1
|
Carnie CJ, Götz MJ, Palma-Chaundler CS, Weickert P, Wanders A, Serrano-Benitez A, Li HY, Gupta V, Awwad SW, Blum CJ, Sczaniecka-Clift M, Cordes J, Zagnoli-Vieira G, D'Alessandro G, Richards SL, Gueorguieva N, Lam S, Beli P, Stingele J, Jackson SP. Decitabine cytotoxicity is promoted by dCMP deaminase DCTD and mitigated by SUMO-dependent E3 ligase TOPORS. EMBO J 2024:10.1038/s44318-024-00108-2. [PMID: 38760575 DOI: 10.1038/s44318-024-00108-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 03/15/2024] [Accepted: 04/16/2024] [Indexed: 05/19/2024] Open
Abstract
The nucleoside analogue decitabine (or 5-aza-dC) is used to treat several haematological cancers. Upon its triphosphorylation and incorporation into DNA, 5-aza-dC induces covalent DNA methyltransferase 1 DNA-protein crosslinks (DNMT1-DPCs), leading to DNA hypomethylation. However, 5-aza-dC's clinical outcomes vary, and relapse is common. Using genome-scale CRISPR/Cas9 screens, we map factors determining 5-aza-dC sensitivity. Unexpectedly, we find that loss of the dCMP deaminase DCTD causes 5-aza-dC resistance, suggesting that 5-aza-dUMP generation is cytotoxic. Combining results from a subsequent genetic screen in DCTD-deficient cells with the identification of the DNMT1-DPC-proximal proteome, we uncover the ubiquitin and SUMO1 E3 ligase, TOPORS, as a new DPC repair factor. TOPORS is recruited to SUMOylated DNMT1-DPCs and promotes their degradation. Our study suggests that 5-aza-dC-induced DPCs cause cytotoxicity when DPC repair is compromised, while cytotoxicity in wild-type cells arises from perturbed nucleotide metabolism, potentially laying the foundations for future identification of predictive biomarkers for decitabine treatment.
Collapse
Affiliation(s)
- Christopher J Carnie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Maximilian J Götz
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Pedro Weickert
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Amy Wanders
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Almudena Serrano-Benitez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Hao-Yi Li
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Samah W Awwad
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | | | - Jacqueline Cordes
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Guido Zagnoli-Vieira
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Giuseppina D'Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sean L Richards
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Nadia Gueorguieva
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Stephen P Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| |
Collapse
|
2
|
Longo GMC, Sayols S, Kotini AG, Heinen S, Möckel MM, Beli P, Roukos V. Linking CRISPR-Cas9 double-strand break profiles to gene editing precision with BreakTag. Nat Biotechnol 2024:10.1038/s41587-024-02238-8. [PMID: 38740992 DOI: 10.1038/s41587-024-02238-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Cas9 can cleave DNA in both blunt and staggered configurations, resulting in distinct editing outcomes, but what dictates the type of Cas9 incisions is largely unknown. In this study, we developed BreakTag, a versatile method for profiling Cas9-induced DNA double-strand breaks (DSBs) and identifying the determinants of Cas9 incisions. Overall, we assessed cleavage by SpCas9 at more than 150,000 endogenous on-target and off-target sites targeted by approximately 3,500 single guide RNAs. We found that approximately 35% of SpCas9 DSBs are staggered, and the type of incision is influenced by DNA:gRNA complementarity and the use of engineered Cas9 variants. A machine learning model shows that Cas9 incision is dependent on the protospacer sequence and that human genetic variation impacts the configuration of Cas9 cuts and the DSB repair outcome. Matched datasets of Cas9 and engineered variant incisions with repair outcomes show that Cas9-mediated staggered breaks are linked with precise, templated and predictable single-nucleotide insertions, demonstrating that a scission-based gRNA design can be used to correct clinically relevant pathogenic single-nucleotide deletions.
Collapse
Affiliation(s)
| | - Sergi Sayols
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Andriana G Kotini
- Department of Biology, Medical School, University of Patras, Patras, Greece
| | - Sabine Heinen
- Institute of Molecular Biology (IMB), Mainz, Germany
| | | | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
- Johannes Gutenberg University (JGU), Mainz, Germany
| | - Vassilis Roukos
- Institute of Molecular Biology (IMB), Mainz, Germany.
- Department of Biology, Medical School, University of Patras, Patras, Greece.
| |
Collapse
|
3
|
Papadopoulos D, Ha SA, Fleischhauer D, Uhl L, Russell TJ, Mikicic I, Schneider K, Brem A, Valanju OR, Cossa G, Gallant P, Schuelein-Voelk C, Maric HM, Beli P, Büchel G, Vos SM, Eilers M. The MYCN oncoprotein is an RNA-binding accessory factor of the nuclear exosome targeting complex. Mol Cell 2024:S1097-2765(24)00285-5. [PMID: 38703770 DOI: 10.1016/j.molcel.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 02/28/2024] [Accepted: 04/10/2024] [Indexed: 05/06/2024]
Abstract
The MYCN oncoprotein binds active promoters in a heterodimer with its partner protein MAX. MYCN also interacts with the nuclear exosome, a 3'-5' exoribonuclease complex, suggesting a function in RNA metabolism. Here, we show that MYCN forms stable high-molecular-weight complexes with the exosome and multiple RNA-binding proteins. MYCN binds RNA in vitro and in cells via a conserved sequence termed MYCBoxI. In cells, MYCN associates with thousands of intronic transcripts together with the ZCCHC8 subunit of the nuclear exosome targeting complex and enhances their processing. Perturbing exosome function results in global re-localization of MYCN from promoters to intronic RNAs. On chromatin, MYCN is then replaced by the MNT(MXD6) repressor protein, inhibiting MYCN-dependent transcription. RNA-binding-deficient alleles show that RNA-binding limits MYCN's ability to activate cell growth-related genes but is required for MYCN's ability to promote progression through S phase and enhance the stress resilience of neuroblastoma cells.
Collapse
Affiliation(s)
- Dimitrios Papadopoulos
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 6, 97080 Würzburg, Germany
| | - Stefanie Anh Ha
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Daniel Fleischhauer
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Leonie Uhl
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Timothy J Russell
- Massachusetts Institute of Technology, Department of Biology, 31 Ames Street, Cambridge, MA 02142, USA
| | - Ivan Mikicic
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, Ackermannweg 4, 55128 Mainz, Germany; Institute of Molecular Biology (IMB), Johannes Gutenberg University, Ackermannweg 4, 55128 Mainz, Germany
| | - Katharina Schneider
- Massachusetts Institute of Technology, Department of Biology, 31 Ames Street, Cambridge, MA 02142, USA
| | - Annika Brem
- Massachusetts Institute of Technology, Department of Biology, 31 Ames Street, Cambridge, MA 02142, USA
| | - Omkar Rajendra Valanju
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, Building D15, 97080 Würzburg, Germany
| | - Giacomo Cossa
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Peter Gallant
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Christina Schuelein-Voelk
- Theodor Boveri Institute, Core Unit High-Content Microscopy, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Hans Michael Maric
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, Building D15, 97080 Würzburg, Germany
| | - Petra Beli
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, Ackermannweg 4, 55128 Mainz, Germany; Institute of Molecular Biology (IMB), Johannes Gutenberg University, Ackermannweg 4, 55128 Mainz, Germany
| | - Gabriele Büchel
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 6, 97080 Würzburg, Germany
| | - Seychelle M Vos
- Massachusetts Institute of Technology, Department of Biology, 31 Ames Street, Cambridge, MA 02142, USA.
| | - Martin Eilers
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
| |
Collapse
|
4
|
Kowald L, Roedig J, Karlowitz R, Wagner K, Smith S, Juretschke T, Beli P, Müller S, van Wijk SJL. USP22 regulates APL differentiation via PML-RARα stabilization and IFN repression. Cell Death Discov 2024; 10:128. [PMID: 38467608 PMCID: PMC10928094 DOI: 10.1038/s41420-024-01894-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
Ubiquitin-specific peptidase 22 (USP22) is a deubiquitinating enzyme (DUB) that underlies tumorigenicity, proliferation, cell death and differentiation through deubiquitination of histone and non-histone targets. Ubiquitination determines stability, localization and functions of cell fate proteins and controls cell-protective signaling pathways to surveil cell cycle progression. In a variety of carcinomas, lymphomas and leukemias, ubiquitination regulates the tumor-suppressive functions of the promyelocytic leukemia protein (PML), but PML-specific DUBs, DUB-controlled PML ubiquitin sites and the functional consequences of PML (de)ubiquitination remain unclear. Here, we identify USP22 as regulator of PML and the oncogenic acute promyelocytic leukemia (APL) fusion PML-RARα protein stability and identify a destabilizing role of PML residue K394. Additionally, loss of USP22 upregulates interferon (IFN) and IFN-stimulated gene (ISG) expression in APL and induces PML-RARα stabilization and a potentiation of the cell-autonomous sensitivity towards all-trans retinoic acid (ATRA)-mediated differentiation. Our findings imply USP22-dependent surveillance of PML-RARα stability and IFN signaling as important regulator of APL pathogenesis, with implications for viral mimicry, differentiation and cell fate regulation in other leukemia subtypes.
Collapse
Affiliation(s)
- Lisa Kowald
- Institute for Experimental Pediatric Hematology and Oncology, Medical Faculty, Goethe-University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Jens Roedig
- Institute for Experimental Pediatric Hematology and Oncology, Medical Faculty, Goethe-University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Rebekka Karlowitz
- Institute for Experimental Pediatric Hematology and Oncology, Medical Faculty, Goethe-University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Kristina Wagner
- Institute of Biochemistry II (IBCII), Medical Faculty, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Sonja Smith
- Institute for Experimental Pediatric Hematology and Oncology, Medical Faculty, Goethe-University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Thomas Juretschke
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Stefan Müller
- Institute of Biochemistry II (IBCII), Medical Faculty, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Sjoerd J L van Wijk
- Institute for Experimental Pediatric Hematology and Oncology, Medical Faculty, Goethe-University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, Frankfurt am Main, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- University Cancer Centre Frankfurt (UCT), University Hospital Frankfurt, Goethe-University Frankfurt, Frankfurt, Germany.
| |
Collapse
|
5
|
Chervova A, Molliex A, Baymaz HI, Coux RX, Papadopoulou T, Mueller F, Hercul E, Fournier D, Dubois A, Gaiani N, Beli P, Festuccia N, Navarro P. Mitotic bookmarking redundancy by nuclear receptors in pluripotent cells. Nat Struct Mol Biol 2024; 31:513-522. [PMID: 38196033 PMCID: PMC10948359 DOI: 10.1038/s41594-023-01195-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 11/30/2023] [Indexed: 01/11/2024]
Abstract
Mitotic bookmarking transcription factors (TFs) are thought to mediate rapid and accurate reactivation after mitotic gene silencing. However, the loss of individual bookmarking TFs often leads to the deregulation of only a small proportion of their mitotic targets, raising doubts on the biological significance and importance of their bookmarking function. Here we used targeted proteomics of the mitotic bookmarking TF ESRRB, an orphan nuclear receptor, to discover a large redundancy in mitotic binding among members of the protein super-family of nuclear receptors. Focusing on the nuclear receptor NR5A2, which together with ESRRB is essential in maintaining pluripotency in mouse embryonic stem cells, we demonstrate conjoint bookmarking activity of both factors on promoters and enhancers of a large fraction of active genes, particularly those most efficiently reactivated in G1. Upon fast and simultaneous degradation of both factors during mitotic exit, hundreds of mitotic targets of ESRRB/NR5A2, including key players of the pluripotency network, display attenuated transcriptional reactivation. We propose that redundancy in mitotic bookmarking TFs, especially nuclear receptors, confers robustness to the reestablishment of gene regulatory networks after mitosis.
Collapse
Affiliation(s)
- Almira Chervova
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Amandine Molliex
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | | | - Rémi-Xavier Coux
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Thaleia Papadopoulou
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Florian Mueller
- Department of Computational Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3691, Imaging and Modeling Unit, Paris, France
| | - Eslande Hercul
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - David Fournier
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Agnès Dubois
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Nicolas Gaiani
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Petra Beli
- Institute of Molecular Biology, Mainz, Germany
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg-Universität, Mainz, Germany
| | - Nicola Festuccia
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France.
- Equipe Labéllisée Ligue Contre le cancer, Paris, France.
| | - Pablo Navarro
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France.
