Single-cell/single-nucleus RNA-seq of Embryonal Tumor with Multilayered Rosettes (ETMR)

Embryonal tumor with multilayered rosettes (ETMR) is a pediatric brain tumor with dismal prognosis. We analyzed eleven ETMR patient samples using single-cell transcriptomics. We reveal a spatially distinct cellular hierarchy that spans highly proliferative neural stem-like cells and more differentiated neuron-like cells. C19MC is predominantly expressed in stem-like cells and controls a transcriptional network governing stemness and lineage commitment. Systematic analysis of receptor-ligand interactions between malignant cell types reveals FGFR and NOTCH signaling as oncogenic pathways. Our study provides fundamental insights into ETMR pathobiology and a powerful rationale for more effective targeted therapies.

Type: Transcriptome Analysis
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

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Dataset ID	Description	Technology	Samples
EGAD50000001379	We analyzed 11 ETMR patient samples using single-cell transcriptomics (6 from fresh and 5 from frozen material). Samples were profilied by paired-end scRNA-sequencing using the Smart-Seq2 protocol on a NextSeq 500 sequencer (Illumina). The dataset contains 8,062 fastq files of 4,031 high-quality single cells/nuclei. Raw fastq files of high-quality cells are shared.	NextSeq 500	16

Publications	Citations
Cellular hierarchies of embryonal tumors with multilayered rosettes are shaped by oncogenic microRNAs and receptor-ligand interactions. Beck A, Gabler-Pamer L, Alencastro Veiga Cruzeiro G, Lambo S, Englinger B, Shaw ML, Hack OA, Liu I, Haase RD, de Biagi CAO, Baumgartner A, Nascimento Silva AD, Klenner M, Freidel PS, Herms J, von Baumgarten L, Tonn JC, Thon N, Bruckner K, Madlener S, Mayr L, Senfter D, Peyrl A, Slavc I, Lötsch D, Dorfer C, Geyregger R, Amberg N, Haberler C, Mack N, Schwalm B, Pfister SM, Korshunov A, Baird LC, Yang E, Chi SN, Alexandrescu S, Gojo J, Kool M, Hovestadt V, Filbin MG. Nat Cancer 6: 2025 1035-1055	0

Publications

Citations

Cellular hierarchies of embryonal tumors with multilayered rosettes are shaped by oncogenic microRNAs and receptor-ligand interactions.
Beck A, Gabler-Pamer L, Alencastro Veiga Cruzeiro G, Lambo S, Englinger B, Shaw ML, Hack OA, Liu I, Haase RD, de Biagi CAO, Baumgartner A, Nascimento Silva AD, Klenner M, Freidel PS, Herms J, von Baumgarten L, Tonn JC, Thon N, Bruckner K, Madlener S, Mayr L, Senfter D, Peyrl A, Slavc I, Lötsch D, Dorfer C, Geyregger R, Amberg N, Haberler C, Mack N, Schwalm B, Pfister SM, Korshunov A, Baird LC, Yang E, Chi SN, Alexandrescu S, Gojo J, Kool M, Hovestadt V, Filbin MG. Nat Cancer 6: 2025 1035-1055