title: Label-Free Protein-RNA Interactome Analysis Identifies Khsrp Signaling Downstream of the p38/Mk2 Kinase Complex as a Critical Modulator of Cell Cycle Progression.
abstract: Growing evidence suggests a key role for RNA binding proteins (RBPs) in genome stability programs. Additionally, recent developments in RNA sequencing technologies, as well as mass-spectrometry techniques, have greatly expanded our knowledge on protein-RNA interactions. We here use full transcriptome sequencing and label-free LC/MS/MS to identify global changes in protein-RNA interactions in response to etoposide-induced genotoxic stress. We show that RBPs have distinct binding patterns in response to genotoxic stress and that inactivation of the RBP regulator module, p38/MK2, can affect the entire spectrum of protein-RNA interactions that take place in response to stress. In addition to validating the role of known RBPs like Srsf1, Srsf2, Elavl1 in the genotoxic stress response, we add a new collection of RBPs to the DNA damage response. We identify Khsrp as a highly regulated RBP in response to genotoxic stress and further validate its role as a driver of the G(1/)S transition through the suppression of Cdkn1a(P21) transcripts. Finally, we identify KHSRP as an indicator of overall survival, as well as disease free survival in glioblastoma multiforme.
authors.affiliation: Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany.
authors.forename: Jorge
authors.initials: J
authors.lastname: Boucas
authors.affiliation: Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Fritz
authors.affiliation: Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany.
authors.forename: Anna
authors.initials: A
authors.lastname: Schmitt
authors.affiliation: Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany.
authors.forename: Arina
authors.initials: A
authors.lastname: Riabinska
authors.affiliation: Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany.
authors.forename: Lisa
authors.initials: L
authors.lastname: Thelen
authors.affiliation: Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Department of Translational Genomics, University of Cologne, Cologne, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Peifer
authors.affiliation: Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany.
authors.forename: Uschi
authors.initials: U
authors.lastname: Leeser
authors.affiliation: Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Nuernberg
authors.affiliation: Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany.
authors.forename: Janine
authors.initials: J
authors.lastname: Altmueller
authors.affiliation: Institute of Biochemistry, Hannover Medical School, Hannover, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Gaestel
authors.affiliation: Computational RNA Biology and Ageing, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann Straße 9b, 50913, Cologne, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Dieterich
authors.affiliation: Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany.
authors.forename: H Christian
authors.initials: HC
authors.lastname: Reinhardt
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D050759:Cyclin-Dependent Kinase Inhibitor p21 / Q000235:genetics; D004249:DNA Damage / Q000235:genetics; D018572:Disease-Free Survival; D000067780:ELAV-Like Protein 1 / Q000235:genetics; D059585:G1 Phase Cell Cycle Checkpoints / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D005909:Glioblastoma / Q000235:genetics; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics*; D051379:Mice; D009687:Nuclear Proteins / Q000235:genetics; D017346:Protein Serine-Threonine Kinases / Q000235:genetics*; D012313:RNA / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000235:genetics*; D012261:Ribonucleoproteins / Q000235:genetics; D000068103:Serine-Arginine Splicing Factors; D015398:Signal Transduction / Q000235:genetics; D015534:Trans-Activators / Q000235:genetics*; D048051:p38 Mitogen-Activated Protein Kinases / Q000235:genetics*; D000099190:MAP-Kinase-Activated Kinase 2
chemical_list: D050759:Cyclin-Dependent Kinase Inhibitor p21; D000067780:ELAV-Like Protein 1; D047908:Intracellular Signaling Peptides and Proteins; D009687:Nuclear Proteins; D017346:Protein Serine-Threonine Kinases; D012313:RNA; D016601:RNA-Binding Proteins; D012261:Ribonucleoproteins; D000068103:Serine-Arginine Splicing Factors; D015534:Trans-Activators; D048051:p38 Mitogen-Activated Protein Kinases; D000099190:MAP-Kinase-Activated Kinase 2; C000593997:Elavl1 protein, mouse; C105789:KHSRP protein, human; C499372:SRSF2 protein, mouse