- Equipe Labéllisée Ligue Contre le cancer, Paris, France.
| |
Collapse
|
6
|
D’Alessandro G, Morales-Juarez DA, Richards SL, Nitiss KC, Serrano-Benitez A, Wang J, Thomas JC, Gupta V, Voigt A, Belotserkovskaya R, Goh CG, Bowden AR, Galanty Y, Beli P, Nitiss JL, Zagnoli-Vieira G, Jackson SP. RAD54L2 counters TOP2-DNA adducts to promote genome stability. Sci Adv 2023; 9:eadl2108. [PMID: 38055822 PMCID: PMC10699776 DOI: 10.1126/sciadv.adl2108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
The catalytic cycle of topoisomerase 2 (TOP2) enzymes proceeds via a transient DNA double-strand break (DSB) intermediate termed the TOP2 cleavage complex (TOP2cc), in which the TOP2 protein is covalently bound to DNA. Anticancer agents such as etoposide operate by stabilizing TOP2ccs, ultimately generating genotoxic TOP2-DNA protein cross-links that require processing and repair. Here, we identify RAD54 like 2 (RAD54L2) as a factor promoting TOP2cc resolution. We demonstrate that RAD54L2 acts through a novel mechanism together with zinc finger protein associated with tyrosyl-DNA phosphodiesterase 2 (TDP2) and TOP2 (ZATT/ZNF451) and independent of TDP2. Our work suggests a model wherein RAD54L2 recognizes sumoylated TOP2 and, using its ATPase activity, promotes TOP2cc resolution and prevents DSB exposure. These findings suggest RAD54L2-mediated TOP2cc resolution as a potential mechanism for cancer therapy resistance and highlight RAD54L2 as an attractive candidate for drug discovery.
Collapse
Affiliation(s)
- Giuseppina D’Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Sean L. Richards
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Almudena Serrano-Benitez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Juanjuan Wang
- Institute of Molecular Biology (IMB), Chromatin Biology & Proteomics, Mainz, Germany
| | - John C. Thomas
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Andrea Voigt
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Rimma Belotserkovskaya
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chen Gang Goh
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Anne Ramsay Bowden
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Yaron Galanty
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), Chromatin Biology & Proteomics, Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | | | - Guido Zagnoli-Vieira
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Stephen P. Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| |
Collapse
|
7
|
Suryo Rahmanto A, Blum CJ, Scalera C, Heidelberger JB, Mesitov M, Horn-Ghetko D, Gräf JF, Mikicic I, Hobrecht R, Orekhova A, Ostermaier M, Ebersberger S, Möckel MM, Krapoth N, Da Silva Fernandes N, Mizi A, Zhu Y, Chen JX, Choudhary C, Papantonis A, Ulrich HD, Schulman BA, König J, Beli P. K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution. Mol Cell 2023; 83:4272-4289.e10. [PMID: 37951215 DOI: 10.1016/j.molcel.2023.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/17/2023] [Accepted: 10/13/2023] [Indexed: 11/13/2023]
Abstract
Reactive aldehydes are produced by normal cellular metabolism or after alcohol consumption, and they accumulate in human tissues if aldehyde clearance mechanisms are impaired. Their toxicity has been attributed to the damage they cause to genomic DNA and the subsequent inhibition of transcription and replication. However, whether interference with other cellular processes contributes to aldehyde toxicity has not been investigated. We demonstrate that formaldehyde induces RNA-protein crosslinks (RPCs) that stall the ribosome and inhibit translation in human cells. RPCs in the messenger RNA (mRNA) are recognized by the translating ribosomes, marked by atypical K6-linked ubiquitylation catalyzed by the RING-in-between-RING (RBR) E3 ligase RNF14, and subsequently resolved by the ubiquitin- and ATP-dependent unfoldase VCP. Our findings uncover an evolutionary conserved formaldehyde-induced stress response pathway that protects cells against RPC accumulation in the cytoplasm, and they suggest that RPCs contribute to the cellular and tissue toxicity of reactive aldehydes.
Collapse
Affiliation(s)
- Aldwin Suryo Rahmanto
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | | | | | | | | | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Justus F Gräf
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Ivan Mikicic
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Anna Orekhova
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | | | | | - Nils Krapoth
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Yajie Zhu
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jia-Xuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany.
| |
Collapse
|
8
|
Stier A, Gilberto S, Mohamed WI, Royall LN, Helenius J, Mikicic I, Sajic T, Beli P, Müller DJ, Jessberger S, Peter M. The CUL4B-based E3 ubiquitin ligase regulates mitosis and brain development by recruiting phospho-specific DCAFs. EMBO J 2023; 42:e112847. [PMID: 37365982 PMCID: PMC10476281 DOI: 10.15252/embj.2022112847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 05/31/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023] Open
Abstract
The paralogs CUL4A and CUL4B assemble cullin-RING E3 ubiquitin ligase (CRL) complexes regulating multiple chromatin-associated cellular functions. Although they are structurally similar, we found that the unique N-terminal extension of CUL4B is heavily phosphorylated during mitosis, and the phosphorylation pattern is perturbed in the CUL4B-P50L mutation causing X-linked intellectual disability (XLID). Phenotypic characterization and mutational analysis revealed that CUL4B phosphorylation is required for efficient progression through mitosis, controlling spindle positioning and cortical tension. While CUL4B phosphorylation triggers chromatin exclusion, it promotes binding to actin regulators and to two previously unrecognized CUL4B-specific substrate receptors (DCAFs), LIS1 and WDR1. Indeed, co-immunoprecipitation experiments and biochemical analysis revealed that LIS1 and WDR1 interact with DDB1, and their binding is enhanced by the phosphorylated N-terminal domain of CUL4B. Finally, a human forebrain organoid model demonstrated that CUL4B is required to develop stable ventricular structures that correlate with onset of forebrain differentiation. Together, our study uncovers previously unrecognized DCAFs relevant for mitosis and brain development that specifically bind CUL4B, but not the CUL4B-P50L patient mutant, by a phosphorylation-dependent mechanism.
Collapse
Affiliation(s)
- Anna Stier
- Institute of BiochemistryETH ZurichZurichSwitzerland
| | - Samuel Gilberto
- Institute of BiochemistryETH ZurichZurichSwitzerland
- Present address:
Monte Rosa TherapeuticsBaselSwitzerland
| | | | - Lars N Royall
- Brain Research InstituteUniversity of ZurichZurichSwitzerland
| | - Jonne Helenius
- Department of Biosystems Science and EngineeringETH ZurichBaselSwitzerland
| | | | - Tatjana Sajic
- Institute of Molecular Systems BiologyETH ZürichZürichSwitzerland
- Present address:
Faculty Unit of Toxicology, CURML, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Petra Beli
- Institute of Molecular BiologyMainzGermany
- Institute of Developmental Biology and Neurobiology (IDN)Johannes Gutenberg UniversityMainzGermany
| | - Daniel J Müller
- Department of Biosystems Science and EngineeringETH ZurichBaselSwitzerland
| | | | | |
Collapse
|
9
|
Shi J, Hauschulte K, Mikicic I, Maharjan S, Arz V, Strauch T, Heidelberger JB, Schaefer JV, Dreier B, Plückthun A, Beli P, Ulrich HD, Wollscheid HP. Nuclear myosin VI maintains replication fork stability. Nat Commun 2023; 14:3787. [PMID: 37355687 PMCID: PMC10290672 DOI: 10.1038/s41467-023-39517-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 06/09/2023] [Indexed: 06/26/2023] Open
Abstract
The actin cytoskeleton is of fundamental importance for cellular structure and plasticity. However, abundance and function of filamentous actin in the nucleus are still controversial. Here we show that the actin-based molecular motor myosin VI contributes to the stabilization of stalled or reversed replication forks. In response to DNA replication stress, myosin VI associates with stalled replication intermediates and cooperates with the AAA ATPase Werner helicase interacting protein 1 (WRNIP1) in protecting these structures from DNA2-mediated nucleolytic attack. Using functionalized affinity probes to manipulate myosin VI levels in a compartment-specific manner, we provide evidence for the direct involvement of myosin VI in the nucleus and against a contribution of the abundant cytoplasmic pool during the replication stress response.
Collapse
Affiliation(s)
- Jie Shi
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Kristine Hauschulte
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Ivan Mikicic
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Srijana Maharjan
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Mainz Biomed N.V., Robert-Koch-Str. 50, D - 55129, Mainz, Germany
| | - Valerie Arz
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Tina Strauch
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Jan B Heidelberger
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Max Planck School Matter to Life, Jahnstr. 29, D - 69120, Heidelberg, Germany
| | - Jonas V Schaefer
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Birgit Dreier
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Andreas Plückthun
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Petra Beli
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 15, D - 55128, Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany.
| | - Hans-Peter Wollscheid
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany.
| |
Collapse
|
10
|
Schindler N, Tonn M, Kellner V, Fung JJ, Lockhart A, Vydzhak O, Juretschke T, Möckel S, Beli P, Khmelinskii A, Luke B. Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase. Nat Commun 2023; 14:1227. [PMID: 36869098 PMCID: PMC9984532 DOI: 10.1038/s41467-023-36866-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
Single ribonucleoside monophosphates (rNMPs) are transiently present in eukaryotic genomes. The RNase H2-dependent ribonucleotide excision repair (RER) pathway ensures error-free rNMP removal. In some pathological conditions, rNMP removal is impaired. If these rNMPs hydrolyze during, or prior to, S phase, toxic single-ended double-strand breaks (seDSBs) can occur upon an encounter with replication forks. How such rNMP-derived seDSB lesions are repaired is unclear. We expressed a cell cycle phase restricted allele of RNase H2 to nick at rNMPs in S phase and study their repair. Although Top1 is dispensable, the RAD52 epistasis group and Rtt101Mms1-Mms22 dependent ubiquitylation of histone H3 become essential for rNMP-derived lesion tolerance. Consistently, loss of Rtt101Mms1-Mms22 combined with RNase H2 dysfunction leads to compromised cellular fitness. We refer to this repair pathway as nick lesion repair (NLR). The NLR genetic network may have important implications in the context of human pathologies.
Collapse
Affiliation(s)
- Natalie Schindler
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany.
| | - Matthias Tonn
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Vanessa Kellner
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.,Department of Biology, New York University, New York, NY, USA
| | - Jia Jun Fung
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Arianna Lockhart
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Olga Vydzhak
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Thomas Juretschke
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Stefanie Möckel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anton Khmelinskii
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Brian Luke
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany. .,Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| |
Collapse
|
11
|
Lampersberger L, Conte F, Ghosh S, Xiao Y, Price J, Jordan D, Matus DQ, Sarkies P, Beli P, Miska EA, Burton NO. Loss of the E3 ubiquitin ligases UBR-5 or HECD-1 restores Caenorhabditis elegans development in the absence of SWI/SNF function. Proc Natl Acad Sci U S A 2023; 120:e2217992120. [PMID: 36689659 PMCID: PMC9945973 DOI: 10.1073/pnas.2217992120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/15/2022] [Indexed: 01/25/2023] Open
Abstract
SWItch/sucrose non-fermenting (SWI/SNF) complexes are a family of chromatin remodelers that are conserved across eukaryotes. Mutations in subunits of SWI/SNF cause a multitude of different developmental disorders in humans, most of which have no current treatment options. Here, we identify an alanine-to-valine-causing mutation in the SWI/SNF subunit snfc-5 (SMARCB1 in humans) that prevents embryonic lethality in Caenorhabditis elegans nematodes harboring a loss-of-function mutation in the SWI/SNF subunit swsn-1 (SMARCC1/2 in humans). Furthermore, we found that the combination of this specific mutation in snfc-5 and a loss-of-function mutation in either of the E3 ubiquitin ligases ubr-5 (UBR5 in humans) or hecd-1 (HECTD1 in humans) can restore development to adulthood in swsn-1 loss-of-function mutants that otherwise die as embryos. Using these mutant models, we established a set of 335 genes that are dysregulated in SWI/SNF mutants that arrest their development embryonically but exhibit near wild-type levels of expression in the presence of suppressor mutations that prevent embryonic lethality, suggesting that SWI/SNF promotes development by regulating some subset of these 335 genes. In addition, we show that SWI/SNF protein levels are reduced in swsn-1; snfc-5 double mutants and partly restored to wild-type levels in swsn-1; snfc-5; ubr-5 triple mutants, consistent with a model in which UBR-5 regulates SWI/SNF levels by tagging the complex for proteasomal degradation. Our findings establish a link between two E3 ubiquitin ligases and SWI/SNF function and suggest that UBR5 and HECTD1 could be potential therapeutic targets for the many developmental disorders caused by missense mutations in SWI/SNF subunits.
