Homeodomain-interacting protein kinase 1 (HIPK1) is majorly found in the nucleoplasm. HIPK1 is associated with cell proliferation, tumor necrosis factor-mediated cellular apoptosis, transcription regulation, and DNA damage response, and thought to play significant roles in health and common diseases such as cancer. Despite this, HIPK1 remains an understudied molecular target. In the present study, based on a systematic screening and mapping approach, we assembled 424 qualitative and 44 quantitative phosphoproteome datasets with 15 phosphosites in HIPK1 reported across multiple studies. These HIPK1 phosphosites were not currently attributed to any functions. Among them, Tyr352 within the kinase domain was identified as the predominant phosphosite modulated in 22 differential datasets. To analyze the functional association of HIPK1 Tyr352, we first employed a stringent criterion to derive its positively and negatively correlated protein phosphosites. Subsequently, we categorized the correlated phosphosites in known interactors, known/predicted kinases, and substrates of HIPK1, for their prioritized validation. Bioinformatics analysis identified their significant association with biological processes such as the regulation of RNA splicing, DNA-templated transcription, and cellular metabolic processes. HIPK1 Tyr352 was also identified to be upregulated in Her2+ cell lines and a subset of pancreatic and cholangiocarcinoma tissues. These data and the systems biology approach undertaken in the present study serve as a platform to explore the functional role of other phosphosites in HIPK1, and by extension, inform cancer drug discovery and oncotherapy innovation. In all, this study highlights the comprehensive phosphosite map of HIPK1 kinase and the first of its kind phosphosite-centric analysis of HIPK1 kinase based on global-level phosphoproteomics datasets derived from human cellular differential experiments across distinct experimental conditions.
Get full access to this article
View all access options for this article.
References
1.
AdachiJ, HashiguchiK, NaganoM, et al.Improved proteome and phosphoproteome analysis on a cation exchanger by a combined acid and salt gradient. Anal Chem, 2016; 88(16):7899–7903; doi: 10.1021/acs.analchem.6b01232
2.
AyatiM, WiredjaD, SchlatzerD, et al.CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis. PLoS Comput Biol, 2019; 15(2):e1006678; doi: 10.1371/journal.pcbi.1006678
BianY, LiL, DongM, et al.Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder. Nat Chem Biol, 2016; 12(11):959–966; doi: 10.1038/nchembio.2178
6.
BoeingS, WilliamsonL, EnchevaV, et al.Multiomic analysis of the UV-induced DNA damage response. Cell Rep, 2016; 15(7):1597–1610; doi: 10.1016/j.celrep.2016.04.047
7.
BorisovaME, VoigtA, TollenaereMAX, et al.P38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage. Nat Commun, 2018; 9(1):1017; doi: 10.1038/s41467-018-03417-3
8.
BrittonD, ZenY, QuagliaA, et al.Quantification of pancreatic cancer proteome and phosphorylome: Indicates molecular events likely contributing to cancer and activity of drug targets. PLoS One, 2014; 9(3):e90948; doi: 10.1371/journal.pone.0090948
9.
BufeA, García Del ArcoA, HenneckeM, et al.Wnt signaling recruits KIF2A to the spindle to ensure chromosome congression and alignment during mitosis. Proc Natl Acad Sci U S A, 2021; 118(34):e2108145118; doi: 10.1073/pnas.2108145118
10.
ChaeSY, NamD, HyeonDY, et al.DNA repair and cholesterol-mediated drug efflux induce dose-dependent chemoresistance in nutrient-deprived neuroblastoma cells. iScience, 2021; 24(4):102325; doi: 10.1016/j.isci.2021.102325
11.
ConteA, PierantoniGM. Update on the regulation of HIPK1, HIPK2 and HIPK3 protein kinases by microRNAs. MicroRNA, 2018; 7(3):178–186; doi: 10.2174/2211536607666180525102330
12.
de GraafEL, KaplonJ, ZhouH, et al.Phosphoproteome dynamics in onset and maintenance of oncogene-induced senescence. Mol Cell Proteomics, 2014; 13(8):2089–100; doi: 10.1074/mcp.M113.035436
13.
de la VegaL, GrishinaI, MorenoR, et al.A redox-regulated SUMO/Acetylation switch of HIPK2 controls the survival threshold to oxidative stress. Mol Cell, 2012; 46(4):472–83; doi: 10.1016/j.molcel.2012.03.003.
