Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage

David R. Ghasemi1,2,3, *, Konstantin Okonechnikov1,2, *, Anne Rademacher4 , Stephan Tirier4,5, Kendra K. Maass1,2,3, Hanna Schumacher6 , Julia Sundheimer1,2,7, Britta Statz1,2, Ahmet S. Rifaioglu6,8, Katharina Bauer9 , Sabrina Schumacher4 , Michele Bortolomeazzi9 , Felice Giangaspero10,11, Kati J. Ernst1,12, Julio Saez-Rodriguez6 , David T. W. Jones1,12, Daisuke Kawauchi13, Jan-Philipp Mallm9 , Karsten Rippe4 , Andrey Korshunov1,14,15, §, Stefan M. Pfister1,2,3, §, Kristian W. Pajtler1,2,3, §

1 Hopp-Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
2 Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
3 Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg; Heidelberg; Germany.
4 Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.
5 Current affiliation: Resolve BioSciences GmbH, Monheim am Rhein, Germany.
6Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany.
7 Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
8 Department of Electrical and Electronics Engineering, İskenderun Technical University, Hatay, Turkey.
9 Single-cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany.
10Department of Radiological, Oncological and Anatomo-Pathological Sciences, Sapienza University of Rome, Italy.
11Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy.
12Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.
13Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan.
14Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
15Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, German


Medulloblastoma with extensive nodularity (MBEN) are cerebellar tumors with two histologically distinct compartments and varying disease course. In some children MBEN progresses, while others show spontaneous differentiation into more benign tumors. However, the mechanisms that control the tug-of-war between proliferation and differentiation are not well understood. Here, we dissected this process with a multimodal single cell transcriptome analysis. We found that the internodular MBEN compartment comprised proliferating early cerebellar granular neuronal precursors (CGNP)-like tumor cells as well as stromal, vascular, and immune cells. In contrast, the nodular compartment consisted of postmitotic, neuronally differentiated MBEN cells. Both compartments were connected through an intermediate cell stage of actively migrating CGNPs. Furthermore, astrocyte-like tumor cells were identified that had branched off the main CGNP developmental trajectory. Cells with an astroglial phenotype were found in close proximity to migrating, late CGNP-like and postmitotic neuronally differentiated cells. Our study reveals how the spatial tissue organization is linked to the developmental trajectory of proliferating tumor cells through a migrating precursor stage into differentiated tumor cells with a more benign phenotype. We anticipate that our framework for integrating single nucleus RNA-sequencing and spatial transcriptomics will help to uncover intercompartmental interactions also in other cancers with varying histology.

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