Collapse
Affiliation(s)
- Lisa Lampersberger
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, CambridgeCB2 1QN, UK
- Department of Genetics, University of Cambridge, CambridgeCB2 3EH, UK
| | | | - Subhanita Ghosh
- Medical Research Council London Institute of Medical Sciences, LondonW12 0NN, UK
| | - Yutong Xiao
- Department of Biochemistry and Cell Biology, Stony Brook University, NY11790
| | - Jonathan Price
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, CambridgeCB2 1QN, UK
- Department of Genetics, University of Cambridge, CambridgeCB2 3EH, UK
| | - David Jordan
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, CambridgeCB2 1QN, UK
- Department of Genetics, University of Cambridge, CambridgeCB2 3EH, UK
| | - David Q. Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, NY11790
| | - Peter Sarkies
- Medical Research Council London Institute of Medical Sciences, LondonW12 0NN, UK
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, UK
| | - Petra Beli
- Institute of Molecular Biology, Mainz55128, Germany
| | - Eric A. Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, CambridgeCB2 1QN, UK
- Department of Genetics, University of Cambridge, CambridgeCB2 3EH, UK
- Department of Biochemistry, University of Cambridge, CambridgeCB2 1QW, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, CambridgeCB10 1SA, UK
| | - Nicholas O. Burton
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI49503
| |
Collapse
|
12
|
Oliveira CAB, Isaakova E, Beli P, Xirodimas DP. A Mass Spectrometry-Based Strategy for Mapping Modification Sites for the Ubiquitin-Like Modifier NEDD8. Methods Mol Biol 2023; 2602:137-149. [PMID: 36446972 DOI: 10.1007/978-1-0716-2859-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The identification of modification sites for ubiquitin and ubiquitin-like modifiers is an essential step in the elucidation of controlled processes. The ubiquitin-like modifier NEDD8 is an important regulator of plethora of biological processes both under homeostatic and proteotoxic stress conditions. Here, we describe a detailed protocol for proteome-wide identification of NEDDylation sites. The approach is based on the use of cell lines stably expressing the NEDD8R74K mutant. Digestion of samples with Lysyl endopeptidase generates peptides with a di-glycine remnant only from proteins modified with NEDD8R74K but not with ubiquitin or ISG15. The isolation of these peptides with anti-di-glycine antibodies (K-ε-GG) allows the identification of NEDDylation sites by liquid chromatography tandem mass spectrometry (LC-MS/MS).
Collapse
Affiliation(s)
| | | | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany.
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany.
| | | |
Collapse
|
13
|
Mosler T, Baymaz HI, Gräf JF, Mikicic I, Blattner G, Bartlett E, Ostermaier M, Piccinno R, Yang J, Voigt A, Gatti M, Pellegrino S, Altmeyer M, Luck K, Ahel I, Roukos V, Beli P. PARP1 proximity proteomics reveals interaction partners at stressed replication forks. Nucleic Acids Res 2022; 50:11600-11618. [PMID: 36350633 PMCID: PMC9723622 DOI: 10.1093/nar/gkac948] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022] Open
Abstract
PARP1 mediates poly-ADP-ribosylation of proteins on chromatin in response to different types of DNA lesions. PARP inhibitors are used for the treatment of BRCA1/2-deficient breast, ovarian, and prostate cancer. Loss of DNA replication fork protection is proposed as one mechanism that contributes to the vulnerability of BRCA1/2-deficient cells to PARP inhibitors. However, the mechanisms that regulate PARP1 activity at stressed replication forks remain poorly understood. Here, we performed proximity proteomics of PARP1 and isolation of proteins on stressed replication forks to map putative PARP1 regulators. We identified TPX2 as a direct PARP1-binding protein that regulates the auto-ADP-ribosylation activity of PARP1. TPX2 interacts with DNA damage response proteins and promotes homology-directed repair of DNA double-strand breaks. Moreover, TPX2 mRNA levels are increased in BRCA1/2-mutated breast and prostate cancers, and high TPX2 expression levels correlate with the sensitivity of cancer cells to PARP-trapping inhibitors. We propose that TPX2 confers a mitosis-independent function in the cellular response to replication stress by interacting with PARP1.
Collapse
Affiliation(s)
| | - H Irem Baymaz
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Justus F Gräf
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Ivan Mikicic
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | | | - Edward Bartlett
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | | | | | - Jiwen Yang
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Marco Gatti
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich CH-8057, Switzerland
| | - Stefania Pellegrino
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich CH-8057, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich CH-8057, Switzerland
| | - Katja Luck
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | | | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| |
Collapse
|
14
|
Winkler R, Mägdefrau AS, Piskor EM, Kleemann M, Beyer M, Linke K, Hansen L, Schaffer AM, Hoffmann ME, Poepsel S, Heyd F, Beli P, Möröy T, Mahboobi S, Krämer OH, Kosan C. Targeting the MYC interaction network in B-cell lymphoma via histone deacetylase 6 inhibition. Oncogene 2022; 41:4560-4572. [PMID: 36068335 PMCID: PMC9525236 DOI: 10.1038/s41388-022-02450-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 08/22/2022] [Indexed: 11/09/2022]
Abstract
Overexpression of MYC is a genuine cancer driver in lymphomas and related to poor prognosis. However, therapeutic targeting of the transcription factor MYC remains challenging. Here, we show that inhibition of the histone deacetylase 6 (HDAC6) using the HDAC6 inhibitor Marbostat-100 (M-100) reduces oncogenic MYC levels and prevents lymphomagenesis in a mouse model of MYC-induced aggressive B-cell lymphoma. M-100 specifically alters protein-protein interactions by switching the acetylation state of HDAC6 substrates, such as tubulin. Tubulin facilitates nuclear import of MYC, and MYC-dependent B-cell lymphoma cells rely on continuous import of MYC due to its high turn-over. Acetylation of tubulin impairs this mechanism and enables proteasomal degradation of MYC. M-100 targets almost exclusively B-cell lymphoma cells with high levels of MYC whereas non-tumor cells are not affected. M-100 induces massive apoptosis in human and murine MYC-overexpressing B-cell lymphoma cells. We identified the heat-shock protein DNAJA3 as an interactor of tubulin in an acetylation-dependent manner and overexpression of DNAJA3 resulted in a pronounced degradation of MYC. We propose a mechanism by which DNAJA3 associates with hyperacetylated tubulin in the cytoplasm to control MYC turnover. Taken together, our data demonstrate a beneficial role of HDAC6 inhibition in MYC-dependent B-cell lymphoma.
Collapse
Affiliation(s)
- René Winkler
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany.,Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias i Pujol, Badalona, 08916, Spain
| | - Ann-Sophie Mägdefrau
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany
| | - Eva-Maria Piskor
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany
| | - Markus Kleemann
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany
| | - Mandy Beyer
- Institute of Toxicology, University Medical Center Mainz, Mainz, 55131, Germany
| | - Kevin Linke
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany
| | - Lisa Hansen
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany
| | - Anna-Maria Schaffer
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany
| | | | - Simon Poepsel
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, University of Cologne, Cologne, 50931, Germany.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, 50931, Germany
| | - Florian Heyd
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, 14195, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
| | - Tarik Möröy
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, H2W 1R7, Canada
| | - Siavosh Mahboobi
- Department of Pharmaceutical/Medicinal Chemistry I, Institute of Pharmacy, University of Regensburg, Regensburg, 93040, Germany
| | - Oliver H Krämer
- Institute of Toxicology, University Medical Center Mainz, Mainz, 55131, Germany
| | - Christian Kosan
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany.
| |
Collapse
|
15
|
Szczęśniak PP, Heidelberger JB, Serve H, Beli P, Wagner SA. VCP inhibition induces an unfolded protein response and apoptosis in human acute myeloid leukemia cells. PLoS One 2022; 17:e0266478. [PMID: 35385564 PMCID: PMC8986003 DOI: 10.1371/journal.pone.0266478] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 03/21/2022] [Indexed: 11/19/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous malignancy characterized by the accumulation of undifferentiated white blood cells (blasts) in the bone marrow. Valosin-containing protein (VCP) is an abundant molecular chaperone that extracts ubiquitylated substrates from protein complexes and cellular compartments prior to their degradation by the proteasome. We found that treatment of AML cell lines with the VCP inhibitor CB-5083 leads to an accumulation of ubiquitylated proteins, activation of unfolded protein response (UPR) and apoptosis. Using quantitative mass spectrometry-based proteomics we assessed the effects of VCP inhibition on the cellular ubiquitin-modified proteome. We could further show that CB-5083 decreases the survival of the AML cell lines THP-1 and MV4-11 in a concentration-dependent manner, and acts synergistically with the antimetabolite cytarabine and the BH3-mimetic venetoclax. Finally, we showed that prolonged treatment of AML cells with CB-5083 leads to development of resistance mediated by mutations in VCP. Taken together, inhibition of VCP leads to a lethal unfolded protein response in AML cells and might be a relevant therapeutic strategy for treatment of AML, particularly when combined with other drugs. The toxicity and development of resistance possibly limit the utility of VCP inhibitors and have to be further explored in animal models and clinical trials.
Collapse
Affiliation(s)
- Paweł P. Szczęśniak
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | | | - Hubert Serve
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sebastian A. Wagner
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt, Germany
- * E-mail:
| |
Collapse
|
16
|
Wegmann S, Meister C, Renz C, Yakoub G, Wollscheid HP, Takahashi DT, Mikicic I, Beli P, Ulrich HD. Linkage reprogramming by tailor-made E3s reveals polyubiquitin chain requirements in DNA-damage bypass. Mol Cell 2022; 82:1589-1602.e5. [PMID: 35263628 PMCID: PMC9098123 DOI: 10.1016/j.molcel.2022.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 01/05/2022] [Accepted: 02/08/2022] [Indexed: 12/22/2022]
Abstract
A polyubiquitin chain can adopt a variety of shapes, depending on how the ubiquitin monomers are joined. However, the relevance of linkage for the signaling functions of polyubiquitin chains is often poorly understood because of our inability to control or manipulate this parameter in vivo. Here, we present a strategy for reprogramming polyubiquitin chain linkage by means of tailor-made, linkage- and substrate-selective ubiquitin ligases. Using the polyubiquitylation of the budding yeast replication factor PCNA in response to DNA damage as a model case, we show that altering the features of a polyubiquitin chain in vivo can change the fate of the modified substrate. We also provide evidence for redundancy between distinct but structurally similar linkages, and we demonstrate by proof-of-principle experiments that the method can be generalized to targets beyond PCNA. Our study illustrates a promising approach toward the in vivo analysis of polyubiquitin signaling.
Collapse
Affiliation(s)
- Sabrina Wegmann
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Cindy Meister
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Christian Renz
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - George Yakoub
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | | | - Diane T Takahashi
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie de Strasbourg, 10413 Illkirch, Strasbourg, France
| | - Ivan Mikicic
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany; Institute for Developmental Biology and Neurobiology, Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany.
| |
Collapse
|
17
|
Bawankar P, Lence T, Paolantoni C, Haussmann IU, Kazlauskiene M, Jacob D, Heidelberger JB, Richter FM, Nallasivan MP, Morin V, Kreim N, Beli P, Helm M, Jinek M, Soller M, Roignant JY. Hakai is required for stabilization of core components of the m 6A mRNA methylation machinery. Nat Commun 2021; 12:3778. [PMID: 34145251 PMCID: PMC8213727 DOI: 10.1038/s41467-021-23892-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/17/2021] [Indexed: 11/10/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification on mRNA which influences most steps of mRNA metabolism and is involved in several biological functions. The E3 ubiquitin ligase Hakai was previously found in complex with components of the m6A methylation machinery in plants and mammalian cells but its precise function remained to be investigated. Here we show that Hakai is a conserved component of the methyltransferase complex in Drosophila and human cells. In Drosophila, its depletion results in reduced m6A levels and altered m6A-dependent functions including sex determination. We show that its ubiquitination domain is required for dimerization and interaction with other members of the m6A machinery, while its catalytic activity is dispensable. Finally, we demonstrate that the loss of Hakai destabilizes several subunits of the methyltransferase complex, resulting in impaired m6A deposition. Our work adds functional and molecular insights into the mechanism of the m6A mRNA writer complex. The E3 ligase Hakai can interact with the m6A methylation machinery but its function is still unclear. Here, the authors show that Hakai is a conserved component of the m6A methyltransferase complex and provide functional and molecular insights into its role in regulating m6A levels in Drosophila.