14.
DeNardoBD, HollowayMP, JiQ, et al.Quantitative phosphoproteomic analysis identifies activation of the RET and IGF-1R/IR signaling pathways in neuroblastoma. PLoS One, 2013; 8(12):e82513; doi: 10.1371/journal.pone.0082513
15.
DinkelH, ChicaC, ViaA, et al.Phospho.ELM: A database of phosphorylation sites—Update 2011. Nucleic Acids Res, 2011; 39(Database issue):D261–D267; doi: 10.1093/nar/gkq1104
16.
DunkerAK, GoughJ. Sequences and topology: Intrinsic disorder in the evolving universe of protein structure. Curr Opin Struct Biol, 2011; 21(3):379–381; doi: 10.1016/j.sbi.2011.04.002
EswaranJ, CyanamD, MudvariP, et al.Transcriptomic landscape of breast cancers through MRNA sequencing. Sci Rep, 2012; 2:264; doi: 10.1038/srep00264
19.
GalanJA, GeraghtyKM, LavoieG, et al.Phosphoproteomic Analysis identifies the tumor suppressor PDCD4 as a RSK substrate negatively regulated by 14-3-3. Proc Natl Acad Sci U S A, 2014; 111(29):E2918–E2927; doi: 10.1073/pnas.1405601111
20.
GoelR, HarshaHC, PandeyA, et al.Human protein reference database and human proteinpedia as resources for phosphoproteome analysis. Mol Biosyst, 2012; 8(2):453–463; doi: 10.1039/c1mb05340j
21.
GossVL, LeeKA, MoritzA, et al.A common phosphotyrosine signature for the Bcr-Abl kinase. Blood, 2006; 107(12):4888–4897; doi: 10.1182/blood-2005-08-3399
22.
HayatA, CarterEP, KingHW, et al.Low HER2 expression in normal breast epithelium enables dedifferentiation and malignant transformation via chromatin opening. Dis Model Mech, 2023; 16(2): dmm049894; doi: 10.1242/dmm.049894
23.
HornbeckPV, ZhangB, MurrayB, et al.PhosphoSitePlus, 2014: Mutations, PTMs and recalibrations. Nucleic Acids Res, 2015; 43(Database issue):D512–D520; doi: 10.1093/nar/gku1267
24.
HuangF-K, ZhangG, LawlorK, et al.Deep coverage of global protein expression and phosphorylation in breast tumor cell lines using TMT 10-plex isobaric labeling. J Proteome Res, 2017; 16(3):1121–1132; doi: 10.1021/acs.jproteome.6b00374
25.
HuangK-Y, WuH-Y, ChenY-J, et al.RegPhos 2.0: An updated resource to explore protein kinase-substrate phosphorylation networks in mammals. Database (Oxford), 2014; 2014(0):bau034; doi: 10.1093/database/bau034
26.
ImamiK, SugiyamaN, ImamuraH, et al.Temporal profiling of lapatinib-suppressed phosphorylation signals in EGFR/HER2 pathways. Mol Cell Proteomics, 2012; 11(12):1741–57; doi: 10.1074/mcp.M112.019919
27.
JohnsonJL, YaronTM, HuntsmanEM, et al.An atlas of substrate specificities for the human serine/threonine kinome. Nature, 2023; 613(7945):759–766; doi: 10.1038/s41586-022-05575-3
28.
KamburovA, HerwigR. ConsensusPathDB 2022: Molecular interactions update as a resource for network biology. Nucleic Acids Res, 2022; 50(D1):D587–D595; doi: 10.1093/nar/gkab1128
KimYH, ChoiCY, LeeSJ, et al.Homeodomain-interacting protein kinases, a novel family of co-repressors for homeodomain transcription factors. J Biol Chem, 1998; 273(40):25875–25879; doi: 10.1074/jbc.273.40.25875
31.
KondoS, LuY, DebbasM, et al.Characterization of cells and gene-targeted mice deficient for the P53-binding kinase homeodomain-interacting protein kinase 1 (HIPK1). Proc Natl Acad Sci U S A, 2003; 100(9):5431–5436; doi: 10.1073/pnas.0530308100
32.
