Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution.
Marie-Ming Aynaud, Olivier Mirabeau, Nadege Gruel, Sandrine Grossetête, Valentina Boeva, Simon Durand, Didier Surdez, Olivier Saulnier, Sakina Zaïdi, Svetlana Gribkova, Aziz Fouché, Ulykbek Kairov, Virginie Raynal, Franck Tirode, Thomas G P Grünewald, Mylene Bohec, Sylvain Baulande, Isabelle Janoueix-Lerosey, Jean-Philippe Vert, Emmanuel Barillot, Olivier Delattre, Andrei Zinovyev
Author Information
Marie-Ming Aynaud: INSERM U830, Équipe Labellisée LNCC, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
Olivier Mirabeau: INSERM U830, Équipe Labellisée LNCC, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
Nadege Gruel: INSERM U830, Équipe Labellisée LNCC, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Institut Curie, PSL Research University, Department of Translational Research, 75005 Paris, France.
Sandrine Grossetête: INSERM U830, Équipe Labellisée LNCC, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
Valentina Boeva: Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Descartes UMR-S1016, 75014 Paris, France; Department of Computer Science, Institute for Machine Learning, Swiss Institute of Bioinformatics (SIB), ETH Zurich, 8092 Zurich, Switzerland; INSERM U900, 75005 Paris, France; Mines ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 75006 Paris, France; Institut Curie, PSL Research University, 75005 Paris, France.
Simon Durand: INSERM U830, Équipe Labellisée LNCC, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
Didier Surdez: INSERM U830, Équipe Labellisée LNCC, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
Olivier Saulnier: INSERM U830, Équipe Labellisée LNCC, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
Sakina Zaïdi: INSERM U830, Équipe Labellisée LNCC, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
Svetlana Gribkova: INSERM U900, 75005 Paris, France; Mines ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 75006 Paris, France; Institut Curie, PSL Research University, 75005 Paris, France; Université Denis Diderot, 75013, Paris, France.
Aziz Fouché: École Normale Supérieure Paris-Saclay, 94230 Cachan, France.
Ulykbek Kairov: Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.
Virginie Raynal: INSERM U830, Équipe Labellisée LNCC, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
Franck Tirode: University of Lyon, Université Claude Bernard Lyon 1, CNRS 5286, INSERM U1052, Cancer Research Centre of Lyon, 69008 Lyon, France.
Thomas G P Grünewald: INSERM U830, Équipe Labellisée LNCC, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Institut Curie, PSL Research University, Department of Translational Research, 75005 Paris, France.
Mylene Bohec: NGS Platform, Institut Curie, 75005 Paris, France.
Sylvain Baulande: NGS Platform, Institut Curie, 75005 Paris, France.
Isabelle Janoueix-Lerosey: INSERM U830, Équipe Labellisée LNCC, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
Jean-Philippe Vert: Mines ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 75006 Paris, France; Google Research, Brain Team, 75009 Paris, France.
Emmanuel Barillot: INSERM U900, 75005 Paris, France; Mines ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 75006 Paris, France; Institut Curie, PSL Research University, 75005 Paris, France.
Olivier Delattre: INSERM U830, Équipe Labellisée LNCC, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France. Electronic address: olivier.delattre@curie.fr.
Andrei Zinovyev: INSERM U900, 75005 Paris, France; Mines ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 75006 Paris, France; Institut Curie, PSL Research University, 75005 Paris, France. Electronic address: andrei.zinovyev@curie.fr.
EWSR1-FLI1, the chimeric oncogene specific for Ewing sarcoma (EwS), induces a cascade of signaling events leading to cell transformation. However, it remains elusive how genetically homogeneous EwS cells can drive the heterogeneity of transcriptional programs. Here, we combine independent component analysis of single-cell RNA sequencing data from diverse cell types and model systems with time-resolved mapping of EWSR1-FLI1 binding sites and of open chromatin regions to characterize dynamic cellular processes associated with EWSR1-FLI1 activity. We thus define an exquisitely specific and direct enhancer-driven EWSR1-FLI1 program. In EwS tumors, cell proliferation and strong oxidative phosphorylation metabolism are associated with a well-defined range of EWSR1-FLI1 activity. In contrast, a subpopulation of cells from below and above the intermediary EWSR1-FLI1 activity is characterized by increased hypoxia. Overall, our study reveals sources of intratumoral heterogeneity within EwS tumors.
