DNA methylation profiling from cerebrospinal fluid as a diagnostic tool for pineoblastoma

Abstract

Pineoblastoma is a rare and aggressive malignancy that often affects pediatric populations. Accurate diagnosis is challenging due to histological overlap with other central nervous system tumors and limited molecular data. DNA methylation profiling and analysis of circulating tumor DNA (derived from both cell dissemination as well as cell-free- cfDNA) in cerebrospinal fluid (CSF) are emerging tools for precise tumor classification, in the field of pediatric central nervous system tumors. Here, we report a challenging case of a 17-year-old refugee girl with a previous diagnosis of a primitive neuroectodermal tumor. Formalin-fixed, paraffin-embedded tissue was not available for histopathological re-evaluation. However, the methylation profiling of low amount of CSF-derived DNA classified the tumor as "pineoblastoma, subtype miRNA processing altered 1, subclass A," enabling patient management. The diagnosis was later confirmed through tissue-based DNA methylation analysis of a secondary lesion, demonstrating that the epigenetic signature faithfully reflected tumor features. This case report highlights the potential of CSF-based DNA methylation profiling as a minimally invasive yet accurate diagnostic tool for pediatric CNS tumors. The concordance between CSF and tissue profiling supports the integration of liquid biopsy into diagnostic workflows, allowing for earlier diagnosis and personalized treatment strategies. However, more studies are needed to demonstrate the reliability of our approach in other CNS malignancies.

Keywords: Cerebrospinal fluid; DNA methylation; Diagnosis; Liquid biopsy; Pineoblastoma.

Fig. 1

A: T1-weighted MRI sagittal images of the patient pre‐surgery, revealing a hypointense region along the spinal cord (red arrow). B: T2-weighted MRI sagittal images of the patient post‐surgery and chemotherapy. C: Cytological analysis on CSF sample confirmed the presence of Synaptophysin positive cancer cells (Magnification 40×). D: t-distributed stochastic neighbor embedding plots of DNA methylation clustering patterns. The patient’s samples, CSF and metastatic tumor tissue biopsy, are outlined in black, and clustered together with pineoblastoma group B (PIN T, PB B). Brain tumor classifier was determined by version 11b4. E: CNV analysis of CSF (upper panel) and tumor tissue (bottom panel) from the same patient, demonstrated multiple and complex chromosome gains (red) and losses (blue). F: T1-weighted MRI sagittal images of the patient in follow-up, showing marked improvement in leptomeningeal disease. G: T1-weighted MRI sagittal images of the patient pre‐surgery, revealing a solid lesion in the sacral canal (red arrow). H: Immunohistochemical features. (a) haematoxylin and eosin staining; immunopositivity for (b) Synaptophysin, (c) Chromogranin and (d) KI-67 proliferation index more than 50% of tumoral cells (Magnification 40×).