Biological and molecular characterization of the cellular origins and progression of atypical teratoid/rhabdoid tumors (AT/RT)

Abstract

Atypical teratoid/rhabdoid tumors (AT/RT) are rare embryonal tumors of the central nervous system that affect very young children and have a poor prognosis. Based on DNA methylation profiles, the different subtypes AT/RT-SHH, AT/RT-TYR, AT/RT-MYC, and AT/RT-SMARCA4 were identified. Although the genetics of these tumors are known, targeted therapies are lacking. Therefore, we aimed to identify the cellular origins of AT/RT and to characterize the mechanisms of tumor progression and recurrence, including therapy resistance. Both should help to develop novel therapeutic approaches. In the first part of the project, we investigated paired primary and recurrent AT/RT using DNA methylation profiling and bulk RNA sequencing, which revealed an increased chromosome 1q gain and chromosome 10 loss in recurrences and differential expression of cancer-associated genes. Single-nucleus RNA sequencing revealed an enrichment of CD1A+ CD207+ dendritic cells (DCs) in recurrences and a high number of AT/RT-MYC tumor cells undergoing partial epithelial-mesenchymal transition. Potentially therapy-resistant cells were identified in AT/RTMYC, which were characterized by increased extracellular matrix remodeling, among others. Overexpression of respective genes and occurrence of CD1A+ CD207+ DCs correlated with an inferior survival of AT/RT patients. All findings were associated with TGF-β signaling – a novel, promising therapeutic target. The second part of this work deals with the identification of the cellular origins of AT/RTSMARCA4 and AT/RT-TYR, because these are completely unknown and mouse models are lacking. We generated different Smarca4-deficient mouse models that targeted distinct cell types at specific timepoints. These mice did not develop tumors, but an important role of Smarca4 in the embryonic development was demonstrated, because Smarca4 loss either resulted in embryonic lethality or neuromuscular disorders. For AT/RT-TYR, we revealed that precursors of the choroid plexus (CP) of the fourth ventricle are potentially the cellular origin. A high proportion of AT/RT-TYR biopsies was intermingled with CP tissue, and immunohistochemistry and RNA sequencing showed that CP marker genes were predominantly expressed in AT/RT-TYR. Deconvolution analyses demonstrated the highest similarity of AT/RT-TYR to the CP. Finally, Foxj1-cre::Smarcb1fl/fl mice displayed a Smarcb1 loss in the CP, resulting in large, atypical, monociliary CP cells. These mice did not develop tumors but demonstrated high similarity to human AT/RT-TYR on gene expression level. In conclusion, our work demonstrated insights into the development of AT/RT, as well as mechanisms of progression and recurrence, which both revealed novel potential therapeutic targets.