Intercellular extrachromosomal DNA copy-number heterogeneity drives neuroblastoma cell state diversity
Maja C. Stöber,
Rocío Chamorro González,
Lotte Brückner,
Thomas Conrad,
Nadine Wittstruck,
Annabell Szymansky,
Angelika Eggert,
Johannes H. Schulte,
Richard P. Koche,
Anton G. Henssen,
Roland F. Schwarz,
Kerstin Haase
Affiliations
Maja C. Stöber
Berlin Institute for Medical Systems Biology at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany; Institute of Pathology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany; Humboldt-Universität zu Berlin, Faculty of Life Science, 10099 Berlin, Germany
Rocío Chamorro González
Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany
Lotte Brückner
Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany
Thomas Conrad
Berlin Institute for Medical Systems Biology at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany; Berlin Institute of Health, 10178 Berlin, Germany
Nadine Wittstruck
Berlin Institute for Medical Systems Biology at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany; Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany
Annabell Szymansky
Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany
Angelika Eggert
Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
Johannes H. Schulte
Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
Richard P. Koche
Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
Anton G. Henssen
Berlin Institute for Medical Systems Biology at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany; Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Berlin Institute of Health, 10178 Berlin, Germany; Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, 13125 Berlin, Germany; Corresponding author
Roland F. Schwarz
Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; BIFOLD - Berlin Institute for the Foundations of Learning and Data, 10587 Berlin, Germany; Berlin Institute for Medical Systems Biology at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany; Corresponding author
Kerstin Haase
Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin, 13353 Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Corresponding author
Summary: Neuroblastoma exhibits significant inter- and intra-tumor genetic heterogeneity and varying clinical outcomes. Extrachromosomal DNAs (ecDNAs) may drive this heterogeneity by independently segregating during cell division, leading to rapid oncogene amplification. While ecDNA-mediated oncogene amplification is linked to poor prognosis in various cancers, the effects of ecDNA copy-number heterogeneity on intermediate phenotypes are poorly understood. Here, we leverage DNA and RNA sequencing from the same single cells in cell lines and neuroblastoma patients to investigate these effects. By analyzing ecDNA amplicon structures, we reveal extensive intercellular ecDNA copy-number heterogeneity. We also provide direct evidence of how this heterogeneity influences the expression of cargo genes, including MYCN and its downstream targets, and the overall transcriptional state of neuroblastoma cells. Our findings highlight the role of ecDNA copy number in promoting rapid adaptability of cellular states within tumors, underscoring the need for ecDNA-specific treatment strategies to address tumor formation and adaptation.