Collapse
Affiliation(s)
- Praveen Bawankar
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Tina Lence
- Institute of Molecular Biology (IMB), Mainz, Germany.,Institute for Molecular Infection Biology (IMIB), Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Irmgard U Haussmann
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK.,Department of Life Science, Faculty of Health, Education and Life Sciences, Birmingham City University, Birmingham, UK
| | | | - Dominik Jacob
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | | | - Florian M Richter
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Mohanakarthik P Nallasivan
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Violeta Morin
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Nastasja Kreim
- Bioinformatics core facility, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany.,Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK. .,Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK.
| | - Jean-Yves Roignant
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany. .,Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
18
|
Wagner SA, Szczesniak PP, Voigt A, Gräf JF, Beli P. Proteomic analysis of tyrosine phosphorylation induced by exogenous expression of oncogenic kinase fusions identified in lung adenocarcinoma. Proteomics 2021; 21:e2000283. [PMID: 33768672 DOI: 10.1002/pmic.202000283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 11/11/2022]
Abstract
Kinase fusions are considered oncogenic drivers in numerous types of cancer. In lung adenocarcinoma 5-10% of patients harbor kinase fusions. The most frequently detected kinase fusion involves the Anaplastic Lymphoma Kinase (ALK) and Echinoderm Microtubule-associated protein-Like 4 (EML4). In addition, oncogenic kinase fusions involving the tyrosine kinases RET and ROS1 are found in smaller subsets of patients. In this study, we employed quantitative mass spectrometry-based phosphoproteomics to define the cellular tyrosine phosphorylation patterns induced by different oncogenic kinase fusions identified in patients with lung adenocarcinoma. We show that exogenous expression of the kinase fusions in HEK 293T cells leads to widespread tyrosine phosphorylation. Direct comparison of different kinase fusions demonstrates that the kinase part and not the fusion partner primarily defines the phosphorylation pattern. The tyrosine phosphorylation patterns differed between ALK, ROS1, and RET fusions, suggesting that oncogenic signaling induced by these kinases involves the modulation of different cellular processes.
Collapse
Affiliation(s)
- Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University School of Medicine, Frankfurt, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Pawel P Szczesniak
- Department of Medicine, Hematology/Oncology, Goethe University School of Medicine, Frankfurt, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Justus F Gräf
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany.,Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, Mainz, Germany
| |
Collapse
|
19
|
Roeschert I, Poon E, Henssen AG, Garcia HD, Gatti M, Giansanti C, Jamin Y, Ade CP, Gallant P, Schülein-Völk C, Beli P, Richards M, Rosenfeldt M, Altmeyer M, Anderson J, Eggert A, Dobbelstein M, Bayliss R, Chesler L, Büchel G, Eilers M. Combined inhibition of Aurora-A and ATR kinase results in regression of MYCN-amplified neuroblastoma. Nat Cancer 2021; 2:312-326. [PMID: 33768209 PMCID: PMC7610389 DOI: 10.1038/s43018-020-00171-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022]
Abstract
Amplification of MYCN is the driving oncogene in a subset of high-risk neuroblastoma. The MYCN protein and the Aurora-A kinase form a complex during S phase that stabilizes MYCN. Here we show that MYCN activates Aurora-A on chromatin, which phosphorylates histone H3 at serine 10 in S phase, promotes the deposition of histone H3.3 and suppresses R-loop formation. Inhibition of Aurora-A induces transcription-replication conflicts and activates the Ataxia telangiectasia and Rad3 related (ATR) kinase, which limits double-strand break accumulation upon Aurora-A inhibition. Combined inhibition of Aurora-A and ATR induces rampant tumor-specific apoptosis and tumor regression in mouse models of neuroblastoma, leading to permanent eradication in a subset of mice. The therapeutic efficacy is due to both tumor cell-intrinsic and immune cell-mediated mechanisms. We propose that targeting the ability of Aurora-A to resolve transcription-replication conflicts is an effective therapy for MYCN-driven neuroblastoma (141 words).
Collapse
Affiliation(s)
- Isabelle Roeschert
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Evon Poon
- Division of Clinical Studies and Cancer Therapeutics, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd. Belmont, Sutton, Surrey SM2 5NG, UK
| | - Anton G. Henssen
- Experimental and Clinical Research Center, Max Delbrück Center and Charité Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
| | - Heathcliff Dorado Garcia
- Experimental and Clinical Research Center, Max Delbrück Center and Charité Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
| | - Marco Gatti
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstraße 190, 8057 Zurich, Switzerland
| | - Celeste Giansanti
- Institute of Molecular Oncology, Center of Molecular Biosciences, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Yann Jamin
- Divisions of Radiotherapy and Imaging, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd. Belmont, Sutton, Surrey SM2 5NG, UK
| | - Carsten P. Ade
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Peter Gallant
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Christina Schülein-Völk
- Theodor Boveri Institute, Core Unit High-Content Microscopy, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Petra Beli
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Mark Richards
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Mathias Rosenfeldt
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, Josef-Schneider-Str. 6, 97080 Würzburg, Germany
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstraße 190, 8057 Zurich, Switzerland
| | - John Anderson
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street London WC1N 1EH, UK
| | - Angelika Eggert
- Experimental and Clinical Research Center, Max Delbrück Center and Charité Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, Center of Molecular Biosciences, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Richard Bayliss
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Louis Chesler
- Division of Clinical Studies and Cancer Therapeutics, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd. Belmont, Sutton, Surrey SM2 5NG, UK
| | - Gabriele Büchel
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 6, 97080 Würzburg, Germany
| | - Martin Eilers
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| |
Collapse
|
20
|
Lobato-Gil S, Heidelberger JB, Maghames C, Bailly A, Brunello L, Rodriguez MS, Beli P, Xirodimas DP. Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation. Cell Rep 2021; 34:108635. [PMID: 33472076 DOI: 10.1016/j.celrep.2020.108635] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 11/20/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
The ubiquitin-like molecule NEDD8 controls several biological processes and is a promising target for therapeutic intervention. NEDDylation occurs through specific NEDD8 enzymes (canonical) or enzymes of the ubiquitin system (atypical). Identification of NEDD8 sites on substrates is critical for delineating the processes controlled by NEDDylation. By combining the use of the NEDD8 R74K mutant with anti-di-glycine (anti-diGly) antibodies, we identified 1,101 unique NEDDylation sites in 620 proteins. Bioinformatics analysis reveals that canonical and atypical NEDDylation have distinct proteomes; the spliceosome/mRNA surveillance/DNA replication and ribosome/proteasome, respectively. The data also reveal the formation of poly-NEDD8, hybrid NEDD8-ubiquitin, and NEDD8-SUMO-2 chains as potential molecular signals. In particular, NEDD8-SUMO-2 chains are induced upon proteotoxic stress (atypical) through NEDDylation of K11 in SUMO-2, and conjugates accumulate in previously described nucleolus-related inclusions. The study uncovers a diverse proteome for NEDDylation and is consistent with the concept of extensive cross-talk between ubiquitin and Ubls under proteotoxic stress conditions.
Collapse
Affiliation(s)
| | | | | | - Aymeric Bailly
- CRBM, University of Montpellier, CNRS, Montpellier, France
| | | | - Manuel S Rodriguez
- Laboratoire de Chimie de Coordination (LCC), UPR 8241, CNRS, Toulouse, France; IPBS-University of Toulouse III-Paul Sabatier, Toulouse, France
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany.
| | | |
Collapse
|
21
|
Roedig J, Kowald L, Juretschke T, Karlowitz R, Ahangarian Abhari B, Roedig H, Fulda S, Beli P, van Wijk SJ. USP22 controls necroptosis by regulating receptor-interacting protein kinase 3 ubiquitination. EMBO Rep 2020; 22:e50163. [PMID: 33369872 PMCID: PMC7857539 DOI: 10.15252/embr.202050163] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 12/27/2022] Open
Abstract
Dynamic control of ubiquitination by deubiquitinating enzymes is essential for almost all biological processes. Ubiquitin-specific peptidase 22 (USP22) is part of the SAGA complex and catalyzes the removal of mono-ubiquitination from histones H2A and H2B, thereby regulating gene transcription. However, novel roles for USP22 have emerged recently, such as tumor development and cell death. Apart from apoptosis, the relevance of USP22 in other programmed cell death pathways still remains unclear. Here, we describe a novel role for USP22 in controlling necroptotic cell death in human tumor cell lines. Loss of USP22 expression significantly delays TNFα/Smac mimetic/zVAD.fmk (TBZ)-induced necroptosis, without affecting TNFα-mediated NF-κB activation or extrinsic apoptosis. Ubiquitin remnant profiling identified receptor-interacting protein kinase 3 (RIPK3) lysines 42, 351, and 518 as novel, USP22-regulated ubiquitination sites during necroptosis. Importantly, mutation of RIPK3 K518 reduced necroptosis-associated RIPK3 ubiquitination and amplified necrosome formation and necroptotic cell death. In conclusion, we identify a novel role of USP22 in necroptosis and further elucidate the relevance of RIPK3 ubiquitination as crucial regulator of necroptotic cell death.
Collapse
Affiliation(s)
- Jens Roedig
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt am Main, Germany
| | - Lisa Kowald
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt am Main, Germany
| | | | - Rebekka Karlowitz
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt am Main, Germany
| | - Behnaz Ahangarian Abhari
- Lighthouse Core Facility, Zentrum für Translationale Zellforschung, Universitaetsklinikum Freiburg, Klinik für Innere Medizin I, Freiburg, Germany
| | - Heiko Roedig
- Pharmazentrum Frankfurt, Institut für Allgemeine Pharmakologie und Toxikologie, Goethe-University, Frankfurt am Main, Germany
| | - Simone Fulda
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt am Main, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Sjoerd Jl van Wijk
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt am Main, Germany
| |
Collapse
|
22
|
Lowe DJ, Herzog M, Mosler T, Cohen H, Felton S, Beli P, Raj K, Galanty Y, Jackson SP. Chronic irradiation of human cells reduces histone levels and deregulates gene expression. Sci Rep 2020; 10:2200. [PMID: 32042076 PMCID: PMC7010678 DOI: 10.1038/s41598-020-59163-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/24/2020] [Indexed: 01/10/2023] Open
Abstract
Over the past decades, there have been huge advances in understanding cellular responses to ionising radiation (IR) and DNA damage. These studies, however, were mostly executed with cell lines and mice using single or multiple acute doses of radiation. Hence, relatively little is known about how continuous exposure to low dose ionising radiation affects normal cells and organisms, even though our cells are constantly exposed to low levels of radiation. We addressed this issue by examining the consequences of exposing human primary cells to continuous ionising γ-radiation delivered at 6-20 mGy/h. Although these dose rates are estimated to inflict fewer than a single DNA double-strand break (DSB) per hour per cell, they still caused dose-dependent reductions in cell proliferation and increased cellular senescence. We concomitantly observed histone protein levels to reduce by up to 40%, which in contrast to previous observations, was not mainly due to protein degradation but instead correlated with reduced histone gene expression. Histone reductions were accompanied by enlarged nuclear size paralleled by an increase in global transcription, including that of pro-inflammatory genes. Thus, chronic irradiation, even at low dose-rates, can induce cell senescence and alter gene expression via a hitherto uncharacterised epigenetic route. These features of chronic radiation represent a new aspect of radiation biology.
Collapse
Affiliation(s)
- Donna J Lowe
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire, OX11 0RQ, UK.
