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bioRxiv · 10.64898/2026.07.16.738862

Single-cell multi-omic analyses resolve the cellular diversity of ALK/ROS1/MET/NTRK-fused gliomas in infants and older children

De Micheli, A. J.·de Biagi-Junior, C. O. A.·Lo Cascio, C.·Machaalani, C.·Postlmayr, A.·Katiyar, S.·Maas, R.·Kancherla, V.·Reimann, R.·Zapotocky, M.·Nobre, L. F.·Eder, S. K.·Rozowsky, J. S.·Ribierre, T.·Zenk, F.·Resnick, A.·Clarke, M.·Gojo, J.·Tabori, U.·Hawkins, C.·Jones, C.·Cavalli, F. M. G.·Filbin, M. G.·Guerreiro Stucklin, A. S.
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Abstract

Pediatric cancers are thought to arise from dysregulation of developmental programs, otherwise tightly regulated in time and space. Infant-type hemispheric gliomas (IHGs) arise in early childhood, driven by characteristic ALK/ROS1/MET/NTRK receptor tyrosine kinase (RTK) gene fusions. We dissected the cellular hierarchies of 24 fusion-positive gliomas, spanning infants through adolescents, using single-cell and single-nucleus RNA/ATAC-seq, and spatial transcriptomics. We identified five cancer cell states, with radial glia-like cells at the apex of a neoplastic hierarchy resembling neuronal- and glial-like trajectories. Neuronal-like cells were enriched in most IHGs but diminished in ROS1-fused IHGs and older patients. Integration of chromatin profiling revealed FOS/JUN-driven oncogenic programs and high inferred plasticity across all cancer cell populations. Myeloid cells, the most abundant non-neoplastic population, comprised distinct subgroups, suggesting context-dependent functions. Despite lacking high-order structure, spatial transcriptomics revealed discrete cellular niches within IHGs. Collectively, our findings elucidate the cellular states and developmental programs underlying IHGs and RTK-fused gliomas in older patients, opening new avenues for research and therapy innovation.

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De Micheli, A. J., de Biagi-Junior, C. O. A., Lo Cascio, C., Machaalani, C., Postlmayr, A., Katiyar, S., Maas, R., Kancherla, V., Reimann, R., Zapotocky, M., Nobre, L. F., Eder, S. K., Rozowsky, J. S., Ribierre, T., Zenk, F., Resnick, A., Clarke, M., Gojo, J., Tabori, U., Hawkins, C., Jones, C., Cavalli, F. M. G., Filbin, M. G., Guerreiro Stucklin, A. S.. 2026-07-16. Single-cell multi-omic analyses resolve the cellular diversity of ALK/ROS1/MET/NTRK-fused gliomas in infants and older children. https://doi.org/10.64898/2026.07.16.738862

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