Page 46 - SDIR5 Abstract book 21 12 2021.

POSTER PRESENTATIONS

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Multi-omic profiling of cancer cells, exosomes, and cell-free DNA isolated from the
cerebrospinal fluid of pediatric brain cancer patients

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Miodrag Gužvić *, Giancarlo Feliciello *, Zbigniew T. Czyz , Jens Warfsmann , Marcus Jakob , Markus J.
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Riemenschneider , Selim Corbacioglu , Jens Warfsmann , Bernhard Polzer , Christoph A. Klein
1 Chair of Experimental Medicine and Therapy Research, University of Regensburg, Regensburg, Germany; Division
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of Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine, Regensburg,
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Germany; Department of Pediatric Hematology, Oncology & Stem Cell Transplantation, University of Regensburg,
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Regensburg, Germany; Department of Neuropathology, University Hospital Regensburg, Regensburg, Germany;
5 Current Address: Department of Urology, University Hospital Regensburg, Regensburg, Germany; *Equal
contribution

Background: Clinical management of pediatric brain tumors is challenging since they often exhibit low
responsiveness to standard treatment resulting in poor survival. Molecular characterization of tumor
tissues may guide novel therapies and monitor their effectiveness. However, brain cancer biopsies are often
difficult to obtain. Therefore, we established a workflow allowing multi-omics analysis of disseminated
cancer cells (DCCs), exosomes, and cell-free-DNA (cfDNA), isolated from cerebrospinal fluid (CSF) aspirates
of pediatric brain cancer patients. Patients and Methods: We used this workflow on CSF samples of two
patients with medulloblastoma and pineal-anlage tumor, respectively. Using centrifugation we separated
cells from the rest of CSF. Since this workflow is used for multiple tumor types, we stained the cells for
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CD45, and both CD45 (immune cells) and CD45 (putative cancer cells) cells were isolated. cfDNA and
exosomes were isolated from the liquid fraction of CSF. We used PCR or RNA-seq to analyze gene
expression in cDNA samples, and DNA-seq to analyze copy number alterations (CNAs) and single nucleotide
variants (SNVs) in genomic DNA. Results: Transcriptome analysis showed that neural lineage markers were
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almost exclusively expressed in CD45 cells. CD45 cells harbored no CNAs. In contrast, all CD45 cells had
CNAs, confirming that they are DCCs. Interestingly, sequencing of cfDNA and exoDNA revealed similar CNA
profile as observed in genomes of DCCs. SNV analysis showed that genomes of DCCs exhibited
heterogeneous profiles of oncogenic mutations. Conclusion: This proof-of-concept study demonstrates
establishment of workflow allowing identification, isolation, and comprehensive molecular characterization
of CSF-derived DCCs, cfDNA and exosomes.
Keywords: Cell-Free Nucleic Acids; Gene Expression; Brain Neoplasms; DNA Copy Number Variations;
Cerebrospinal Fluid; Mutation

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