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
| | - Mareike Herzog
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
| | | | - Howard Cohen
- Elizabeth House Surgery, Warlingham, Surrey, CR6 9LF, UK
| | - Sarah Felton
- Department of Dermatology, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire, OX11 0RQ, UK
| | - Yaron Galanty
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
| | - Stephen P Jackson
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
| |
Collapse
|
23
|
Dold A, Han H, Liu N, Hildebrandt A, Brüggemann M, Rücklé C, Hänel H, Busch A, Beli P, Zarnack K, König J, Roignant JY, Lasko P. Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation. PLoS Genet 2020; 16:e1008581. [PMID: 31978041 PMCID: PMC7001992 DOI: 10.1371/journal.pgen.1008581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 02/05/2020] [Accepted: 12/20/2019] [Indexed: 11/18/2022] Open
Abstract
Makorins are evolutionary conserved proteins that contain C3H-type zinc finger modules and a RING E3 ubiquitin ligase domain. In Drosophila, maternal Makorin 1 (Mkrn1) has been linked to embryonic patterning but the mechanism remained unsolved. Here, we show that Mkrn1 is essential for axis specification and pole plasm assembly by translational activation of oskar (osk). We demonstrate that Mkrn1 interacts with poly(A) binding protein (pAbp) and binds specifically to osk 3’ UTR in a region adjacent to A-rich sequences. Using Drosophila S2R+ cultured cells we show that this binding site overlaps with a Bruno1 (Bru1) responsive element (BREs) that regulates osk translation. We observe increased association of the translational repressor Bru1 with osk mRNA upon depletion of Mkrn1, indicating that both proteins compete for osk binding. Consistently, reducing Bru1 dosage partially rescues viability and Osk protein level in ovaries from Mkrn1 females. We conclude that Mkrn1 controls embryonic patterning and germ cell formation by specifically activating osk translation, most likely by competing with Bru1 to bind to osk 3’ UTR. To ensure accurate development of the Drosophila embryo, proteins and mRNAs are positioned at specific sites within the embryo. Many of these factors are produced and localized during the development of the egg in the mother. One protein essential for this process that has been heavily studied is Oskar (Osk), which is positioned at the posterior pole. During the localization of osk mRNA, its translation is repressed by the RNA-binding protein Bruno1 (Bru1), ensuring that Osk protein is not present outside of the posterior where it is harmful. At the posterior pole, osk mRNA is activated through mechanisms that are not yet understood. In this work, we show that the conserved protein Makorin 1 (Mkrn1) is a novel factor involved in the translational activation of osk. Mkrn1 binds specifically to osk mRNA, overlapping with a binding site of Bru1, thus alleviating the association of Bru1 with osk. Moreover, Mkrn1 is stabilized by poly(A) binding protein (pAbp), a translational activator that binds osk mRNA in close proximity to one Mkrn1 binding site. Our work thus helps to answer a long-standing question in the field, providing insight about the function of Mkrn1 and more generally into embryonic patterning in animals.
Collapse
Affiliation(s)
- Annabelle Dold
- RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Hong Han
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Niankun Liu
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Andrea Hildebrandt
- Chromatin Biology and Proteomics, Institute of Molecular Biology, Mainz, Germany.,Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Cornelia Rücklé
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Heike Hänel
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Anke Busch
- Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany
| | - Petra Beli
- Chromatin Biology and Proteomics, Institute of Molecular Biology, Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Julian König
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Jean-Yves Roignant
- RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany.,Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Paul Lasko
- Department of Biology, McGill University, Montréal, Québec, Canada.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| |
Collapse
|
24
|
Bekbulat F, Schmitt D, Feldmann A, Huesmann H, Eimer S, Juretschke T, Beli P, Behl C, Kern A. RAB18 Loss Interferes With Lipid Droplet Catabolism and Provokes Autophagy Network Adaptations. J Mol Biol 2019; 432:1216-1234. [PMID: 31874152 DOI: 10.1016/j.jmb.2019.12.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/16/2019] [Accepted: 12/16/2019] [Indexed: 12/18/2022]
Abstract
Autophagy is dependent on appropriate lipid supply for autophagosome formation. The regulation of lipid acquisition and the autophagy network response to lipid-limiting conditions are mostly elusive. Here, we show that the knockout of the RAB GTPase RAB18 interferes with lipid droplet catabolism, causing an impaired fatty acid release. The resulting reduced lipid-droplet-derived lipid availability influences autophagy and provokes adaptive modifications of the autophagy network. These adjustments include increased expression and phosphorylation of ATG2B as well as augmented formation of the ATG12-ATG5 conjugate. Moreover, ATG9A shows an enhanced phosphorylation at amino acid residues tyrosine 8 and serine 14, resulting in an increased ATG9A trafficking. Via pharmacological inhibition of Y8 phosphorylation, we demonstrate that this ATG9A modification is important to maintain basal autophagy under RAB18 knockout conditions. However, while the network adaptations are sufficient to maintain basal autophagic activity, they are incapable of ensuring autophagy induction upon starvation, which is characterized by an enhanced lipid demand. Thus, here, we define the molecular role of RAB18 in connecting lipid droplets and autophagy, emphasize the significance of lipid droplets as lipid sources for the degradative pathway, and uncover a remarkable autophagy network plasticity, including phosphorylation-dependent ATG9A activation, to compensate reduced lipid availability in order to rescue basal autophagic activity.
Collapse
Affiliation(s)
- Fazilet Bekbulat
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Duesbergweg 6, 55128 Mainz, Germany
| | - Daniel Schmitt
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Duesbergweg 6, 55128 Mainz, Germany
| | - Anne Feldmann
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Duesbergweg 6, 55128 Mainz, Germany
| | - Heike Huesmann
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Duesbergweg 6, 55128 Mainz, Germany
| | - Stefan Eimer
- Department of Structural Cell Biology, Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt, Germany
| | - Thomas Juretschke
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Christian Behl
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Duesbergweg 6, 55128 Mainz, Germany.
| | - Andreas Kern
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Duesbergweg 6, 55128 Mainz, Germany.
| |
Collapse
|
25
|
Hildebrandt A, Brüggemann M, Rücklé C, Boerner S, Heidelberger JB, Busch A, Hänel H, Voigt A, Möckel MM, Ebersberger S, Scholz A, Dold A, Schmid T, Ebersberger I, Roignant JY, Zarnack K, König J, Beli P. The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. Genome Biol 2019; 20:216. [PMID: 31640799 PMCID: PMC6805484 DOI: 10.1186/s13059-019-1814-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 09/04/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Cells have evolved quality control mechanisms to ensure protein homeostasis by detecting and degrading aberrant mRNAs and proteins. A common source of aberrant mRNAs is premature polyadenylation, which can result in non-functional protein products. Translating ribosomes that encounter poly(A) sequences are terminally stalled, followed by ribosome recycling and decay of the truncated nascent polypeptide via ribosome-associated quality control. RESULTS Here, we demonstrate that the conserved RNA-binding E3 ubiquitin ligase Makorin Ring Finger Protein 1 (MKRN1) promotes ribosome stalling at poly(A) sequences during ribosome-associated quality control. We show that MKRN1 directly binds to the cytoplasmic poly(A)-binding protein (PABPC1) and associates with polysomes. MKRN1 is positioned upstream of poly(A) tails in mRNAs in a PABPC1-dependent manner. Ubiquitin remnant profiling and in vitro ubiquitylation assays uncover PABPC1 and ribosomal protein RPS10 as direct ubiquitylation substrates of MKRN1. CONCLUSIONS We propose that MKRN1 mediates the recognition of poly(A) tails to prevent the production of erroneous proteins from prematurely polyadenylated transcripts, thereby maintaining proteome integrity.
Collapse
Affiliation(s)
- Andrea Hildebrandt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Cornelia Rücklé
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Susan Boerner
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Jan B Heidelberger
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Heike Hänel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Martin M Möckel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | | | - Anica Scholz
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Annabelle Dold
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Tobias Schmid
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Ingo Ebersberger
- Department for Applied Bioinformatics, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Straße 14-16, 60325, Frankfurt am Main, Germany
| | - Jean-Yves Roignant
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Génopode Building, CH-1015, Lausanne, Switzerland
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| |
Collapse
|
26
|
Szybinski J, Sasca D, Heidelberger J, Klumb K, Shah V, Dolnik A, Theobald M, Bullinger L, Beli P, Kindler T. Abstract 5223: Epigenetic silencing mediated by non-phosphorylated STAT5B prevents differentiation in acute myeloid leukemia. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-5223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
STAT5 proteins are transcription factors involved in the regulation of proliferation, apoptosis and differentiation. Upon ligand-mediated activation, phosphorylated STAT5A (pSTAT5A) and pSTAT5B form homo- or heterodimers, translocate to the nucleus and activate transcription. Recent data indicate an important role of un-phosphorylated STAT5 (uSTAT5) in the regulation of differentiation. For example, the presence of uStat5 shifts the balance toward the maintenance of leukemic stem cells, whereas genetic depletion of Stat5induced differentiation. Further, uSTAT5 has been shown to act as a repressor of megakaryocytic differentiation via restricting the access of ERG to its target genes. To further investigate the function of uSTAT5 in mammalian AML, we established several cell line models expressing doxycycline-inducible shRNA directed against either STAT5A or STAT5B. In uSTAT5-expressing AML cells targeting of STAT5A or STAT5B suppressed cell growth and induced differentiation. These effects were significantly stronger upon knockdown of STAT5B compared to STAT5A. Global RNA sequencing demonstrated enrichment of differentiation programs upon downregulation of uSTAT5B. To further explore the biological function of uSTAT5, we performed SILAC-based global proteomics after pulldown of either STAT5A or STAT5B. While uSTAT5A was found to be associated with proteins involved in RNA processing, uSTAT5B primarily co-precipitated with chromatin- and histone-binding proteins, like the transcriptional repressor ETV6 or the histone H3K4 demethylase KDM5C. To dissect the specific roles of pSTAT5B and uSTAT5B, we performed co-immunoprecipitation assay upon treatment of AML cells with GM-CSF or vehicle control. As expected, GM-CSF treatment caused strong phosphorylation of STAT5A/B, however, uSTAT5B-binding of ETV6 was almost completely abolished, indicating a specific association only with uSTAT5B. As depletion of uSTAT5B induced differentiation and uSTAT5B interacts with KDM5C and ETV6, we hypothesized that uSTAT5B prevents transcription of genes involved in differentiation. To address this question, we performed H3K4me3 ChIP-seq analysis in THP-1 cells upon knockdown of STAT5B. Downregulation of uSTAT5B caused strong accumulation of H3K4me3 at promoter regions of previously silenced genes. Finally, we wanted to investigate whether targeting of KDM5C can reverse disturbed differentiation in AML cells. Treatment with the KDM5 inhibitor CPI-455 significantly inhibited proliferation and induced apoptosis, but only in AML samples expressing uSTAT5B. In summary, our data provide evidence that uSTAT5B specifically blocks differentiation in AML cells via its interaction with KDM5C followed by repression of H3K4me3 at distinct promoter regions. Targeting of uSTAT5B or its interacting partners might represent an interesting novel strategy in AML therapy.
Citation Format: Jakub Szybinski, Daniel Sasca, Jan Heidelberger, Karolin Klumb, Viral Shah, Anna Dolnik, Matthias Theobald, Lars Bullinger, Petra Beli, Thomas Kindler. Epigenetic silencing mediated by non-phosphorylated STAT5B prevents differentiation in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5223.
Collapse
Affiliation(s)
| | - Daniel Sasca
- 1University Medical Center of Mainz, Mainz, Germany
| | | | | | - Viral Shah
- 1University Medical Center of Mainz, Mainz, Germany
| | - Anna Dolnik
- 3Charité, University Medical Center, Berlin, Germany
| | | | | | - Petra Beli
- 2Institute of Molecular Biology, Mainz, Germany
| | | |
Collapse
|
27
|
Balmus G, Pilger D, Coates J, Demir M, Sczaniecka-Clift M, Barros AC, Woods M, Fu B, Yang F, Chen E, Ostermaier M, Stankovic T, Ponstingl H, Herzog M, Yusa K, Martinez FM, Durant ST, Galanty Y, Beli P, Adams DJ, Bradley A, Metzakopian E, Forment JV, Jackson SP. ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks. Nat Commun 2019; 10:87. [PMID: 30622252 PMCID: PMC6325118 DOI: 10.1038/s41467-018-07729-2] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/15/2018] [Indexed: 02/02/2023] Open
Abstract
Mutations in the ATM tumor suppressor gene confer hypersensitivity to DNA-damaging chemotherapeutic agents. To explore genetic resistance mechanisms, we performed genome-wide CRISPR-Cas9 screens in cells treated with the DNA topoisomerase I inhibitor topotecan. Thus, we here establish that inactivating terminal components of the non-homologous end-joining (NHEJ) machinery or of the BRCA1-A complex specifically confer topotecan resistance to ATM-deficient cells. We show that hypersensitivity of ATM-mutant cells to topotecan or the poly-(ADP-ribose) polymerase (PARP) inhibitor olaparib reflects delayed engagement of homologous recombination at DNA-replication-fork associated single-ended double-strand breaks (DSBs), allowing some to be subject to toxic NHEJ. Preventing DSB ligation by NHEJ, or enhancing homologous recombination by BRCA1-A complex disruption, suppresses this toxicity, highlighting a crucial role for ATM in preventing toxic LIG4-mediated chromosome fusions. Notably, suppressor mutations in ATM-mutant backgrounds are different to those in BRCA1-mutant scenarios, suggesting new opportunities for patient stratification and additional therapeutic vulnerabilities for clinical exploitation.
