Cell Reports (Oct 2024)
NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors
- Noah Bonine,
- Vittorio Zanzani,
- Annelies Van Hemelryk,
- Bavo Vanneste,
- Christian Zwicker,
- Tinne Thoné,
- Sofie Roelandt,
- Sarah-Lee Bekaert,
- Jan Koster,
- Isabelle Janoueix-Lerosey,
- 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
Affiliations
- Noah Bonine
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Vittorio Zanzani
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Laboratory for Computational Biology, Integromics and Gene Regulation (CBIGR), Ghent University, Ghent, Belgium
- Annelies Van Hemelryk
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Bavo Vanneste
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Christian Zwicker
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Tinne Thoné
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Sofie Roelandt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Sarah-Lee Bekaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Jan Koster
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam, the Netherlands
- Isabelle Janoueix-Lerosey
- Inserm U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France
- Cécile Thirant
- Inserm U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France
- Stéphane Van Haver
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Stephen S. Roberts
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
- Liselot M. Mus
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Bram De Wilde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Nadine Van Roy
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Celine Everaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Frank Speleman
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Vanessa Vermeirssen
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Laboratory for Computational Biology, Integromics and Gene Regulation (CBIGR), Ghent University, Ghent, Belgium
- Charlotte L. Scott
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium; Corresponding author
- Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Corresponding author
- Journal volume & issue
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Vol. 43,
no. 10
p. 114804
Abstract
Summary: 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.
