Gene signatures of quiescent glioblastoma cells reveal mesenchymal shift and interactions with niche microenvironmentResearch in context
Rut Tejero,
Yong Huang,
Igor Katsyv,
Michael Kluge,
Jung-Yi Lin,
Jessica Tome-Garcia,
Nicolas Daviaud,
Yuanshuo Wang,
Bin Zhang,
Nadejda M. Tsankova,
Caroline C. Friedel,
Hongyan Zou,
Roland H. Friedel
Affiliations
Rut Tejero
Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Yong Huang
Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Igor Katsyv
Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Michael Kluge
Institut für Informatik, Ludwig-Maximilians-Universität München, Munich, Germany
Jung-Yi Lin
Tisch Cancer Institute, Biostatistics Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Jessica Tome-Garcia
Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Nicolas Daviaud
Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Yuanshuo Wang
Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Bin Zhang
Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Nadejda M. Tsankova
Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Caroline C. Friedel
Institut für Informatik, Ludwig-Maximilians-Universität München, Munich, Germany
Hongyan Zou
Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Corresponding authors at: Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Roland H. Friedel
Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Corresponding authors at: Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Background: Glioblastoma (GBM), a highly malignant brain tumor, invariably recurs after therapy. Quiescent GBM cells represent a potential source of tumor recurrence, but little is known about their molecular underpinnings. Methods: Patient-derived GBM cells were engineered by CRISPR/Cas9-assisted knock-in of an inducible histone2B-GFP (iH2B-GFP) reporter to track cell division history. We utilized an in vitro 3D GBM organoid approach to isolate live quiescent GBM (qGBM) cells and their proliferative counterparts (pGBM) to compare stem cell properties and therapy resistance. Gene expression programs of qGBM and pGBM cells were analyzed by RNA-Seq and NanoString platforms. Findings: H2B-GFP-retaining qGBM cells exhibited comparable self-renewal capacity but higher therapy resistance relative to pGBM. Quiescent GBM cells expressed distinct gene programs that affect cell cycle control, metabolic adaptation, and extracellular matrix (ECM) interactions. Transcriptome analysis also revealed a mesenchymal shift in qGBM cells of both proneural and mesenchymal GBM subtypes. Bioinformatic analyses and functional assays in GBM organoids established hypoxia and TGFβ signaling as potential niche factors that promote quiescence in GBM. Finally, network co-expression analysis of TCGA glioma patient data identified gene modules that are enriched for qGBM signatures and also associated with survival rate. Interpretation: Our in vitro study in 3D GBM organoids supports the presence of a quiescent cell population that displays self-renewal capacity, high therapy resistance, and mesenchymal gene signatures. It also sheds light on how GBM cells may acquire and maintain quiescence through ECM organization and interaction with niche factors such as TGFβ and hypoxia. Our findings provide a starting point for developing strategies to tackle the quiescent population of GBM. Fund: National Institutes of Health (NIH) and Deutsche Forschungsgemeinschaft (DFG). Keywords: Glioblastoma, Tumor quiescence, H2B-GFP, GBM organoid, Proneural-mesenchymal transition, Stem cell niche