Collapse
Affiliation(s)
- Gabriel Balmus
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- UK Dementia Research Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Domenic Pilger
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Julia Coates
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Mukerrem Demir
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Matylda Sczaniecka-Clift
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Ana C Barros
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Michael Woods
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Elisabeth Chen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Tatjana Stankovic
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Hannes Ponstingl
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Mareike Herzog
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Kosuke Yusa
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Francisco Munoz Martinez
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Stephen T Durant
- DNA Damage Response Biology, Bioscience Oncology IMED Biotech Unit, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Yaron Galanty
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Allan Bradley
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Emmanouil Metzakopian
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- UK Dementia Research Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Josep V Forment
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
- DNA Damage Response Biology, Bioscience Oncology IMED Biotech Unit, AstraZeneca, Cambridge, CB4 0WG, UK.
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
| |
Collapse
|
28
|
Dev H, Chiang TWW, Lescale C, de Krijger I, Martin AG, Pilger D, Coates J, Sczaniecka-Clift M, Wei W, Ostermaier M, Herzog M, Lam J, Shea A, Demir M, Wu Q, Yang F, Fu B, Lai Z, Balmus G, Belotserkovskaya R, Serra V, O'Connor MJ, Bruna A, Beli P, Pellegrini L, Caldas C, Deriano L, Jacobs JJL, Galanty Y, Jackson SP. Shieldin complex promotes DNA end-joining and counters homologous recombination in BRCA1-null cells. Nat Cell Biol 2018; 20:954-965. [PMID: 30022119 PMCID: PMC6145444 DOI: 10.1038/s41556-018-0140-1] [Citation(s) in RCA: 250] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/11/2018] [Indexed: 02/02/2023]
Abstract
BRCA1 deficiencies cause breast, ovarian, prostate and other cancers, and render tumours hypersensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. To understand the resistance mechanisms, we conducted whole-genome CRISPR-Cas9 synthetic-viability/resistance screens in BRCA1-deficient breast cancer cells treated with PARP inhibitors. We identified two previously uncharacterized proteins, C20orf196 and FAM35A, whose inactivation confers strong PARP-inhibitor resistance. Mechanistically, we show that C20orf196 and FAM35A form a complex, 'Shieldin' (SHLD1/2), with FAM35A interacting with single-stranded DNA through its C-terminal oligonucleotide/oligosaccharide-binding fold region. We establish that Shieldin acts as the downstream effector of 53BP1/RIF1/MAD2L2 to promote DNA double-strand break (DSB) end-joining by restricting DSB resection and to counteract homologous recombination by antagonizing BRCA2/RAD51 loading in BRCA1-deficient cells. Notably, Shieldin inactivation further sensitizes BRCA1-deficient cells to cisplatin, suggesting how defining the SHLD1/2 status of BRCA1-deficient tumours might aid patient stratification and yield new treatment opportunities. Highlighting this potential, we document reduced SHLD1/2 expression in human breast cancers displaying intrinsic or acquired PARP-inhibitor resistance.
Collapse
Affiliation(s)
- Harveer Dev
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
- Academic Urology Group, Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK
| | - Ting-Wei Will Chiang
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chloe Lescale
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Inge de Krijger
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan , Amsterdam, the Netherlands
| | - Alistair G Martin
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Domenic Pilger
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Julia Coates
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Matylda Sczaniecka-Clift
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Wenming Wei
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | | | - Mareike Herzog
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jonathan Lam
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Abigail Shea
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Mukerrem Demir
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Qian Wu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Gabriel Balmus
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Rimma Belotserkovskaya
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Violeta Serra
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Alejandra Bruna
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, Paris, France.
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan , Amsterdam, the Netherlands.
| | - Yaron Galanty
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Stephen P Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| |
Collapse
|
29
|
Borisova ME, Voigt A, Tollenaere MAX, Sahu SK, Juretschke T, Kreim N, Mailand N, Choudhary C, Bekker-Jensen S, Akutsu M, Wagner SA, Beli P. p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage. Nat Commun 2018. [PMID: 29523821 PMCID: PMC5845016 DOI: 10.1038/s41467-018-03417-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ultraviolet (UV) light radiation induces the formation of bulky photoproducts in the DNA that globally affect transcription and splicing. However, the signaling pathways and mechanisms that link UV-light-induced DNA damage to changes in RNA metabolism remain poorly understood. Here we employ quantitative phosphoproteomics and protein kinase inhibition to provide a systems view on protein phosphorylation patterns induced by UV light and uncover the dependencies of phosphorylation events on the canonical DNA damage signaling by ATM/ATR and the p38 MAP kinase pathway. We identify RNA-binding proteins as primary substrates and 14-3-3 as direct readers of p38-MK2-dependent phosphorylation induced by UV light. Mechanistically, we show that MK2 phosphorylates the RNA-binding subunit of the NELF complex NELFE on Serine 115. NELFE phosphorylation promotes the recruitment of 14-3-3 and rapid dissociation of the NELF complex from chromatin, which is accompanied by RNA polymerase II elongation. UV-light-induced DNA damage affects RNA metabolism but the underlying signalling pathways are largely unexplored. Here, the authors show that UV light triggers p38-MK2-mediated phosphorylation of the NELF complex, promoting its release from chromatin and concurrent transcriptional elongation.
Collapse
Affiliation(s)
- Marina E Borisova
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Maxim A X Tollenaere
- Cellular Stress Signaling Group, Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, Blegdamsvej 3C, 2200, Copenhagen, Denmark
| | - Sanjeeb Kumar Sahu
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Thomas Juretschke
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Nastasja Kreim
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Niels Mailand
- Ubiquitin Signaling Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Chunaram Choudhary
- Proteomics and Cell Signaling Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Simon Bekker-Jensen
- Cellular Stress Signaling Group, Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, Blegdamsvej 3C, 2200, Copenhagen, Denmark
| | - Masato Akutsu
- Institute of Biochemistry II, Goethe University Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von Laue-Strasse 15, 60438, Frankfurt, Germany
| | - Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.,German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.,German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| |
Collapse
|
30
|
Heidelberger JB, Voigt A, Borisova ME, Petrosino G, Ruf S, Wagner SA, Beli P. Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function. EMBO Rep 2018; 19:embr.201744754. [PMID: 29467282 DOI: 10.15252/embr.201744754] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 01/17/2018] [Accepted: 01/26/2018] [Indexed: 12/20/2022] Open
Abstract
Valosin-containing protein (VCP) is an evolutionarily conserved ubiquitin-dependent ATPase that mediates the degradation of proteins through the ubiquitin-proteasome pathway. Despite the central role of VCP in the regulation of protein homeostasis, identity and nature of its cellular substrates remain poorly defined. Here, we combined chemical inhibition of VCP and quantitative ubiquitin remnant profiling to assess the effect of VCP inhibition on the ubiquitin-modified proteome and to probe the substrate spectrum of VCP in human cells. We demonstrate that inhibition of VCP perturbs cellular ubiquitylation and increases ubiquitylation of a different subset of proteins compared to proteasome inhibition. VCP inhibition globally upregulates K6-linked ubiquitylation that is dependent on the HECT-type ubiquitin E3 ligase HUWE1. We report ~450 putative VCP substrates, many of which function in nuclear processes, including gene expression, DNA repair and cell cycle. Moreover, we identify that VCP regulates the level and activity of the transcription factor c-Myc.
Collapse
Affiliation(s)
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Mainz, Germany
| | | | | | - Stefanie Ruf
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University School of Medicine, Frankfurt, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
| |
Collapse
|
31
|
Hildebrandt A, Alanis-Lobato G, Voigt A, Zarnack K, Andrade-Navarro MA, Beli P, König J. Interaction profiling of RNA-binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin system. Sci Rep 2017; 7:16582. [PMID: 29185492 PMCID: PMC5707401 DOI: 10.1038/s41598-017-16695-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 09/14/2017] [Indexed: 11/09/2022] Open
Abstract
RNA-binding ubiquitin ligases (RBULs) have the potential to link RNA-mediated mechanisms to protein ubiquitylation. Despite this, the cellular functions, substrates and interaction partners of most RBULs remain poorly characterized. Affinity purification (AP) combined with quantitative mass spectrometry (MS)-based proteomics is a powerful approach for analyzing protein functions. Mapping the physiological interaction partners of RNA-binding proteins has been hampered by their intrinsic properties, in particular the existence of low-complexity regions, which are prone to engage in non-physiological interactions. Here, we used an adapted AP approach to identify the interaction partners of human RBULs harboring different RNA-binding domains. To increase the likelihood of recovering physiological interactions, we combined control and bait-expressing cells prior to lysis. In this setup, only stable interactions that were originally present in the cell will be identified. We exploit gene function similarity between the bait proteins and their interactors to benchmark our approach in its ability to recover physiological interactions. We reveal that RBULs engage in stable interactions with RNA-binding proteins involved in different steps of RNA metabolism as well as with components of the ubiquitin conjugation machinery and ubiquitin-binding proteins. Our results thus demonstrate their capacity to link posttranscriptional regulation with the ubiquitin system.
Collapse
Affiliation(s)
- Andrea Hildebrandt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Gregorio Alanis-Lobato
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.,Faculty of Biology, Johannes Gutenberg University, Gresemundweg 2, 55128, Mainz, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Miguel A Andrade-Navarro
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.,Faculty of Biology, Johannes Gutenberg University, Gresemundweg 2, 55128, Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| |
Collapse
|
32
|
Mahendrarajah N, Borisova ME, Reichardt S, Godmann M, Sellmer A, Mahboobi S, Haitel A, Schmid K, Kenner L, Heinzel T, Beli P, Krämer OH. HSP90 is necessary for the ACK1-dependent phosphorylation of STAT1 and STAT3. Cell Signal 2017; 39:9-17. [DOI: 10.1016/j.cellsig.2017.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/07/2017] [Accepted: 07/19/2017] [Indexed: 12/24/2022]
|
33
|
Schunter S, Villa R, Flynn V, Heidelberger JB, Classen AK, Beli P, Becker PB. Ubiquitylation of the acetyltransferase MOF in Drosophila melanogaster. PLoS One 2017; 12:e0177408. [PMID: 28510597 PMCID: PMC5433716 DOI: 10.1371/journal.pone.0177408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/26/2017] [Indexed: 01/26/2023] Open
Abstract
The nuclear acetyltransferase MOF (KAT8 in mammals) is a subunit of at least two multi-component complexes involved in transcription regulation. In the context of complexes of the ‘Non-Specific-Lethal’ (NSL) type it controls transcription initiation of many nuclear housekeeping genes and of mitochondrial genes. While this function is conserved in metazoans, MOF has an additional, specific function in Drosophila in the context of dosage compensation. As a subunit of the male-specific-lethal dosage compensation complex (MSL-DCC) it contributes to the doubling of transcription output from the single male X chromosome by acetylating histone H4. Proper dosage compensation requires finely tuned levels of MSL-DCC and an appropriate distribution of MOF between the regulatory complexes. The amounts of DCC formed depends directly on the levels of the male-specific MSL2, which orchestrates the assembly of the DCC, including MOF recruitment. We found earlier that MSL2 is an E3 ligase that ubiquitylates most MSL proteins, including MOF, suggesting that ubiquitylation may contribute to a quality control of MOF’s overall levels and folding state as well as its partitioning between the complex entities. We now used mass spectrometry to map the lysines in MOF that are ubiquitylated by MSL2 in vitro and identified in vivo ubiquitylation sites of MOF in male and female cells. MSL2-specific ubiquitylation in vivo could not be traced due to the dominance of other, sex-independent ubiquitylation events and conceivably may be rare or transient. Expressing appropriately mutated MOF derivatives we assessed the importance of the ubiquitylated lysines for dosage compensation by monitoring DCC formation and X chromosome targeting in cultured cells, and by genetic complementation of the male-specific-lethal mof2 allele in flies. Our study provides a comprehensive analysis of MOF ubiquitylation as a reference for future studies.
