Multi-omics characterization of the blood-brain barrier in molecular groups of ependymoma 

Julia K. Sundheimer 1,2 , Julia Benzel 1 , Aniello Federico 1 , Maximilian Knoll 6 , Cornelia Gansert 1,2 , Britta Statz 1,2 , Christian Seitz 4,5 , Marcel Kool 1 , Stefan M. Pfister 1,3 , Kendra K. Maaß 1,3 , Kristian W. Pajtler 1,3 
[1]     Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
[2]     Faculty of Biosciences, Im Neuenheimer Feld 234, 69120 Heidelberg University, Germany
[3]     Department of Pediatric Hematology, Oncology and Immunology, Heidelberg University Hospital, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany 
[4]     DFG Cluster of Excellence 2180 'Image-guided and Functional Instructed Tumor Therapy' (iFIT), University of Tuebingen, Tuebingen, Germany.
[5]     Department of Pediatric Hematology and Oncology, University Hospital Tuebingen, Tuebingen, Germany.
[6]     Division of Molecular & Translational Radiation Oncology, Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg University Hospital (UKHD), Heidelberg, Germany; German Cancer Consortium (DKTK) Core-Center, German Cancer Research Center (DKFZ), Heidelberg, Germany; Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), German Cancer Research Center (DKFZ), Heidelberg University Hospital (UKHD), Faculty of Medicine (MFHD) of the Heidelberg University, and Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany; CCU Translational Radiation Oncology, CCU Radiation Oncology, CCU Neurooncology, National Center for Tumor Diseases (NCT) German Cancer Research Center (DKFZ), Heidelberg University Hospital (UKHD), Heidelberg, Germany; Departments of Neurology, Neurosurgery and Radiation Oncology, Heidelberg University Hospital (UKHD), Heidelberg, Germany.  

Correspondence: This email address is being protected from spambots. You need JavaScript enabled to view it.  

Ependymoma (EPN) represents the third most common pediatric CNS tumor. While recurrence rates remain high, systemic therapies have so far failed to lead to clinical benefit. A better understanding of pathophysiological blood-brain barrier (BBB) characteristics represents an important component in developing effective (pre-)clinical trials. 

Our study seeks to increase knowledge of molecular EPN group-specific BBB compositions as a proof-of-concept for other brain tumor entities. Furthermore, we explore the correlation between BBB characteristics and their functional impact to adapt an established in silico model that currently predicts drug penetration over the healthy BBB.

T-distributed stochastic neighbor embedding (tSNE)-based clustering analyses using the most relevant  tight  junction  and  transporter  gene  sets  revealed  distinct  molecular  EPN  group-specific expression patterns. While PDX models (n=20) showed high similarity with patient tumor samples, IUE mouse models (n=2) did not fully recapitulate these BBB characteristics. Single-cell analyses and spatial mapping of protein abundance allowed dissection of BBB gene expression patterns in endothelial cells (e.g. Claudin5). Functional validation on protein level showed that coherence of RNA and protein is BBB gene-dependent.

The  differences  in  BBB  markers  between  molecular  EPN  groups  may  partly  explain  drug resistance of aggressive EPN as especially ZFTA fusion-positive tumors are characterized by high tight junction expression suggestive of low BBB permeability. Our multi-omics approach is intended to develop a score that further complements our established in silico prediction tool for BBB drug penetration. These findings will be validated in preclinical studies while molecular BBB characterization will be further expanded to other brain tumor entities.