Mapping the Human Kinome in Response to DNA Damage

Michel Owusu,Peter Bannauer,Joana Ferreira Da Silva,Thanos P Mourikis,Alistair Jones,Peter Májek,Michael Caldera,Marc Wiedner,Charles-Hugues Lardeau,André C Mueller,Jörg Menche,Stefan Kubicek,Francesca D Ciccarelli,Joanna I Loizou

doi:10.1016/j.celrep.2018.12.087

Michel Owusu, Peter Bannauer + Show 12 more

Open Access

https://doi.org/10.1016/j.celrep.2018.12.087

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Abstract

We provide a catalog for the effects of the human kinome on cell survival in response to DNA-damaging agents, covering all major DNA repair pathways. By treating 313 kinase-deficient cell lines with ten diverse DNA-damaging agents, including seven commonly used chemotherapeutics, we identified examples of vulnerability and resistance that are kinase specific. To investigate synthetic lethal interactions, we tested the response to carmustine for 25 cell lines by establishing a phenotypic fluorescence-activated cell sorting (FACS) assay designed to validate gene-drug interactions. We show apoptosis, cell cycle changes, and DNA damage and proliferation after alkylation- orcrosslink-induced damage. In addition, we reconstitute the cellular sensitivity of DYRK4, EPHB6, MARK3, and PNCK as a proof of principle for our study. Furthermore, using global phosphoproteomics on cells lacking MARK3, we provide evidence for its role in the DNA damage response. Our data suggest that cancers with inactivating mutations in kinases, including MARK3, are particularly vulnerable to alkylating chemotherapeutic agents.

Highlights

The DNA damage response (DDR) is elicited by a complex and far-reaching network of proteins that are commonly deregulated in human pathologies, including cancer (Jackson and Bartek, 2009)
Protein kinases are an important group of signal transducers and are often deregulated in human cancer (Fleuren et al, 2016), making them interesting to study within the signaling context of the DNA damage response
We performed global phosphoproteomics to reveal alterations in phospho-signaling in the absence of MARK3, a kinase that is frequently mutated in cancer and we identified as displaying a vulnerability to alkylation damage, showing a role for MARK3 in the DNA damage response

Summary

Introduction

The DNA damage response (DDR) is elicited by a complex and far-reaching network of proteins that are commonly deregulated in human pathologies, including cancer (Jackson and Bartek, 2009). Protein kinases are an important group of signal transducers and are often deregulated in human cancer (Fleuren et al, 2016), making them interesting to study within the signaling context of the DNA damage response. Due to their enzymatic function, kinases represent an important group of drug targets (Klaeger et al, 2017) and results from loss-of-function studies with kinases are more likely to be translated into a therapeutic setting

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