STAR Protocols (Sep 2023)
Isolation and profiling of viable tumor cells from human ex vivo glioblastoma cultures through single-cell transcriptomics
- Junyi Zhang,
- Jakob Straehle,
- Kevin Joseph,
- Nicolas Neidert,
- Simon Behringer,
- Jonathan Göldner,
- Andreas Vlachos,
- Marco Prinz,
- Christian Fung,
- Jürgen Beck,
- Oliver Schnell,
- Dieter Henrik Heiland,
- Vidhya M. Ravi
Affiliations
- Junyi Zhang
- 3D-Brain Models for Neurodegenerative Diseases, Medical Center, University of Freiburg, Freiburg, Germany; Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Freiburg, Germany; Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; Translational NeuroOncology Research Group, Medical Center - University of Freiburg, Freiburg, Germany
- Jakob Straehle
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany; Center of Advanced Surgical Tissue Analysis (CAST), University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Kevin Joseph
- NeuroEngineering Laboratory, Medical Centre, University of Freiburg, Freiburg, Germany; Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany; Center of Advanced Surgical Tissue Analysis (CAST), University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; Translational NeuroOncology Research Group, Medical Center - University of Freiburg, Freiburg, Germany
- Nicolas Neidert
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Simon Behringer
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Jonathan Göldner
- 3D-Brain Models for Neurodegenerative Diseases, Medical Center, University of Freiburg, Freiburg, Germany; Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Freiburg, Germany; Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; Translational NeuroOncology Research Group, Medical Center - University of Freiburg, Freiburg, Germany
- Andreas Vlachos
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; BrainLinks-BrainTools Center, University of Freiburg, Freiburg, Germany; Center for Basics in Neuromodulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for NeuroModulation (NeuroModul), University of Freiburg, Freiburg, Germany
- Marco Prinz
- Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Basics in Neuromodulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for NeuroModulation (NeuroModul), University of Freiburg, Freiburg, Germany; Institute of Neuropathology, Medical Center - University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Christian Fung
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Jürgen Beck
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany; Center of Advanced Surgical Tissue Analysis (CAST), University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Basics in Neuromodulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany; Comprehensive Cancer Center Freiburg (CCCF), Faculty of Medicine and Medical Center- University of Freiburg, Freiburg, Germany
- Oliver Schnell
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany; Center of Advanced Surgical Tissue Analysis (CAST), University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; Translational NeuroOncology Research Group, Medical Center - University of Freiburg, Freiburg, Germany
- Dieter Henrik Heiland
- Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Freiburg, Germany; Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany; Center of Advanced Surgical Tissue Analysis (CAST), University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; Translational NeuroOncology Research Group, Medical Center - University of Freiburg, Freiburg, Germany; Comprehensive Cancer Center Freiburg (CCCF), Faculty of Medicine and Medical Center- University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK), Partner Site Freiburg; Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Vidhya M. Ravi
- 3D-Brain Models for Neurodegenerative Diseases, Medical Center, University of Freiburg, Freiburg, Germany; Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany; Center of Advanced Surgical Tissue Analysis (CAST), University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; Translational NeuroOncology Research Group, Medical Center - University of Freiburg, Freiburg, Germany; Freiburg Institute of Advanced Studies (FRIAS), Freiburg, Germany; Corresponding author
- Journal volume & issue
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Vol. 4,
no. 3
p. 102383
Abstract
Summary: Single-cell RNA-sequencing (scRNA-seq) is becoming a ubiquitous method in profiling the cellular transcriptomes of both malignant and non-malignant cells from the human brain. Here, we present a protocol to isolate viable tumor cells from human ex vivo glioblastoma cultures for single-cell transcriptomic analysis. We describe steps including surgical tissue collection, sectioning, culturing, primary tumor cells inoculation, growth tracking, fluorescence-based cell sorting, and population-enriched scRNA-seq. This comprehensive methodology empowers in-depth understanding of brain tumor biology at the single-cell level.For complete details on the use and execution of this protocol, please refer to Ravi et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
