The nuclear DEK interactome supports multi‐functionality

Abstract

DEK is an oncoprotein that is overexpressed in many forms of cancer and participates in numerous cellular pathways. Of these different pathways, relevant interacting partners and functions of DEK are well described in regard to the regulation of chromatin structure, epigenetic marks, and transcription. Most of this understanding was derived by investigating DNA-binding and chromatin processing capabilities of the oncoprotein. To facilitate the generation of mechanism-driven hypotheses regarding DEK activities in underexplored areas, we have developed the first DEK interactome model using tandem-affinity purification and mass spectrometry. With this approach, we identify IMPDH2, DDX21, and RPL7a as novel DEK binding partners, hinting at new roles for the oncogene in de novo nucleotide biosynthesis and ribosome formation. Additionally, a hydroxyurea-specific interaction with replication protein A (RPA) was observed, suggesting that a DEK-RPA complex may form in response to DNA replication fork stalling. Taken together, these findings highlight diverse activities for DEK across cellular pathways and support a model wherein this molecule performs a plethora of functions.DDX21, DEK, IMPDH2, interactome, mass spectrometry, ribosome, RPA | I N TR ODU C TI ONDEK is a DNA-binding and predominantly nuclear protein that was first identified as a DEK-NUP214 fusion protein in AML. 1 Since this discovery, DEK has been classified as an oncoprotein and shown to be overexpressed in many diverse tumor types, 2 wherein the degree of overexpression was linked to worse prognosis, advanced stage tumors, and chemotherapy resistance. 3-9 Cellular functions of the oncoprotein include activities in modifying chromatin structure, 2,10-13 histone chaperoning, 14,15 epigenetic modification and transcription regulation, [16][17][18][19]20,21 DNA repair,22,23 DNA replication fork restart, 24 mitotic non-disjunction events, 25 evasion of senescence and apoptosis, 19,26,27 proliferation 28-30 cancer stem cell fitness and invasion, 28,31 inflammation, 32,33 and metabolic reprogramming. 34 Precise molecular mechanisms whereby DEK regulates these cellular processes remain unclear in many cases. For instance, while DEK is necessary for optimal non-homologous end joining (NHEJ) DNA repair, the mechanism of action or interacting partners remain elusive. 23 For an oncogene that is widely implicated in human carcinogenesis and outcome, determining how DEK operates is imperative. However, this has proven challenging as the oncoprotein DEK has no known enzymatic activity or paralogs. 2 While significant progress has been made to understand molecular DEK activities in transcription via chromatin remodeling, 2,[10][11][12][13][16][17][18][19] there is a dearth of information regarding 88 | V C 2017 Wiley Periodicals, Inc.wileyonlinelibrary.com/journal/prot Proteins. 2018;86:88-97.

NUP214 in Leukemia: It’s More than Transport

“…In support of its multifunctional roles, a recent study on the interactome of DEK in human cells identified hundreds of interactors, including chromatin remodeling, RNA processing, ribosome biogenesis, and stress response factors [118]. Gene ontology (GO) analysis further unveiled that proteins involved in translation were among the most frequent hits [118].…”

“…In support of its multifunctional roles, a recent study on the interactome of DEK in human cells identified hundreds of interactors, including chromatin remodeling, RNA processing, ribosome biogenesis, and stress response factors [118]. Gene ontology (GO) analysis further unveiled that proteins involved in translation were among the most frequent hits [118]. In this context, it was previously shown that DEK-NUP214 activates the mTOR signaling pathway and the eukaryotic translation initiation factor 4E (EIF4E), which coincided with increased protein production [119,120].…”

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

“…DEK is considered a potential therapeutic target and a biomarker for breast and ovarian cancer [23–25], retinoblastoma [26], colorectal [27] and bladder cancer [28] as well as for melanoma progression [29, 30]. DEK has a pleiotropic mode of action and can influence diverse regulatory circuits in the cell, a notion supported also by the recent elucidation of its interactome [31]. Downregulation of DEK expression increases the susceptibility to DNA damage [21, 32], attenuates apoptosis [33] and senescence [22], and affects proliferation and chemoresistance [24, 34, 35].…”

Diverse Roles of DEAD/DEAH-Box Helicases in Innate Immunity and Diseases

“…DDX21, also known as nucleolar RNA helicase II, is an ATP-independent helicase associated with many nuclear and nucleolar events, such as ribosomal RNA biogenesis [158] or unwinding of R-loops [159] and RNA guanine quadruplexes [160]. DDX21 also interacts with mitotic regulator PP1 [161] and oncoprotein DEK [162]. Additionally, upregulated DDX21 has been found to promote tumorigenesis in breast cancer by phosphorylating c-Jun, a component of AP-1 transcription factor involved in cell survival pathways [163].…”