Medulloblastoma cerebrospinal fluid reveals metabolites and lipids indicative of hypoxia and cancer-specific RNAs

Abstract

Medulloblastoma (MB) is the most common malignant brain tumor in children. There remains an unmet need for diagnostics to sensitively detect the disease, particularly recurrences. Cerebrospinal fluid (CSF) provides a window into the central nervous system, and liquid biopsy of CSF could provide a relatively non-invasive means for disease diagnosis. There has yet to be an integrated analysis of the transcriptomic, metabolomic, and lipidomic changes occurring in the CSF of children with MB. CSF samples from patients with (n = 40) or without (n = 11; no cancer) MB were subjected to RNA-sequencing and high-resolution mass spectrometry to identify RNA, metabolite, and lipid profiles. Differentially expressed transcripts, metabolites, and lipids were identified and their biological significance assessed by pathway analysis. The DIABLO multivariate analysis package (R package mixOmics) was used to integrate the molecular changes characterizing the CSF of MB patients. Differentially expressed transcripts, metabolites, and lipids in CSF were discriminatory for the presence of MB but not the exact molecular subtype. One hundred and ten genes and ten circular RNAs were differentially expressed in MB CSF compared with normal, representing TGF-β signaling, TNF-α signaling via NF-kB, and adipogenesis pathways. Tricarboxylic acid cycle and other metabolites (malate, fumarate, succinate, α-ketoglutarate, hydroxypyruvate, N-acetyl-aspartate) and total triacylglycerols were significantly upregulated in MB CSF compared with normal CSF. Although separating MBs into subgroups using transcriptomic, metabolomic, and lipid signatures in CSF was challenging, we were able to identify a group of omics signatures that could separate cancer from normal CSF. Metabolic and lipidomic profiles both contained indicators of tumor hypoxia. Our approach provides several candidate signatures that deserve further validation, including the novel circular RNA circ_463, and insights into the impact of MB on the CSF microenvironment.

LC–MS-Based Urine Metabolomics Analysis for the Diagnosis and Monitoring of Medulloblastoma

“…Several studies have established that metabolism is altered in MB patients, including decreased fatty acid oxidation and increased lipogenesis (19), which is consistent with our results. Previous CSF metabolomics analysis suggests that a state of hypoxia might occur in MB patients, reflected by the accumulation of lipids and an increased TCA cycle (14). Additionally, CSF metabolomics analysis of MB patients discovered strongly upregulated lipid hormones (20).…”

“…The tricarboxylic acid cycle and total triacylglycerols were found to be significantly upregulated in MB patients. A group of omics signatures, including indicators of tumor hypoxia, was found to separate MB from normal samples (14).…”

Pathological implications of metabolic reprogramming and its therapeutic potential in medulloblastoma

“…Recent studies are now focusing on the possible use of CSF as an indicator of MB disease status and also as a source of novel biomarkers. Metabolomic studies on MB CSF samples revealed high levels of metabolites that are typically secreted under hypoxia, such as α-KG, fumarate, hydroxypyruvate, malate and succinate as well as triacylglycerol ( Lee et al, 2022 ). Moreover, recurrent MB patients-derived CSF samples show high concentrations of hypoxia-induced amino acids such as tryptophan, methionine, serine and lysine respectively ( Reichl et al, 2020 ).…”

The Tumor Microenvironment of Medulloblastoma: An Intricate Multicellular Network with Therapeutic Potential

“…In addition, higher levels of CXCL1, IL-6, and IL-8 were observed in MYC-amplified group 3 MB patients [ 157 ]. More in-depth evaluations of the CSF of recurrent MB patients revealed that proteins (GPR37, ADAMTS1, and GAP43), metabolites, and lipids (tryptophan, methionine, serine, triglycerides) indicative of tumor-associated hypoxia were upregulated compared to the CSF of patients without cancer [ 158 , 159 ]. These studies point out that analysis of the CSF can reveal markers of metastatic MB progression and give insights into the impact of MB on the CSF microenvironment.…”