Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_01.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_19.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_06.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_16.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_14.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_03.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_08.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_13.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_17.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_18.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_07.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_04.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_09.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/20231027_E2_Neo_ColID_AUR01_25cm_TRAP_SK_MS-0037_WP_sample_02.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067752/Proteome_Search.zipprimaryOK200wbecker@ukaachen.deSebastian KallabisMass SpectrometryBottom-up proteomicsData-independent acquisitionRfx7Dyrk1aDyrk1bA549P53https://www.ebi.ac.uk/pride/archive/projects/PXD067752Cell CultureSample preparation for MS analysis: A549 tetON cells were harvested 24 h after treatment by adding 1 ml of Accutase, pelleted by centrifugation (4 °C, 150 g, 10 min), and subsequently frozen at −80 °C. Pelleted cells were lysed with guanidine hydrochloride (GuHCl) lysis buffer containing 6 M GuHCl (Merck), 5 mM Bond-Breaker TCEP solution (Thermo), 10 mM 2-chloroacetamide (Merck), and 100 mM Tris-HCl buffer pH 8.5. Samples were incubated at 90 °C and 800 rpm in a thermo shaker for 10 minutes. DNA was sheared by incubation with Benzonase (15 U/sample, Merck, #E1014-25KU) for 30 minutes at 37 °C, and the samples were centrifuged at 15,000 g for 10 minutes. Supernatants were transferred to fresh tubes, and protein concentrations were determined with the Pierce 660 nm protein assay (Thermo). Samples were diluted to < 1 M GuHCl with 25 mM Tris-HCl, and trypsin / Lys-C (Promega) was added in a 1:100 enzyme-to-protein ratio and digested at 37 °C overnight. The next day, samples were acidified with formic acid (final concentration of 1 %) and desalted using C18 cartridges (Waters). In brief, the C18 sorbent was activated with 1 ml each of 100 % isopropanol and washed twice with buffer A (0.1 % formic acid in LC-MS-grade water). Solvents were pushed through the cartridges by applying positive pressure. Samples were loaded completely onto the cartridges and washed twice with buffer A. For peptide elution, buffer B (80% acetonitrile, 0.1% formic acid in LC-MS-grade water) was added to the cartridges and the flow-through was collected in clean reaction tubes. Samples were dried completely by vacuum centrifugation, redissolved in buffer R (2% acetonitrile, 0.1% formic acid in LC-MS-grade water), and peptide concentrations were determined. For each LCMS/MS measurement, 200 ng of peptides were injected into the LC-MS system. Liquid chromatography-mass spectrometry: A liquid chromatography-tandem mass spectrometry system consisting of a Vanquish Neo UHPCL operated in trap mode, and an Orbitrap Exploris 480 MS (both Thermo Fisher Scientific) was used for proteomics analysis. Peptides were separated with a 90-minute chromatographic gradient consisting of a binary buffer system with buffer A and buffer B. An IonOpticks Aurora Ultimate analytical column was used for peptide separation. Starting at 5% buffer B, the amount of B was linearly increased to 25 % over 71 minutes, followed by a linear increase to 55% over 9 minutes. Lastly, the analytical column was washed at 95% B for 10 minutes. Eluting peptides were online injected into the mass spectrometer by electrospray ionization using a nanoFlex ion source operated at 2.5 kV. The MS was operated in data-independent acquisition (DIA) mode with staggered DIA windows. In brief, full spectra were acquired at a resolution of 120,000, an injection time of 55 ms and an AGC target of 300%. Ions were collected within a range of 380 – 1,020 m/z. For MS/MS fragment spectra, ions were isolated from 24 equal-sized windows of 24 m/z within a range of 400 – 1,000 m/z. The acquisition was performed at a resolution of 15,000, an injection time of 22 ms and an AGC target of 1,000%. Fragmentation was achieved by higher-energy collisional dissociation (HCD) at 31% relative collision energy. For every second cycle, the isolation windows for MS/MS acquisition were shifted by 12 m/z.PrideNot availableMS raw data processing was performed in Spectronaut (version 19.1.240724.62635) using the implemented directDIA search strategy. For spectral library generation, the SWISS-PROT Homo sapiens database was used (downloaded 2024-08-01). The default settings for peptide identification and quantification were used. Protein group intensities were LFQ (label-free quantification) normalised with directLFQ (Ammar et al. 2023). The statistical analysis was performed with Perseus (v. 1.6.15, Tyanova et al. 2016). Protein LFQ intensities were log2 transformed and filtered for data completeness in at least one condition. Missing protein intensities were replaced sample-wise by random selection of values from 1.8 standard deviations downshifted, 0.3 standard deviations broad normal distribution. 1D annotation enrichment tests (Benjamini-Hochberg FDR = 0.02, Cox and Mann 2012) were performed for identification of enriched RFX7 target gene sets (selection based on Coronel et al. 2021; Schwab et al. 2023). Statistical differences from multiple comparisons in Figure 6E were identified, as previously described in the statistical methods section, using a generalized mixed model (PROC GLIMMIX, SAS 9.4, SAS Institute Inc., Cary, NC, USA) based on log₂-transformed LFQ intensities. Statistical significance for Figure 6B was determined using a Wilcoxon matched-pairs signed rank test (GraphPad Prism 9; GraphPad Software, San Diego,California, USA).ProteomicsWalter BeckerInstitute of Pharmacology and Toxicology, RWTH Aachen University, 52074 Aachen, Germany;PARTIALHomo Sapiens (human)kallabis@uni-bonn.de10.1038/S41419-026-08660-XCore Facility Translational Proteomics Medical Faculty University Bonn Venusberg - Campus 1 53127 Bonn GermanyGermanyfalseThe protein kinase DYRK1B is a p53 target gene and functions as a negative feedback regulator of the transcription factor RFX7 - ProteomeThe tumor suppressor protein p53 orchestrates cellular responses to stress by regulating the transcription of target genes involved in processes such as cell cycle control, DNA damage repair and apoptosis. The protein kinase DYRK1B, known to promote cancer cell survival and contribute to DNA damage repair, is overexpressed in various tumor types. Here, we demonstrate that expression of DYRK1B - but not its closely related paralog DYRK1A - is upregulated by cytostatic drugs (Actinomycin D, Doxorubicin) in multiple cancer cell lines. This induction required functional p53 and was mediated by p53-dependent activation of the transcription factor RFX7. Furthermore, we show that DYRK1B physically interacts with RFX7 and counteracts its activation by p53, thereby establishing a negative feedback loop that attenuates RFX7- dependent gene expression. This inhibitory effect of DYRK1B was strictly dependent on its catalytic activity and could be blocked by using small-molecule DYRK1 inhibitors. In conclusion, our study identifies DYRK1B as an indirect p53 target that suppresses p53- mediated activation of RFX7. These findings suggest that pharmacological inhibition of DYRK1B may represent a therapeutic strategy to enhance RFX7 tumor suppressor 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