Collapse
Affiliation(s)
- Sarah Schunter
- Molecular Biology Division, Biomedical Center and Center for integrated Protein Science Ludwig-Maximilians-University, Munich, Germany
| | - Raffaella Villa
- Molecular Biology Division, Biomedical Center and Center for integrated Protein Science Ludwig-Maximilians-University, Munich, Germany
| | - Victoria Flynn
- Molecular Biology Division, Biomedical Center and Center for integrated Protein Science Ludwig-Maximilians-University, Munich, Germany
| | | | | | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Peter B. Becker
- Molecular Biology Division, Biomedical Center and Center for integrated Protein Science Ludwig-Maximilians-University, Munich, Germany
- * E-mail:
| |
Collapse
|
34
|
Diamanti MA, Gupta J, Bennecke M, De Oliveira T, Ramakrishnan M, Braczynski AK, Richter B, Beli P, Hu Y, Saleh M, Mittelbronn M, Dikic I, Greten FR. IKKα controls ATG16L1 degradation to prevent ER stress during inflammation. J Exp Med 2017; 214:423-437. [PMID: 28082356 PMCID: PMC5294863 DOI: 10.1084/jem.20161867] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 11/29/2016] [Accepted: 12/27/2016] [Indexed: 12/29/2022] Open
Abstract
Inhibition of the IκB kinase complex (IKK) has been implicated in the therapy of several chronic inflammatory diseases including inflammatory bowel diseases. In this study, using mice with an inactivatable IKKα kinase (IkkαAA/AA), we show that loss of IKKα function markedly impairs epithelial regeneration in a model of acute colitis. Mechanistically, this is caused by compromised secretion of cytoprotective IL-18 from IKKα-mutant intestinal epithelial cells because of elevated caspase 12 activation during an enhanced unfolded protein response (UPR). Induction of the UPR is linked to decreased ATG16L1 stabilization in IkkαAA/AA mice. We demonstrate that both TNF-R and nucleotide-binding oligomerization domain stimulation promote ATG16L1 stabilization via IKKα-dependent phosphorylation of ATG16L1 at Ser278. Thus, we propose IKKα as a central mediator sensing both cytokine and microbial stimulation to suppress endoplasmic reticulum stress, thereby assuring antiinflammatory function during acute intestinal inflammation.
Collapse
Affiliation(s)
- Michaela A Diamanti
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt am Main, Germany
| | - Jalaj Gupta
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt am Main, Germany
| | - Moritz Bennecke
- Institute of Molecular Immunology, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Tiago De Oliveira
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt am Main, Germany
| | - Mallika Ramakrishnan
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt am Main, Germany
| | - Anne K Braczynski
- Edinger Institute (Institute of Neurology), Goethe University Hospital, Goethe University, 60323 Frankfurt, Germany
| | - Benjamin Richter
- Institute of Biochemistry II, Buchmann Institute for Molecular Life Sciences, Goethe University School of Medicine, Goethe University, 60323 Frankfurt, Germany
| | - Petra Beli
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Yinling Hu
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Maya Saleh
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Michel Mittelbronn
- Edinger Institute (Institute of Neurology), Goethe University Hospital, Goethe University, 60323 Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Buchmann Institute for Molecular Life Sciences, Goethe University School of Medicine, Goethe University, 60323 Frankfurt, Germany
| | - Florian R Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt am Main, Germany
| |
Collapse
|
35
|
Abstract
Protein phosphorylation plays central regulatory roles in DNA damage repair and signaling. Protein kinases of the phosphatidylinositol 3-kinase-related kinase family ATM, ATR, and DNA-PKcs mediate phosphorylation of hundreds of substrates after DNA damage and thereby orchestrate the cellular response to DNA damage. Protein phosphorylation can be studied using antibodies that specifically recognize phosphorylated protein species; however, this approach is limited by existing antibodies and does not permit unbiased discovery of phosphorylation sites or analyzing phosphorylation sites in a high-throughput manner. Mass spectrometry (MS)-based proteomics has emerged as a powerful method for identification of phosphorylation sites on individual proteins and proteome-wide. To identify phosphorylation sites, proteins are digested into peptides and phosphopeptides are enriched using titanium dioxide (TiO2)-based chromatography followed by the identification by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Quantitative proteomics approaches, such as stable isotope labeling with amino acids in cell culture (SILAC), enable relative quantification of phosphopeptide abundance in different conditions. Here, we describe a streamlined protocol for enrichment of phosphopeptides using TiO2-based chromatography, and outline the application of quantitative phosphoproteomics for the identification of DNA damage-induced phosphorylation and substrates of kinases functioning after DNA damage.
Collapse
Affiliation(s)
| | - Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
| |
Collapse
|
36
|
Wagner SA, Oehler H, Voigt A, Dalic D, Freiwald A, Serve H, Beli P. ATR inhibition rewires cellular signaling networks induced by replication stress. Proteomics 2016; 16:402-16. [PMID: 26572502 DOI: 10.1002/pmic.201500172] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 10/15/2015] [Accepted: 11/09/2015] [Indexed: 12/27/2022]
Abstract
The slowing down or stalling of replication forks is commonly known as replication stress and arises from multiple causes such as DNA lesions, nucleotide depletion, RNA-DNA hybrids, and oncogene activation. The ataxia telangiectasia and Rad3-related kinase (ATR) plays an essential role in the cellular response to replication stress and inhibition of ATR has emerged as therapeutic strategy for the treatment of cancers that exhibit high levels of replication stress. However, the cellular signaling induced by replication stress and the substrate spectrum of ATR has not been systematically investigated. In this study, we employed quantitative MS-based proteomics to define the cellular signaling after nucleotide depletion-induced replication stress and replication fork collapse following ATR inhibition. We demonstrate that replication stress results in increased phosphorylation of a subset of proteins, many of which are involved in RNA splicing and transcription and have previously not been associated with the cellular replication stress response. Furthermore, our data reveal the ATR-dependent phosphorylation following replication stress and discover novel putative ATR target sites on MCM6, TOPBP1, RAD51AP1, and PSMD4. We establish that ATR inhibition rewires cellular signaling networks induced by replication stress and leads to the activation of the ATM-driven double-strand break repair signaling.
Collapse
Affiliation(s)
- Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hannah Oehler
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Denis Dalic
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Anja Freiwald
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Hubert Serve
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
| |
Collapse
|
37
|
Zurnic I, Hütter S, Lehmann U, Stanke N, Reh J, Kern T, Lindel F, Gerresheim G, Hamann M, Müllers E, Lesbats P, Cherepanov P, Serrao E, Engelman A, Lindemann D, Da Silva Santos C, Tartour K, Cimarelli A, Burdick R, Chen J, Sastri J, Hu WS, Pathak V, Keppler OT, Pradeau K, Eiler S, Levy N, Lennon S, Cianferani S, Emiliani S, Ruff M, Parissi V, Rato S, Rausell A, Munoz M, Telenti A, Ciuffi A, Zhyvoloup A, Melamed A, Anderson I, Planas D, Kriston-Vizi J, Ketteler R, Lee CH, Merritt A, Ancuta P, Bangham C, Fassati A, Rodari A, Van Driessche B, Galais M, Delacourt N, Fauquenoy S, Vanhulle C, Kula A, Burny A, Rohr O, Van Lint C, van Montfort T, van der Sluis R, Speijer D, Berkhout B, Meng B, Rutkowski A, Berry N, Dölken L, Lever A, Schuster T, Asbach B, Wagner R, Gross C, Wiesmann V, Kalmer M, Wittenberg T, Gettemans J, Thoma-Kress AK, Li M, Freed EO, Liu SL, Müller J, Münch J, Sewald X, Uchil P, Ladinsky M, Beloor J, Pi R, Herrmann C, Motamedi N, Murooka T, Brehm M, Greiner D, Mempel T, Bjorkman P, Kumar P, Mothes W, Joas S, Parrish E, Gnanadurai CW, Lump E, Stürzel CM, Parrish NF, Sauermann U, Töpfer K, Schultheiss T, Bosinger S, Silvestri G, Apetrei C, Huot N, Müller-Trutwin M, Sauter D, Hahn BH, Stahl-Hennig C, Kirchhoff F, Schumann G, Jung-Klawitter S, Fuchs NV, Upton KR, Muñoz-Lopez M, Shukla R, Wang J, Garcia-Canadas M, Lopez-Ruiz C, Gerhardt DJ, Sebe A, Grabundzija I, Gerdes P, Merkert S, Pulgarin A, Bock A, Held U, Witthuhn A, Haase A, Wolvetang EJ, Martin U, Ivics Z, Izsvák Z, Garcia-Perez J, Faulkner GJ, Hurst T, Katzourakis A, Magiorkinis G, Schott K, Derua R, Seifried J, Reuter A, Schmitz H, Tondera C, Brandariz-Nuñez A, Diaz-Griffero F, Janssens V, König R, Baldauf HM, Stegmann L, Schwarz SM, Trotard M, Martin M, Lenzi G, Burggraf M, Pan X, Fregoso OI, Lim ES, Abraham L, Erikson E, Nguyen L, Ambiel I, Rutsch F, Kim B, Emerman M, Fackler OT, Wittmann S, Behrendt R, Volkmann B, Eissmann K, Gramberg T, Bolduan S, Koppensteiner H, Regensburg S, Brack-Werner R, Draenert R, Schindler M, Ducroux A, Xu S, Ponnurangam A, Franz S, Malassa A, Ewald E, Goffinet C, Fung SY, Chan CP, Yuen CK, Kok KH, Chan CP, Jin DY, Dittmer U, Kmiec D, Iyer S, Stürzel C, Hahn B, Ariumi Y, Yasuda-Inoue M, Kawano K, Tateishi S, Turelli P, Compton A, Roy N, Porrot F, Billet A, Casartelli N, Yount J, Liang C, Schwartz O, Magnus C, Reh L, Moore P, Uhr T, Weber J, Morris L, Trkola A, Grindberg RV, Schlaepfer E, Schreiber G, Simon V, Speck RF, Debyser Z, Vranckx L, Demeulemeester J, Saleh S, Verdin E, Cereseto A, Christ F, Gijsbers R, Wang G, Zhao N, Das AT, Köstler J, Perdiguero B, Esteban M, Jacobs BL, Montefiori DC, LaBranche CC, Yates NL, Tomaras GD, Ferrari G, Foulds KE, Roederer M, Landucci G, Forthal DN, Seaman MS, Hawkins N, Self SG, Phogat S, Tartaglia J, Barnett SW, Burke B, Cristillo AD, Ding S, Heeney JL, Pantaleo G, Stab V, Ensser A, Tippler B, Burton D, Tenbusch M, Überla K, Alter G, Lofano G, Dugast AS, Kulkarni V, Suscovich T, Opazo T, Barraza F, Herrera D, Garces A, Schwenke T, Tapia D, Cancino J, Arriagada G, Haußner C, Damm D, Rohrhofer A, Schmidt B, Eichler J, Midgley