KurokawaK, AkaikeY, MasudaK, et al.Downregulation of serine/arginine-rich splicing factor 3 induces G1 cell cycle arrest and apoptosis in colon cancer cells. Oncogene, 2014; 33(11):1407–1417; doi: 10.1038/onc.2013.86
33.
LeeD, ParkS-J, SungKS, et al.Mdm2 associates with ras effector NORE1 to induce the degradation of oncoprotein HIPK1. EMBO Rep, 2012; 13(2):163–169; doi: 10.1038/embor.2011.235
34.
LiX, LuoY, YuL, et al.SENP1 mediates TNF-Induced desumoylation and cytoplasmic translocation of HIPK1 to enhance ASK1-dependent apoptosis. Cell Death Differ, 2008; 15(4):739–750; doi: 10.1038/sj.cdd.4402303
35.
LiX, ZhangR, LuoD, et al.Tumor necrosis factor alpha-induced desumoylation and cytoplasmic translocation of homeodomain-interacting protein kinase 1 are critical for apoptosis signal-regulating kinase 1-JNK/P38 activation. J Biol Chem, 2005; 280(15):15061–15070; doi: 10.1074/jbc.M414262200
36.
LindingR, JensenLJ, PasculescuA, et al.NetworKIN: A resource for exploring cellular phosphorylation networks. Nucleic Acids Res, 2008; 36(Database issue):D695–D699; doi: 10.1093/nar/gkm902
37.
LiuZ, YanH, YangY, et al.Down-regulation of CIT can inhibit the growth of human bladder cancer cells. Biomed Pharmacother, 2020; 124:109830; doi: 10.1016/j.biopha.2020.109830
38.
LuY, LiX, ZhaoK, et al.Proteomic and phosphoproteomic profiling reveals the oncogenic role of protein kinase D family kinases in cholangiocarcinoma. Cells, 2022; 11(19):3088; doi: 10.3390/cells11193088
Martinez-FabregasJ, WangL, PohlerE, et al.CDK8 fine-tunes IL-6 transcriptional activities by limiting STAT3 resident time at the gene loci. Cell Rep, 2020; 33(12):108545; doi: 10.1016/j.celrep.2020.108545
41.
MatreV, NordgårdO, Alm-KristiansenAH, et al.HIPK1 interacts with C-Myb and modulates its activity through phosphorylation. Biochem Biophys Res Commun, 2009; 388(1):150–154; doi: 10.1016/j.bbrc.2009.07.139
42.
MauriM, ElliT, CavigliaG, et al.RAWGraphs. In: Proceedings of the 12th Biannual Conference on Italian SIGCHI Chapter ACM: New York, NY, USA; 2017; pp. 1–5; doi: 10.1145/3125571.3125585
43.
MertinsP, ManiDR, Ruggles KV, et al.Proteogenomics Connects somatic mutations to signalling in breast cancer. Nature, 2016; 534(7605):55–62; doi: 10.1038/nature18003
44.
MertinsP, YangF, LiuT, et al.Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels. Mol Cell Proteomics, 2014; 13(7):1690–1704; doi: 10.1074/mcp.M113.036392
45.
MooneySM, QiuR, KimJJ, et al.Cancer/testis antigen PAGE4, a regulator of c-Jun transactivation, is phosphorylated by homeodomain-interacting protein kinase 1, a component of the stress-response pathway. Biochemistry, 2014; 53(10):1670–1679; doi: 10.1021/bi500013w
46.
NishiH, HashimotoK, PanchenkoAR. Phosphorylation in protein-protein binding: Effect on stability and function. Structure, 2011; 19(12):1807–1815; doi: 10.1016/j.str.2011.09.021
47.
OkanishiH, OhgakiR, XuM, et al.Phosphoproteomics revealed cellular signals immediately responding to disruption of cancer amino acid homeostasis induced by inhibition of L-type amino acid transporter 1. Cancer Metab, 2022; 10(1):18; doi: 10.1186/s40170-022-00295-8
48.
OughtredR, RustJ, ChangC, et al.The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Sci, 2021; 30(1):187–200; doi: 10.1002/pro.3978
49.
ParcaL, ArianoB, CabibboA, et al.Kinome-wide identification of phosphorylation networks in eukaryotic proteomes. Bioinformatics, 2019; 35(3):372–379; doi: 10.1093/bioinformatics/bty545
50.
