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

• DOI: 10.1016/j.celrep.2024.114804
• Publication Date: 2024-10-03T21:48:54Z
• Authors: Noah Bonine; Vittorio Zanzani; Annelies Van Heme...; Bavo Vanneste; Christian Zwicker; Tinne Thoné; Sofie Roelandt; Sarah-Lee Bekaert; Jan Koster; Isabelle Janoueix...; Cécile Thirant; Stéphane Van Haver; Stephen S. Roberts; Liselot M. Mus; Bram De Wilde; Nadine Van Roy; Celine Everaert; Frank Speleman; Vanessa Vermeirssen; Charlotte L. Scott; Katleen De Preter
• Keywords: LANDSCAPE; QH301-705.5; Gene Expression Profiling; Biology and Life Sciences; PHENOTYPES; DENDRITIC CELLS; MODEL; Gene Expression Regulation, Neoplastic; Neuroblastoma; DISEASE-ASSOCIATED MICROGLIA; SEQ; MARKERS; REVEALS; Medicine and Health Sciences; Humans; MACROPHAGES; Biology (General); Single-Cell Analysis; Transcriptome; CP: Cancer; GENE-EXPRESSION

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.