Deciphering the cellular heterogeneity of infant-type hemispheric gliomas using single-nuclei multi-omics

Abstract Infant-type hemispheric gliomas (IHGs) have recently been recognized as a new tumor entity. Compared to other types of pediatric gliomas, most IHGs distinctively harbor a fusion in a cluster of receptor tyrosine kinase (RTK) genes: the NTRK family, ROS1, ALK, or MET. Clinically, IHG patients appear to be associated with better outcomes compared to older children with high-grade tumors. While large-scale genomic studies have helped uncovered the complex molecular landscape and clinical features of IHGs, little is known about the underlying biology – specifically how tumor heterogeneity may explain the spectrum of clinical presentations and progression of the disease. Using single-nuclei multi-omic (RNA/ATAC-seq) profiling, we assembled a comprehensive atlas of IHG tumor cells from a cohort of patients spanning different age groups and RTK fusion subtypes. We measured that tumor single-nuclei transcriptomes clustered into distinct subpopulations and contained genes expressed by the normal brain cell lineages. Data integration with single-cell atlases from the developing brain allowed us to rank tumor cell subpopulations according to their developmental stage, with age- and fusion-specific differences. Using trajectory inference and gene expression velocity modeling, we describe a hierarchical and dynamic organization between subpopulations, potentially illustrating the role of phenotypic plasticity in glioma formation. Moreover, we measured in fragments of open chromatin a cell-type specific enrichment of binding sites for transcription factors known to regulate brain cell maturation. Taken together, our multi-modal atlas describes the cellular and functional heterogeneity of IHGs, paving the way towards a greater understating of its unique biology and clinical consequences.