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Ribosomal protein S11 influences glioma response to TOP2 poisons

Oncogene volume 39, pages 5068–5081 (2020)Cite this article

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Abstract

Topoisomerase II poisons are one of the most common class of chemotherapeutics used in cancer. We and others had shown that a subset of glioblastomas, the most malignant of all primary brain tumors in adults, is responsive to TOP2 poisons. To identify genes that confer susceptibility to this drug in gliomas, we performed a genome-scale CRISPR knockout screen with etoposide. Genes involved in protein synthesis and DNA damage were implicated in etoposide susceptibility. To define potential biomarkers for TOP2 poisons, CRISPR hits were overlapped with genes whose expression correlates with susceptibility to this drug across glioma cell lines, revealing ribosomal protein subunit RPS11, 16, and 18 as putative biomarkers for response to TOP2 poisons. Loss of RPS11 led to resistance to etoposide and doxorubicin and impaired the induction of proapoptotic gene APAF1 following treatment. The expression of these ribosomal subunits was also associated with susceptibility to TOP2 poisons across cell lines from gliomas and multiple other cancers.

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Fig. 1: CRISPR screen in glioma cells reveals genes that confer susceptibility to etoposide.
Fig. 2: DNA damage and repair response contribute to GBM shared genetic susceptibility to TOP2 poisons.
Fig. 3: Ribosomal subunit proteins control GBM susceptibility to TOP2 poisons and are biomarker for favorable response.
Fig. 4: Ribosomal subunit proteins 11, 16, and 18 influences etoposide response across cell lines from different cancers.
Fig. 5: RPS11 confers susceptibility to TOP2 poisons by controlling nascent proteins and upregulating proapoptosome machinery APAF1.

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Acknowledgements

This work was funded by 5DP5OD021356-05 (AMS), P50CA221747 SPORE for Translational Approaches to Brain Cancer (AMS), and Developmental funds from The Robert H. Lurie NCI Cancer Center Support Grant #P30CA060553 (AMS), and generous philanthropic support from Dan and Sharon Moceri. We thank Dr. Ichiro Nakano (University of Alabama), Dr. Charles David James (Northwestern University), and Dr. Shi-Yuan Cheng (Northwestern University) for the kind gift of the GBM xenografts. We thank Dr. Peng Zhang (Northwestern University) for technical support with culture of GBM PDX. We thank Synthego, CA, USA, for the gifts of RPS11 sgRNA guides. Immunofluorescence imaging work was performed at the Center for Advanced Microscopy/Nikon Imaging Center and RHLCCC - Flow Cytometry Core, Northwestern University supported by NCI CCSG P30 CA060553 awarded to the Robert H. Lurie Comprehensive Cancer Center. BG was supported by the NVKP 16-1-2016-0037 grant.

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Authors and Affiliations

  1. Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University , Chicago, IL, United States

    Chidiebere U. Awah, Li Chen, Louisa Warnke, Edgar Gonzalez-Buendia, Cheol Park, Daniel Zhang, Eric Feldstein, Dou Yu, Markella Zannikou, Irina V. Balyasnikova, Roger Stupp, Atique Ahmed & Adam M. Sonabend

  2. Psychogenic Inc., Paramus, NJ, USA

    Mukesh Bansal

  3. Department of Neurological Surgery, Columbia University Medical Center, Columbia University, New York City, NY, USA

    Aayushi Mahajan

  4. Functional Genomics and Signaling, German Center for Cancer Research, Heidelberg, Germany

    Jan Winter

  5. Mailman School of Public Health, Columbia University, New York City, NY, USA

    Meeki Lad

  6. Department of Pathology, Columbia University Medical Centre, Columbia University, New York City, NY, USA

    Regina Martuscello

  7. Molecular and Cell Biology, Salk Institute, La Jolla, CA, USA

    Silvana Konerman & Patrick Hsu

  8. MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary

    Balázs Győrffy

  9. 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary

    Balázs Győrffy

  10. Department of Preventive Medicine, Northwestern University, Chicago, IL, USA

    Kirsten B. Burdett & Denise M. Scholtens

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Contributions

AMS and CUA conceived the idea of this project. CUA, AM, and LC performed the genome-scale CRISPR screen. JW and CUA performed the screen analysis. MB and CUA performed the combinatorial analysis to predict biomarkers. CUA performed the single-gene editing and all validations. ML contributed to organizing and curating the large-scale data used in this work. CUA, LW, and ZD performed western blots. EF contributed in cell culture. DY and CUA performed the immunohistochemistry, EBG and CP transduced lentivirus with RPS11 overexpression vector. MZ and CUA performed the flow cytometry analysis. SK contributed to the CRISPR screen. IVB contributed reagents and corrected the manuscript. CUA and RM performed the DNA damage analysis on edited cells and GBM cell lines, respectively, and LC performed 53BP1 staining. BG, KBB, and DMS performed oversaw statistical analysis. AMS, PH, and AH supervised the project. CUA, MZ, and AMS prepared figures. CUA and AMS wrote the manuscript.

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Correspondence to Adam M. Sonabend.

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Awah, C.U., Chen, L., Bansal, M. et al. Ribosomal protein S11 influences glioma response to TOP2 poisons. Oncogene 39, 5068–5081 (2020). https://doi.org/10.1038/s41388-020-1342-0

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