NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors

• Published in: Cell reports (Cambridge) Vol. 43; no. 10; p. 114804
• Main Authors: Bonine, Noah, Zanzani, Vittorio, Van Hemelryk, Annelies, Vanneste, Bavo, Zwicker, Christian, Thoné, Tinne, Roelandt, Sofie, Bekaert, Sarah-Lee, Koster, Jan, Janoueix-Lerosey, Isabelle, Thirant, Cécile, Van Haver, Stéphane, Roberts, Stephen S., Mus, Liselot M., De Wilde, Bram, Van Roy, Nadine, Everaert, Celine, Speleman, Frank, Vermeirssen, Vanessa, Scott, Charlotte L., De Preter, Katleen
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 22-10-2024; Elsevier
• Subjects: CP: Cancer; integration; NBAtlas; neuroblastoma; single cell; single nucleus; transcriptomics; reference; single cell; atlas; CP: Cancer; NBAtlas; single nucleus; transcriptomics; neuroblastoma; integration
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2024.114804

Neuroblastoma, a rare embryonic tumor arising from neural crest development, is responsible for 15% of pediatric cancer-related deaths. Recently, several single-cell transcriptome studies were performed on neuroblastoma patient samples to investigate the cell of origin and tumor heterogeneity. However, these individual studies involved a small number of tumors and cells, limiting the conclusions that could be drawn. To overcome this limitation, we integrated seven single-cell or single-nucleus datasets into a harmonized cell atlas covering 362,991 cells across 61 patients. We use this atlas to decipher the transcriptional landscape of neuroblastoma at single-cell resolution, revealing associations between transcriptomic profiles and clinical outcomes within the tumor compartment. In addition, we characterize the complex immune-cell landscape and uncover considerable heterogeneity among tumor-associated macrophages. Finally, we showcase the utility of our atlas as a resource by expanding it with additional data and using it as a reference for data-driven cell-type annotation.
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•The NBAtlas includes single-cell/nucleus RNA-seq data from 61 neuroblastoma patients•Malignant neuroendocrine cells comprise cycling high-risk vs. differentiated low-risk cells•Macrophage heterogeneity is considerable and includes high-risk-associated TREM2+-cells•The NBAtlas enables accurate reference-based mapping of new data
Bonine et al. integrate neuroblastoma tumor single-cell/nucleus RNA-sequencing data from 61 patients into “NBAtlas,” further unraveling the transcriptional landscape of neuroblastoma as well as highlighting some technical challenges. This resource will aid future single-cell investigations.