1
|
Gonzalez-Buendia E, Zhao J, Wang L, Mukherjee S, Zhang D, Arrieta VA, Feldstein E, Kane JR, Kang SJ, Lee-Chang C, Mahajan A, Chen L, Realubit R, Karan C, Magnuson L, Horbinski C, Marshall SA, Sarkaria JN, Mohyeldin A, Nakano I, Bansal M, James CD, Brat DJ, Ahmed A, Canoll P, Rabadan R, Shilatifard A, Sonabend AM. TOP2B Enzymatic Activity on Promoters and Introns Modulates Multiple Oncogenes in Human Gliomas. Clin Cancer Res 2021; 27:5669-5680. [PMID: 34433651 PMCID: PMC8818263 DOI: 10.1158/1078-0432.ccr-21-0312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/07/2021] [Accepted: 07/28/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE The epigenetic mechanisms involved in transcriptional regulation leading to malignant phenotype in gliomas remains poorly understood. Topoisomerase IIB (TOP2B), an enzyme that decoils and releases torsional forces in DNA, is overexpressed in a subset of gliomas. Therefore, we investigated its role in epigenetic regulation in these tumors. EXPERIMENTAL DESIGN To investigate the role of TOP2B in epigenetic regulation in gliomas, we performed paired chromatin immunoprecipitation sequencing for TOP2B and RNA-sequencing analysis of glioma cell lines with and without TOP2B inhibition and in human glioma specimens. These experiments were complemented with assay for transposase-accessible chromatin using sequencing, gene silencing, and mouse xenograft experiments to investigate the function of TOP2B and its role in glioma phenotypes. RESULTS We discovered that TOP2B modulates transcription of multiple oncogenes in human gliomas. TOP2B regulated transcription only at sites where it was enzymatically active, but not at all native binding sites. In particular, TOP2B activity localized in enhancers, promoters, and introns of PDGFRA and MYC, facilitating their expression. TOP2B levels and genomic localization was associated with PDGFRA and MYC expression across glioma specimens, which was not seen in nontumoral human brain tissue. In vivo, TOP2B knockdown of human glioma intracranial implants prolonged survival and downregulated PDGFRA. CONCLUSIONS Our results indicate that TOP2B activity exerts a pleiotropic role in transcriptional regulation of oncogenes in a subset of gliomas promoting a proliferative phenotype.
Collapse
Affiliation(s)
- Edgar Gonzalez-Buendia
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Junfei Zhao
- Department of Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Lu Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Subhas Mukherjee
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Daniel Zhang
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Víctor A Arrieta
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- PECEM, Facultad de Medicina, Universidad Nacional Autónoma de México, México
| | - Eric Feldstein
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - J Robert Kane
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Seong Jae Kang
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Catalina Lee-Chang
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Aayushi Mahajan
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Li Chen
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ronald Realubit
- High-Throughput Screening Genome Center, Columbia University, New York, New York
| | - Charles Karan
- High-Throughput Screening Genome Center, Columbia University, New York, New York
| | - Lisa Magnuson
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Craig Horbinski
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Ahmed Mohyeldin
- Department of Neurosurgery, Ohio State University, Columbus, Ohio
| | - Ichiro Nakano
- Department of Neurosurgery, University of Alabama, Birmingham, Alabama
| | - Mukesh Bansal
- Department of Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Charles D James
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Daniel J Brat
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Atique Ahmed
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Raul Rabadan
- Department of Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Adam M Sonabend
- Department of Neurosurgery, Feinberg School of Medicine, Northwestern University and Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.
| |
Collapse
|