ParkB-W, ParkS, KooJS, et al.Homeodomain-interacting protein kinase 1 (HIPK1) expression in breast cancer tissues. Jpn J Clin Oncol, 2012; 42(12):1138–1145; doi: 10.1093/jjco/hys163
51.
PartynskaA, GomulkiewiczA, DziegielP, et al.The role of zyxin in carcinogenesis. Anticancer Res, 2020; 40(11):5981–5988; doi: 10.21873/anticanres.14618
52.
PedersenA-K, PfeifferA, KaremoreG, et al.Proteomic investigation of Cbl and Cbl-b in neuroblastoma cell differentiation highlights roles for SHP-2 and CDK16. iScience, 2021; 24(4):102321; doi: 10.1016/j.isci.2021.102321
53.
Polonio-VallonT, KirkpatrickJ, KrijgsveldJ, et al.Src kinase modulates the apoptotic P53 pathway by altering HIPK2 localization. Cell Cycle, 2014; 13(1):115–125; doi: 10.4161/cc.26857
54.
RajuR, PaulAM, AsokachandranV, et al.The triple-negative breast cancer database: An omics platform for reference, integration and analysis of triple-negative breast cancer data. Breast Cancer Res, 2014; 16(6):490; doi: 10.1186/s13058-014-0490-y
55.
RaudvereU, KolbergL, KuzminI, et al.G:Profiler: A web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Res, 2019; 47(W1):W191–W198; doi: 10.1093/nar/gkz369
56.
RuiY, XuZ, LinS, et al.Axin stimulates P53 functions by activation of HIPK2 kinase through multimeric complex formation. EMBO J, 2004; 23(23):4583–4594; doi: 10.1038/sj.emboj.7600475
57.
SaulVV, de la VegaL, MilanovicM, et al.HIPK2 kinase activity depends on cis-autophosphorylation of its activation loop. J Mol Cell Biol, 2013; 5(1):27–38; doi: 10.1093/jmcb/mjs053
58.
SchmitzML, Rodriguez-GilA, HornungJ. Integration of stress signals by homeodomain interacting protein kinases. Biol Chem, 2014; 395(4):375–386; doi: 10.1515/hsz-2013-0264
59.
SealRL, BraschiB, GrayK, et al.Genenames.Org: The HGNC resources in 2023. Nucleic Acids Res, 2023; 51(D1):D1003–D1009; doi: 10.1093/nar/gkac888
60.
ShannonP, MarkielA, OzierO, et al.Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res, 2003; 13(11):2498–2504; doi: 10.1101/gr.1239303
61.
SolankiHS, WelshEA, FangB, et al.Cell type-specific adaptive signaling responses to KRASG12C inhibition. Clin Cancer Res, 2021; 27(9):2533–2548; doi: 10.1158/1078-0432.CCR-20-3872
62.
TsitsiridisG, SteinkampR, GiurgiuM, et al.CORUM: The comprehensive resource of mammalian protein complexes-2022. Nucleic Acids Res, 2023; 51(D1):D539–D545; doi: 10.1093/nar/gkac1015
63.
UniProt Consortium. UniProt: The universal protein knowledgebase in 2023. Nucleic Acids Res, 2023; 51(D1):D523–D531; doi: 10.1093/nar/gkac1052
64.
van der LadenJ, SoppaU, BeckerW. Effect of tyrosine autophosphorylation on catalytic activity and subcellular localisation of homeodomain-interacting protein kinases (HIPK). Cell Commun Signal, 2015; 13:3; doi: 10.1186/s12964-014-0082-6
65.
YangM, WuM, XiaP, et al.The role of microtubule-associated protein 1B in axonal growth and neuronal migration in the central nervous system. Neural Regen Res, 2012; 7(11):842–848; doi: 10.3969/j.issn.1673-5374.2012.11.008
66.
ZhangZ, ZhangY, LiY, et al.Quantitative phosphoproteomics reveal cellular responses from caffeine, coumarin and quercetin in treated HepG2 cells. Toxicol Appl Pharmacol, 2022; 449:116110; doi: 10.1016/j.taap.2022.116110
Supplementary Material
Please find the following supplemental material available below.
For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.
For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.
