor's genetic profile and disease status.

1. Non-Invasive Nature:

1. ctDNA can be obtained from CSF via lumbar puncture or intraoperative sampling, avoiding the need for surgical biopsy, which carries risks in CNS tumors.

2. High Sensitivity:

1. ctDNA analysis can detect tumor-specific genetic alterations, such as copy-number alterations (CNAs) and mutations, even in cases where traditional tumor markers (e.g., β-hCG and AFP) are negative.

3. Specificity:

1. Tumor-derived DNA in CSF is enriched compared to peripheral blood due to the blood-brain barrier, allowing for higher specificity in detecting CNS tumor signatures.

4. Real-Time Monitoring:

1. ctDNA levels in CSF can be monitored longitudinally to evaluate treatment response, detect minimal residual disease (MRD), and predict recurrence.

5. Complementary to Imaging:

1. ctDNA can help clarify indeterminate imaging findings and guide clinical decisions when radiological evidence is inconclusive.

1. Detection of Marker-Negative Germinomas:

1. Germinomas often lack elevated serum or CSF tumor markers. ctDNA can provide a genetic signature for diagnosis, improving accuracy in such cases.

2. Non-Germinomatous GCTs (NGGCTs):

1. NGGCTs, which are more biologically heterogeneous, may show distinct CNAs or mutations detectable through ctDNA analysis. This aids in differentiating subtypes and tailoring treatments.

3. Early Detection and Prognostic Insights:

1. ctDNA can be used to detect CNS-GCTs at early stages, offering a potential advantage over imaging and traditional marker-based diagnostics.

4. Stratification and Risk Assessment:

1. By analyzing ctDNA, clinicians can stratify patients based on tumor burden or genetic risk factors, informing treatment intensity and monitoring strategies.

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1. Technical Limitations:

1. Low-pass whole genome sequencing (LP-WGS), while cost-effective, may miss low-frequency mutations. Sensitivity may vary depending on tumor size, ctDNA abundance, and sequencing depth.

2. Access to CSF:

1. While lumbar punctures are less invasive than surgery, they are still a procedure with risks, particularly in patients with raised intracranial pressure.

3. Standardization:

1. Protocols for ctDNA extraction, sequencing, and interpretation are not yet fully standardized, making reproducibility across centers a concern.

4. Cost and Availability:

1. Advanced sequencing methods require infrastructure and expertise, which may limit widespread adoption in resource-limited settings.

5. Correlation with Clinical Outcomes:

1. More studies are needed to validate the correlation between ctDNA levels and long-term patient outcomes, such as relapse-free survival.

1. Improved Sensitivity:

1. Development of advanced sequencing techniques, such as ultra-deep sequencing or targeted NGS, to detect low-abundance ctDNA.

2. Biomarker Panels:

1. Combining ctDNA analysis with traditional markers (β-hCG, AFP) and imaging to create robust diagnostic algorithms.

3. Longitudinal Studies:

1. Conducting prospective studies to establish ctDNA thresholds for MRD detection and recurrence prediction.

4. Integration with Clinical Workflow:

1. Establishing guidelines for integrating ctDNA analysis into standard diagnostic and monitoring protocols for CNS-GCTs.

5. Artificial Intelligence (AI) Tools:

1. Leveraging AI for data analysis, improving the accuracy of CNAs and mutation detection from ctDNA.

Circulating tumor DNA in CSF represents a transformative tool for the diagnosis and management of CNS germ cell tumors. Its high sensitivity and specificity, coupled with the ability to monitor disease dynamics in real-time, offer significant advantages over traditional methods. Despite current limitations, ongoing technological and clinical advancements are likely to establish ctDNA as a cornerstone in the precision diagnosis and personalized treatment of CNS-GCTs.

A study aimed to establish the detectability of circulating tumor DNA (ctDNA) from cerebrospinal fluid (CSF) of children with Central Nervous System Germ Cell Tumor as a potential biomarker. They obtained CSF from patients with CNS-GCT by lumbar puncture or intra-operatively. Cell-free DNA (cfDNA) was extracted and subjected to low-pass whole genome sequencing (LP-WGS). Copy-number alterations (CNAs) were inferred and served as a marker of measurable residual disease (MRD). Comparisons with imaging findings and tumor marker levels were made. A total of 29 CSF samples from 21 patients (16 with germinoma, 5 with non-germinomatous GCT) were sequenced. Twenty samples from 19 patients were collected at diagnosis, and 9 samples from 7 patients were collected during or after therapy. Among the diagnostic samples, CNAs were detected in samples from 17/19 patients (89%), which included 8 with marker-negative tumors. Specific clinical scenarios suggested that serial cfDNA analysis may carry utility in tracking treatment responses as well as clarifying indeterminate imaging findings. The results provide evidence for the high sensitivity in detecting ctDNA from CSF of CNS-GCT patients using LP-WGS, with potential utility for non-invasive diagnosis and disease monitoring in upcoming CNS-GCT studies ¹⁾.

The study by Nakano et al. represents a significant advance in the non-invasive assessment of CNS-GCTs. The high detection rate of ctDNA in CSF using LP-WGS demonstrates the potential for this technique to revolutionize diagnosis and disease monitoring in CNS tumors. However, the study’s small sample size and lack of comparative or long-term data warrant caution in interpreting the findings. With further validation in larger cohorts and real-world clinical settings, ctDNA analysis could become a cornerstone of precision oncology for pediatric CNS-GCTs.

Zhang et al. investigated the translational significance of cerebrospinal fluid (CSF) circulating tumor DNA (ctDNA) in pediatric NGGCTs to identify characteristic features of CNS NGGCTs and to identify a subset of patients for whom the presence of residual disease is a risk factor and an indicator of shorter progression-free survival (PFS) and overall survival (OS).

Medical records of patients with CNS NGGCTs between January 1, 2018 and December 31, 2022 were reviewed retrospectively.

The cohort consisted of 11 male and six female patients. Tumor markers were elevated in four of the five people who underwent surgery. The remaining 12 patients were diagnosed with malignant NGGCTs according to elevated tumor markers. Among them, ctDNA before chemotherapy as well as ctDNA clearance were consistently associated with PFS and OS (p < .05). By setting a ctDNA positivity threshold of 6%, patients with high ctDNA (above the threshold) levels, which had a limitation due to the selection based on optimal statistic from the survival analysis, had significantly inferior 5-year PFS and OS compared to those with low levels (below the threshold). ctDNA or ctDNA clearance combined with the presence of residual disease predicted significantly worse OS and PFS (p < .05).

CSF ctDNA might allow the study of genomic evolution and the characterization of tumors in pediatric NGGCTs. CSF ctDNA analysis may facilitate the clinical management of pediatric NGGCT patients and aid in designing personalized therapeutic strategies ²⁾.

This study by Zhang et al. underscores the potential of CSF ctDNA as a biomarker for diagnosis, monitoring, and prognostication in pediatric CNS NGGCTs. While the findings are promising, the study's small cohort size and retrospective nature highlight the need for further research. With prospective validation and detailed genomic analyses, ctDNA could become an integral component of personalized medicine in pediatric neuro-oncology.