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posted on 2025-01-15, 08:21 authored by Selin Jessa, Antonella De Cola, Bhavyaa Chandarana, Michael McNicholas, Steven Hébert, Adam Ptack, Damien Faury, Jessica W. Tsai, Andrey Korshunov, Timothy N. Phoenix, Benjamin Ellezam, David T.W. Jones, Michael D. Taylor, Pratiti Bandopadhayay, Manav Pathania, Nada Jabado, Claudia L. Kleinman NB-FOXR2 tumors transcriptionally resemble interneurons and OPC cells. A,t-Distributed stochastic neighbor embedding (t-SNE) of bulk RNA-seq profiles of pediatric brain tumors (left) and pediatric brain tumors with stage 4 high-risk EC-NBs from Gartlgruber and colleagues (ref. 21; right) using ssGSEA scores for N = 374 cell type–specific gene signatures from reference scRNA-seq datasets. t-Distributed stochastic neighbor embedding perplexity = 10 for left and perplexity = 30 for right. Color legend for pediatric brain tumors in the right panel matches labels in the left panel. FOXR2+ tumors, normalized expression >2. B, Tally of the top-scoring signatures across NB-FOXR2 bulk tumors (N = 25). The X-axis indicates the number of samples in which each signature is the top match by ssGSEA (Supplementary Table S10). HF nIN4/HF nIN5, human fetal interneuron 4 and 5; F-e12 CINHN, forebrain E12 cortical inhibitory neurons; F-e12 MGINH, forebrain E12 MGE inhibitory neurons; human fetal GE MGE/CGE, human fetal GE progenitors. C, Uniform Manifold Approximation and Projection joint representation of NB-FOXR2 tumors (N = 6) profiled by snRNA-seq. Top, points colored by consensus cell type annotation based on a reference dataset of the developing mouse brain. Gray, nonmalignant cells. Bottom, points colored by sample. Samples are joined without integration or batch correction. D, Number of malignant cells per consensus projected cell type across NB-FOXR2 tumors profiled by snRNA-seq (N = 6). Cell classes comprising >2% cells per sample are shown. E, Volcano plot for differential ssGSEA enrichment of cell type–specific signatures in bulk NB-FOXR2 compared with other tumor entities. Point size reflects −log10(adjusted P value). Differential testing was performed with t tests between NB-FOXR2 tumors and glial tumors (HGGs, DIPGs, posterior fossa group A ependymoma), followed by multiple testing correction using the Benjamini–Hochberg procedure. A positive FC represents enrichment in NB-FOXR2. Each point represents one signature, and signatures with positive log FCs and adjusted P value < 0.01 are colored. Color legend as in F. F, Differential ssGSEA enrichment as in E, comparing NB-FOXR2 tumors with neuronal tumors (ETMR, MB-SHH, and MB-WNT). Amp, amplified; EP-PFA, posterior fossa group A ependymoma; IPC, intermediate progenitor cell; NonAmp, nonamplified; RGC, radial glial cells.
Funding
Canadian Institutes of Health Research (CIHR)
Natural Sciences and Engineering Research Council of Canada (NSERC)
National Institute of Neurological Disorders and Stroke (NINDS)
United States Department of Health and Human Services
Find out more...Genome Canada (GC)
Fondation Charles-Bruneau (Charles Bruneau Foundation)
Fonds de Recherche du Québec - Santé (FRQS)
Cancer Research UK Cambridge Institute, University of Cambridge (CRUK CI)
Brain Research UK (BRUK)
Great Ormond Street Hospital Charity (GOSH)
Emily Parsons Donation
Cancer Research UK (CRUK)
St. Baldrick’s Foundation (SBF)
Alex’s Lemonade Stand Foundation for Childhood Cancer (ALSF)
Helen Gurley Brown Presidential Initiative
Griffin’s Guardians
Pedals for Pediatrics
Rally Foundation (Rally Foundation, Inc.)
Kids Join the Fight
Lady Davis Institute for Medical Research (LDI)
Faculty of Medicine, McGill University (McGill Faculty of Medicine)
Calcul Quebec
History
ARTICLE ABSTRACT
Central nervous system neuroblastoma with forkhead box R2 (FOXR2) activation (NB-FOXR2) is a high-grade tumor of the brain hemispheres and a newly identified molecular entity. Tumors express dual neuronal and glial markers, leading to frequent misdiagnoses, and limited information exists on the role of FOXR2 in their genesis. To identify their cellular origins, we profiled the transcriptomes of NB-FOXR2 tumors at the bulk and single-cell levels and integrated these profiles with large single-cell references of the normal brain. NB-FOXR2 tumors mapped to LHX6+/DLX+ lineages derived from the medial ganglionic eminence, a progenitor domain in the ventral telencephalon. In vivo prenatal Foxr2 targeting to the ganglionic eminences in mice induced postnatal cortical tumors recapitulating human NB-FOXR2–specific molecular signatures. Profiling of FOXR2 binding on chromatin in murine models revealed an association with ETS transcriptional networks, as well as direct binding of FOXR2 at key transcription factors that coordinate initiation of gliogenesis. These data indicate that NB-FOXR2 tumors originate from LHX6+/DLX+ interneuron lineages, a lineage of origin distinct from that of other FOXR2-driven brain tumors, highlight the susceptibility of ventral telencephalon–derived interneurons to FOXR2-driven oncogenesis, and suggest that FOXR2-induced activation of glial programs may explain the mixed neuronal and oligodendroglial features in these tumors. More broadly, this work underscores systematic profiling of brain development as an efficient approach to orient oncogenic targeting for in vivo modeling, critical for the study of rare tumors and development of therapeutics.Significance: Profiling the developing brain enabled rationally guided modeling of FOXR2-activated CNS neuroblastoma, providing a strategy to overcome the heterogeneous origins of pediatric brain tumors that hamper tumor modeling and therapy development.See related commentary by Orr, p. 195
