Systematic Kinase Inhibitor Profiling Identifies CDK9 as a Synthetic Lethal Target in NUT Midline Carcinoma

Johannes Brägelmann; Marcel A Dammert; Felix Dietlein; Johannes M Heuckmann; Axel Choidas; Stefanie Böhm; André Richters; Debjit Basu; Verena Tischler; Carina Lorenz; Peter Habenberger; Zhizhou Fang; Sandra Ortiz-Cuaran; Frauke Leenders; Jan Eickhoff; Uwe Koch; Matthäus Getlik; Martin Termathe; Muhammad Sallouh; Zoltán Greff; Zoltán Varga; Hyatt Balke-Want; Christopher A French; Martin Peifer; H Christian Reinhardt; László Örfi; György Kéri; Sascha Ansén; Lukas C Heukamp; Reinhard Büttner; Daniel Rauh; Bert M Klebl; Roman K Thomas; Martin L Sos

doi:10.1016/j.celrep.2017.08.082

Systematic Kinase Inhibitor Profiling Identifies CDK9 as a Synthetic Lethal Target in NUT Midline Carcinoma

Cell Rep. 2017 Sep 19;20(12):2833-2845. doi: 10.1016/j.celrep.2017.08.082.

Authors

Johannes Brägelmann¹, Marcel A Dammert¹, Felix Dietlein², Johannes M Heuckmann³, Axel Choidas⁴, Stefanie Böhm¹, André Richters⁵, Debjit Basu⁵, Verena Tischler⁶, Carina Lorenz¹, Peter Habenberger⁴, Zhizhou Fang⁵, Sandra Ortiz-Cuaran⁶, Frauke Leenders⁶, Jan Eickhoff⁴, Uwe Koch⁴, Matthäus Getlik⁵, Martin Termathe⁵, Muhammad Sallouh⁵, Zoltán Greff⁷, Zoltán Varga⁷, Hyatt Balke-Want⁸, Christopher A French⁹, Martin Peifer⁶, H Christian Reinhardt¹⁰, László Örfi¹¹, György Kéri⁷, Sascha Ansén², Lukas C Heukamp¹², Reinhard Büttner¹³, Daniel Rauh⁵, Bert M Klebl⁴, Roman K Thomas¹⁴, Martin L Sos¹⁵

Affiliations

¹ Molecular Pathology, Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany.
² Department I of Internal Medicine and Center for Integrated Oncology, University Hospital of Cologne, Kerpener Str. 62, 50937 Cologne, Germany.
³ NEO New Oncology GmbH, Gottfried-Hagen-Str. 20, 51105 Cologne, Germany.
⁴ Lead Discovery Center (LDC) GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany.
⁵ Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44221 Dortmund, Germany.
⁶ Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany.
⁷ Vichem Chemie Research Ltd., Herman Ottó u. 15, Budapest, Hungary.
⁸ Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany; Department I of Internal Medicine and Center for Integrated Oncology, University Hospital of Cologne, Kerpener Str. 62, 50937 Cologne, Germany.
⁹ Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
¹⁰ Department I of Internal Medicine and Center for Integrated Oncology, University Hospital of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany.
¹¹ Vichem Chemie Research Ltd., Herman Ottó u. 15, Budapest, Hungary; Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes E. U.9, Budapest, Hungary.
¹² Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany; Institute of Pathology, Medical Faculty, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany.
¹³ Institute of Pathology, Medical Faculty, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany.
¹⁴ Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany; Institute of Pathology, Medical Faculty, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany. Electronic address: roman.thomas@uni-koeln.de.
¹⁵ Molecular Pathology, Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany. Electronic address: martin.sos@uni-koeln.de.

Abstract

Kinase inhibitors represent the backbone of targeted cancer therapy, yet only a limited number of oncogenic drivers are directly druggable. By interrogating the activity of 1,505 kinase inhibitors, we found that BRD4-NUT-rearranged NUT midline carcinoma (NMC) cells are specifically killed by CDK9 inhibition (CDK9i) and depend on CDK9 and Cyclin-T1 expression. We show that CDK9i leads to robust induction of apoptosis and of markers of DNA damage response in NMC cells. While both CDK9i and bromodomain inhibition over time result in reduced Myc protein expression, only bromodomain inhibition induces cell differentiation and a p21-induced cell-cycle arrest in these cells. Finally, RNA-seq and ChIP-based analyses reveal a BRD4-NUT-specific CDK9i-induced perturbation of transcriptional elongation. Thus, our data provide a mechanistic basis for the genotype-dependent vulnerability of NMC cells to CDK9i that may be of relevance for the development of targeted therapies for NMC patients.

Keywords: CDK9 inhibitor; NUT midline carcinoma; high-throughput screen; transcriptional elongation.

MeSH terms

Cell Cycle Proteins
Cell Line, Tumor
Cyclin T / metabolism
Cyclin-Dependent Kinase 9 / antagonists & inhibitors
Cyclin-Dependent Kinase 9 / metabolism
HEK293 Cells
High-Throughput Screening Assays
Humans
Molecular Targeted Therapy*
Neoplasms / enzymology*
Neoplasms / genetics
Neoplasms / pathology*
Nuclear Proteins / antagonists & inhibitors
Nuclear Proteins / metabolism
Protein Kinase Inhibitors / chemistry
Protein Kinase Inhibitors / pharmacology*
RNA Polymerase II / metabolism
Transcription Elongation, Genetic / drug effects
Transcription Factors / antagonists & inhibitors
Transcription Factors / metabolism
Transcription, Genetic / drug effects

Substances

BRD4 protein, human
Cell Cycle Proteins
Cyclin T
Nuclear Proteins
Protein Kinase Inhibitors
Transcription Factors
CDK9 protein, human
Cyclin-Dependent Kinase 9
RNA Polymerase II