The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer

Stephin J Vervoort; Sarah A Welsh; Jennifer R Devlin; Elisa Barbieri; Deborah A Knight; Sarah Offley; Stefan Bjelosevic; Matteo Costacurta; Izabela Todorovski; Conor J Kearney; Jarrod J Sandow; Zheng Fan; Benjamin Blyth; Victoria McLeod; Joseph H A Vissers; Karolina Pavic; Ben P Martin; Gareth Gregory; Elena Demosthenous; Magnus Zethoven; Isabella Y Kong; Edwin D Hawkins; Simon J Hogg; Madison J Kelly; Andrea Newbold; Kaylene J Simpson; Otto Kauko; Kieran F Harvey; Michael Ohlmeyer; Jukka Westermarck; Nathanael Gray; Alessandro Gardini; Ricky W Johnstone

doi:10.1016/j.cell.2021.04.022

The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer

Cell. 2021 Jun 10;184(12):3143-3162.e32. doi: 10.1016/j.cell.2021.04.022. Epub 2021 May 17.

Authors

Stephin J Vervoort¹, Sarah A Welsh², Jennifer R Devlin³, Elisa Barbieri⁴, Deborah A Knight³, Sarah Offley⁵, Stefan Bjelosevic³, Matteo Costacurta³, Izabela Todorovski³, Conor J Kearney³, Jarrod J Sandow⁶, Zheng Fan³, Benjamin Blyth⁷, Victoria McLeod⁷, Joseph H A Vissers⁸, Karolina Pavic⁹, Ben P Martin³, Gareth Gregory¹⁰, Elena Demosthenous⁷, Magnus Zethoven⁷, Isabella Y Kong⁶, Edwin D Hawkins⁶, Simon J Hogg³, Madison J Kelly³, Andrea Newbold³, Kaylene J Simpson⁷, Otto Kauko⁹, Kieran F Harvey¹¹, Michael Ohlmeyer¹², Jukka Westermarck⁹, Nathanael Gray¹³, Alessandro Gardini¹⁴, Ricky W Johnstone¹⁵

Affiliations

¹ Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia. Electronic address: [email protected].
² The Wistar Institute, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
³ Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia.
⁴ The Wistar Institute, Philadelphia, PA 19104, USA.
⁵ The Wistar Institute, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
⁶ The Walter and Eliza Hall Institute, Parkville 3010, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville 3010, VIC, Australia.
⁷ Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia.
⁸ Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia; Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville 3010, VIC, Australia.
⁹ Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku FI-20014, Finland; Institute of Biomedicine, University of Turku, Turku FI-20014, Finland.
¹⁰ Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton 3168, VIC, Australia.
¹¹ Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia; Department of Anatomy and Developmental Biology, and Biomedicine Discovery Institute, Monash University, Clayton 3168, VIC, Australia.
¹² Mount Sinai School of Medicine, New York, NY 10029, USA; Atux Iskay LLC, Plainsboro, NJ 08536, USA.
¹³ Dana Farber Cancer Institute, Boston, MA 02215, USA.
¹⁴ The Wistar Institute, Philadelphia, PA 19104, USA. Electronic address: [email protected].
¹⁵ Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia. Electronic address: [email protected].

Abstract

Gene expression by RNA polymerase II (RNAPII) is tightly controlled by cyclin-dependent kinases (CDKs) at discrete checkpoints during the transcription cycle. The pausing checkpoint following transcription initiation is primarily controlled by CDK9. We discovered that CDK9-mediated, RNAPII-driven transcription is functionally opposed by a protein phosphatase 2A (PP2A) complex that is recruited to transcription sites by the Integrator complex subunit INTS6. PP2A dynamically antagonizes phosphorylation of key CDK9 substrates including DSIF and RNAPII-CTD. Loss of INTS6 results in resistance to tumor cell death mediated by CDK9 inhibition, decreased turnover of CDK9 phospho-substrates, and amplification of acute oncogenic transcriptional responses. Pharmacological PP2A activation synergizes with CDK9 inhibition to kill both leukemic and solid tumor cells, providing therapeutic benefit in vivo. These data demonstrate that fine control of gene expression relies on the balance between kinase and phosphatase activity throughout the transcription cycle, a process dysregulated in cancer that can be exploited therapeutically.

Keywords: CDK9; CRISPR-Cas9 screen; CTD; Integrator; PP2A; PP2A activation; RNA polymerase II; cancer; pause-release; phosphatase; transcriptional elongation.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cell Line, Tumor
Cyclin-Dependent Kinase 9 / antagonists & inhibitors
Cyclin-Dependent Kinase 9 / metabolism*
Drug Resistance, Neoplasm / genetics
Gene Expression Regulation, Neoplastic
Humans
Mice
Mice, Inbred NOD
Molecular Targeted Therapy*
Neoplasms / drug therapy*
Neoplasms / genetics*
Phosphorylation
Protein Binding
Protein Phosphatase 2 / metabolism*
RNA Polymerase II / chemistry
RNA Polymerase II / metabolism
RNA-Binding Proteins / metabolism*
Substrate Specificity
Transcription, Genetic*
Tumor Suppressor Proteins / metabolism*

Substances

INTS6 protein, human
RNA-Binding Proteins
Tumor Suppressor Proteins
CDK9 protein, human
Cyclin-Dependent Kinase 9
RNA Polymerase II
Protein Phosphatase 2

Abstract

Publication types

MeSH terms

Substances

Grants and funding