The oncoprotein DEK affects the outcome of PARP1/2 inhibition during mild replication stress

Abstract

DNA replication stress is a major source of genomic instability and is closely linked to tumor formation and progression. Poly(ADP-ribose)polymerases1/2 (PARP1/2) enzymes are activated in response to replication stress resulting in poly(ADP-ribose) (PAR) synthesis. PARylation plays an important role in the remodelling and repair of impaired replication forks, providing a rationale for targeting highly replicative cancer cells with PARP1/2 inhibitors. The human oncoprotein DEK is a unique, non-histone chromatin architectural protein whose deregulated expression is associated with the development of a wide variety of human cancers. Recently, we showed that DEK is a high-affinity target of PARylation and that it promotes the progression of impaired replication forks. Here, we investigated a potential functional link between PAR and DEK in the context of replication stress. Under conditions of mild replication stress induced either by topoisomerase1 inhibition with camptothecin or nucleotide depletion by hydroxyurea, we found that the effect of acute PARP1/2 inhibition on replication fork progression is dependent on DEK expression. Reducing DEK protein levels also overcomes the restart impairment of stalled forks provoked by blocking PARylation. Non-covalent DEK-PAR interaction via the central PAR-binding domain of DEK is crucial for counteracting PARP1/2 inhibition as shown for the formation of RPA positive foci in hydroxyurea treated cells. Finally, we show by iPOND and super resolved microscopy that DEK is not directly associated with the replisome since it binds to DNA at the stage of chromatin formation. Our report sheds new light on the still enigmatic molecular functions of DEK and suggests that DEK expression levels may influence the sensitivity of cancer cells to PARP1/2 inhibitors.

Super-resolution microscopy reveals the nanoscale organization of the DEK protein cancer biomarker

“…This approach allowed us to quantitatively compare the DEK pattern in MCF10A and MDAMB231 cells, representing the normal-like breast basal epithelial cells and triple negative, metastatic basal breast cancer cells, respectively. Previous studies indicate that DEK protein locates mostly within the cell nucleus (4,10,18), and, more precisely, it can be associated with euchromatin (i.e., the active compartments of chromatin) (19). Considering the overexpression of DEK in breast cancer samples, we speculated that its nanoscale organization would differ if compared to normal-like cells.…”

“…It is well established that the DEK protein is overexpressed in highly proliferating cells (38), such as cancer cells, and can alter the chromatin topology (7). Our recent study using super-resolution techniques suggested that the commonly observed dispersed nuclear DEK pattern (18,31) is composed of nanoclusters (10). In this work, we investigated the nanoscale characteristics of such clusters in normal-like and aggressive type of breast cancer cell lines to study if DEK’s overexpression correlates with its cluster features.…”

“…When observed with diffraction-limited fluorescence microscopy, DEK is commonly described as uniformly distributed within the cell nucleus (18,31). However, our recent study employing SMLM suggests the formation of cluster-like DEK structures (10).…”

“…One of the non-histone chromatin architectural factors is DEK, which has a pleiotropic mode of action by influencing several regulatory cellular pathways. DEK is involved in chromatin structure and chromatin-related processes regulation, such as transcriptional activation and repression (4)(5)(6), DNA replication (7)(8)(9)(10), and DNA damage response and repair (11)(12)(13)(14)(15). DEK binds to many highly and commonly expressed genes (5) and is involved in gene regulation in breast cancer cells (16).…”

Poly(ADP-Ribosyl) Code Functions

“…The interaction of the DEK oncoprotein with PAR also turns out to be dependent on the polymer length. DEK is involved in various intracellular processes: replication [ 87 , 88 ], DNA repair [ 89 ], RNA processing [ 90 ], and transcription regulation [ 91 , 92 , 93 ]. High DEK levels were shown to contribute to cell immortalization, as well as suppress aging and apoptosis [ 94 , 95 ].…”