H2A.Z histone variants facilitate HDACi-dependent removal of H3.3K27M mutant protein in pediatric high-grade glioma cells
Katarzyna B. Leszczynska,
Amanda Freitas-Huhtamäki,
Chinchu Jayaprakash,
Monika Dzwigonska,
Francisca N.L. Vitorino,
Cynthia Horth,
Kamil Wojnicki,
Bartlomiej Gielniewski,
Paulina Szadkowska,
Beata Kaza,
Javad Nazarian,
Maciej K. Ciolkowski,
Joanna Trubicka,
Wieslawa Grajkowska,
Benjamin A. Garcia,
Jacek Majewski,
Bozena Kaminska,
Jakub Mieczkowski
Affiliations
Katarzyna B. Leszczynska
Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland; Corresponding author
Amanda Freitas-Huhtamäki
Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
Chinchu Jayaprakash
Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
Monika Dzwigonska
Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
Francisca N.L. Vitorino
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
Cynthia Horth
Department of Human Genetics, McGill University, Montreal, QC, Canada
Kamil Wojnicki
Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
Bartlomiej Gielniewski
Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
Paulina Szadkowska
Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
Beata Kaza
Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
Javad Nazarian
Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, USA; Department of Pediatrics, University Children’s Hospital Zürich, Zürich, Switzerland
Maciej K. Ciolkowski
Children’s Memorial Health Institute, Warsaw, Poland
Joanna Trubicka
Children’s Memorial Health Institute, Warsaw, Poland
Wieslawa Grajkowska
Children’s Memorial Health Institute, Warsaw, Poland
Benjamin A. Garcia
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
Jacek Majewski
Department of Human Genetics, McGill University, Montreal, QC, Canada
Bozena Kaminska
Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
Jakub Mieczkowski
Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland; 3P-Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland; Corresponding author
Summary: Diffuse intrinsic pontine gliomas (DIPGs) are deadly pediatric brain tumors, non-resectable due to brainstem localization and diffusive growth. Over 80% of DIPGs harbor a mutation in histone 3 (H3.3 or H3.1) resulting in a lysine-to-methionine substitution (H3K27M). Patients with DIPG have a dismal prognosis with no effective therapy. We show that histone deacetylase (HDAC) inhibitors lead to a significant reduction in the H3.3K27M protein (up to 80%) in multiple glioma cell lines. We discover that the SB939-mediated H3.3K27M loss is partially blocked by a lysosomal inhibitor, chloroquine. The H3.3K27M loss is facilitated by co-occurrence of H2A.Z, as evidenced by the knockdown of H2A.Z isoforms. Chromatin immunoprecipitation sequencing (ChIP-seq) analysis confirms the occupancy of H3.3K27M and H2A.Z at the same SB939-inducible genes. We discover a mechanism showing that HDAC inhibition in DIPG leads to pharmacological modulation of the oncogenic H3.3K27M protein levels. These findings show the possibility of directly targeting the H3.3K27M oncohistone.