R, Wheeldon J, Piguet V, Khopkar P, Rohamare M, Kulkarni S, Godinho-Santos A, Hance A, Goncalves J, Mammano F, Gasser R, Hamoudi M, Pellicciotta M, Zhou Z, Visdeloup C, Colin P, Braibant M, Lagane B, Negroni M, Wamara J, Bannert N, Mesplede T, Osman N, Anstett K, Liang JC, Pham HT, Wainberg M, Shao W, Shan J, Kearney M, Wu X, Maldarelli F, Mellors J, Luke B, Coffin J, Hughes S, Fricke T, Opp S, Shepard C, Ivanov D, Valle-Casuso J, Kanja M, Cappy P, Negroni M, Lener D, Knyazhanskaya E, Anisenko A, Zatsepin T, Gottikh M, Komkov A, Minervina A, Nugmanov G, Nazarov V, Khodosevich K, Mamedov I, Lebedev Y, Colomer-Lluch M, Serra-Moreno R, Sarracino A, Gharu L, Pasternak A, Marcello A, McCartin AM, Kulkarni A, Le Douce V, Gautier V, Baeyens A, Naessens E, Van Nuffel A, Weening K, Reilly AM, Claeys E, Trypsteen W, Vandekerckhove L, Eyckerman S, Gevaert K, Verhasselt B, Mok HP, Norton N, Fun A, Hirst J, Wills M, Miklik D, Senigl F, Hejnar J, Sakuragi JI, Sakuragi S, Yokoyama M, Shioda T, Sato H, Bodem J, Moschall R, Denk S, Erkelenz S, Schenk C, Schaal H, Donhauser N, Socher E, Millen S, Sticht H, Gross C, Mann M, Wei G, Betts MJ, Liu Y, Kehl T, Russell RB, Löchelt M, Hohn O, Mostafa S, Hanke K, Norley S, Chen CY, Shingai M, Borrego P, Taveira N, Strebel K, Hellmund C, Meng B, Friedrich M, Hahn F, Setz C, Rauch P, Fraedrich K, Matthaei A, Henklein P, Traxdorf M, Fossen T, Schubert U, Khwaja A, Galilee M, Alian A, Schwalbe B, Hauser H, Schreiber M, Scherpenisse M, Cho YK, Kim J, Jeong D, Trejbalova K, Benesova M, Kucerova D, Vernerova Z, Amouroux R, Hajkova P, Elleder D, Hron T, Farkasova H, Padhi A, Paces J, Zhu H, Gifford R, Murcia P, Carrozza ML, Niewiadomska AM, Mazzei M, Abi-Said M, Hughes J, Hué S, Gifford R, Obasa A, Jacobs G, Engelbrecht S, Mack K, Starz K, Geyer M, Bibollet-Ruche F, Stürzel C, Leoz M, Plantier JC, Argaw-Denboba A, Balestrieri E, Serafino A, Bucci I, Cipriani C, Spadafora C, Sinibaldi-Vallebona P, Matteucci C, Jayashree SN, Neogi U, Chhangani AK, Rathore SS, Mathur BRJ, Abati A, Koç BT, Oğuzoğlu TÇ, Shimauchi T, Caucheteux S, Turpin J, Finsterbusch K, Tokura Y, Souriant S, Balboa L, Pingris K, Kviatcowsky D, Raynaud-Messina B, Cougoule C, Mercier I, Kuroda M, González-Montaner P, Inwentarz S, Moraña EJ, del Carmen Sasiain M, Neyrolles O, Maridonneau-Parini I, Lugo-Villarino G, Vérollet C, Herrmann A, Thomas D, Bouzas NF, Lahaye X, Bhargava A, Satoh T, Gentili M, Cerboni S, Silvin A, Conrad C, Ahmed-Belkacem H, Rodriguez EC, Guichou JF, Bosquet N, Piel M, Le Grand R, King M, Pawlotsky JM, Manel N, Hofmann H, Vanwalscappel B, Bloch N, Landau N, Indik S, Hagen B, Valle-Casuso JC, Allouch A, David A, Barré-Sinoussi F, Benkirane M, Pancino G, Saez-Cirion A, Lee WY, Sloan R, Schulte B, Opp S, Blomberg J, Vargiu L, Rodriguez-Tomé P, Tramontano E, Sperber G, Kumari N, Ammosova T, Diaz S, Oneal P, Nekhai S, Fahrny A, Gers-Huber G, Audigé A, Jayaprakash A, Sachidanandam R, Hernandez M, Dillon-White M, Souriant S, Pingris K, Raynaud-Messina B, Cougoule C, Mercier I, Neyrolles O, Maridonneau-Parini I, Lugo-Villarino G, Maze E, Ham C, Almond N, Towers G, Belshaw R, de Sousa-Pereira P, Abrantes J, Pizzato M, Esteves PJ, Kahle T, Schmitt S, Merkel L, Reuter N, Stamminger T, Rosa ID, Bishop K, Spinazzola A, Groom H, Vieyres G, Müsken M, Zillinger T, Hornung V, Barchet W, Häussler S, Pietschmann T, Javed A, Leuchte N, Salinas G, Opitz L, Sopper S, Mummert C, Hofmann C, Hückelhoven AG, Bergmann S, Müller-Schmucker SM, Harrer EG, Dörrie J, Schaft N, Harrer T, Cardinaux L, Zahno ML, Vogt HR, Zanoni R, Bertoni G, Muenchhoff M, Goulder P, Keppler O, Rebensburg S, Helfer M, Zhang Y, Chen H, Bernier A, Gosselin A, Routy JP, Wöhrl B, Schneider A, Corona A, Spöring I, Jordan M, Buchholz B, Maccioni E, Di Santo R, Schweimer K, Schölz C, Weinert B, Wagner S, Beli P, Miyake Y, Qi J, Jensen L, Streicher W, McCarthy A, Westwood N, Lain S, Cox J, Matthias P, Mann M, Bradner J, Choudhary C, Stern M, Valletta E, Frezza C, Marino-Merlo F, Grelli S, Serafino AL, Mastino A, Macchi B, Kaulfuß M, Windmann S, Bayer W, Mikasi S, Jacobs G, Heß R, Bonsmann MSG, Kirschning C, Lepenies B, Kolenbrander A, Temchura V, Iijima K, Kobayashi J, Ishizaka Y. Proceedings of the Frontiers of Retrovirology Conference 2016. Retrovirology 2016. [PMCID: PMC5046194 DOI: 10.1186/s12977-016-0294-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Oral presentations Session 1: Entry & uncoating O1 Host cell polo-like kinases (PLKs) promote early prototype foamy virus (PFV) replication Irena Zurnic, Sylvia Hütter, Ute Lehmann, Nicole Stanke, Juliane Reh, Tobias Kern, Fabian Lindel, Gesche Gerresheim, Martin Hamann, Erik Müllers, Paul Lesbats, Peter Cherepanov, Erik Serrao, Alan Engelman, Dirk Lindemann O2 A novel entry/uncoating assay reveals the presence of at least two species of viral capsids during synchronized HIV-1 infection Claire Da Silva Santos, Kevin Tartour, Andrea Cimarelli O3 Dynamics of nuclear envelope association and nuclear import of HIV-1 complexes Rya Burdick, Jianbo Chen, Jaya Sastri, Wei-Shau Hu, Vinay Pathak O4 Human papillomavirus protein E4 potently enhances the susceptibility to HIV infection Oliver T. Keppler Session 2: Reverse transcription & integration O5 Structure and function of HIV-1 integrase post translational modifications Karine Pradeau, Sylvia Eiler, Nicolas Levy, Sarah Lennon, Sarah Cianferani, Stéphane Emiliani, Marc Ruff O6 Regulation of retroviral integration by RNA polymerase II associated factors and chromatin structure Vincent Parissi Session 3: Transcription and latency O7 A novel single-cell analysis pipeline to identify specific biomarkers of HIV permissiveness Sylvie Rato, Antonio Rausell, Miguel Munoz, Amalio Telenti, Angela Ciuffi O8 A capsid-dependent integration program linking T cell activation to HIV-1 gene expression Alexander Zhyvoloup, Anat Melamed, Ian Anderson, Delphine Planas, Janos Kriston-Vizi, Robin Ketteler, Chen-Hsuin Lee, Andy Merritt, Petronela Ancuta, Charles Bangham, Ariberto Fassati O9 Characterisation of new RNA polymerase III and RNA polymerase II transcriptional promoters in the Bovine Leukemia Virus genome Anthony Rodari, Benoit Van Driessche, Mathilde Galais, Nadége Delacourt, Sylvain Fauquenoy, Caroline Vanhulle, Anna Kula, Arsène Burny, Olivier Rohr, Carine Van Lint O10 Tissue-specific dendritic cells differentially modulate latent HIV-1 reservoirs Thijs van Montfort, Renee van der Sluis, Dave Speijer, Ben Berkhout Session 4: RNA trafficking & packaging O11 A novel cis-acting element affecting HIV replication Bo Meng, Andrzej Rutkowski, Neil Berry, Lars Dölken, Andrew Lever O12 Tolerance of HIV’s late gene expression towards stepwise codon adaptation Thomas Schuster, Benedikt Asbach, Ralf Wagner Session 5: Assembly & release O13 Importance of the tax-inducible actin-bundling protein fascin for transmission of human T cell leukemia virus Type 1 (HTLV-1) Christine Gross, Veit Wiesmann, Martina Kalmer, Thomas Wittenberg, Jan Gettemans, Andrea K. Thoma-Kress O14 Lentiviral nef proteins antagonize TIM-mediated inhibition of viral release Minghua Li, Eric O. Freed, Shan-Lu Liu Session 6: Pathogenesis & evolution O15 SEVI and semen prolong the half-life of HIV-1 Janis Müller, Jan Münch O16 CD169+ macrophages mediate retrovirus trans-infection of permissive lymphocytes to establish infection in vivo Xaver Sewald, Pradeep Uchil, Mark Ladinsky, Jagadish Beloor, Ruoxi Pi, Christin Herrmann, Nasim Motamedi, Thomas Murooka, Michael Brehm, Dale Greiner, Thorsten Mempel, Pamela Bjorkman, Priti Kumar, Walther Mothes O17 Efficient replication of a vpu containing SIVagm construct in African Green Monkeys requires an HIV-1 nef gene Simone Joas, Erica Parrish, Clement Wesley Gnanadurai, Edina Lump, Christina M. Stürzel, Nicholas F. Parrish, Ulrike Sauermann, Katharina Töpfer, Tina Schultheiss, Steven Bosinger, Guido Silvestri, Cristian Apetrei, Nicholas Huot, Michaela Müller-Trutwin, Daniel Sauter, Beatrice H. Hahn, Christiane Stahl-Hennig, Frank Kirchhoff O18 Reprogramming initiates mobilization of endogenous mutagenic LINE-1, Alu and SVA retrotransposons in human induced pluripotent stem cells with consequences for host gene expression Gerald Schumann, Sabine Jung-Klawitter, Nina V. Fuchs, Kyle R. Upton, Martin Muñoz-Lopez, Ruchi Shukla, Jichang Wang, Marta Garcia-Canadas, Cesar Lopez-Ruiz, Daniel J. Gerhardt, Attila Sebe, Ivana Grabundzija, Patricia Gerdes, Sylvia Merkert, Andres Pulgarin, Anja Bock, Ulrike Held, Anett Witthuhn, Alexandra Haase, Ernst J. Wolvetang, Ulrich Martin, Zoltán Ivics, Zsuzsanna Izsvák, J. Garcia-Perez, Geoffrey J. Faulkner O19 NF-κB activation induces expression of human endogenous retrovirus and particle production Tara Hurst, Aris Katzourakis, Gkikas Magiorkinis Session 7a and b: Innate sensing & intrinsic immunity O20 Identification of the phosphatase acting on T592 in SAMHD1 during M/G1 transition Kerstin Schott, Rita Derua, Janna Seifried, Andreas Reuter, Heike Schmitz, Christiane Tondera, Alberto Brandariz-Nuñez, Felipe Diaz-Griffero, Veerle Janssens, Renate König O21 Vpx overcomes a SAMHD1-independent block to HIV reverse transcription that is specific to resting CD4 T cells Hanna-Mari Baldauf, Lena Stegmann, Sarah-Marie Schwarz, Maud Trotard, Margarethe Martin, Gina Lenzi, Manja Burggraf, Xiaoyu Pan, Oliver I. Fregoso, Efrem S. Lim, Libin Abraham, Elina Erikson, Laura Nguyen, Ina Ambiel, Frank Rutsch, Renate König, Baek Kim, Michael Emerman, Oliver T. Fackler, Oliver T. Keppler O22 The role of SAMHD1 in antiviral restriction and immune sensing in the mouse Sabine Wittmann, Rayk Behrendt, Bianca Volkmann, Kristin Eissmann, Thomas Gramberg O23 T cells expressing reduced restriction factors are preferentially infected in therapy naïve HIV-1 patients Sebastian Bolduan, Herwig Koppensteiner, Stefanie Regensburg, Ruth Brack-Werner, Rika Draenert, Michael Schindler O24 cGAS-mediated innate immunity spreads through HIV-1 env-induced membrane fusion sites from infected to uninfected primary HIV-1 target cells Aurélie Ducroux, Shuting Xu, Aparna Ponnurangam, Sergej Franz, Angelina Malassa, Ellen Ewald, Christine Goffinet O25 Perturbation of innate RNA and DNA sensing by human T cell leukemia virus type 1 oncoproteins Sin-Yee Fung, Ching-Ping Chan, Chun-Kit Yuen, Kin-Hang Kok, Chin-Ping Chan, Dong-Yan Jin O26 Induction and anti-viral activity of Interferon α subtypes in HIV-1 infection Ulf Dittmer O27 Vpu-mediated counteraction of tetherin is a major determinant of HIV-1 interferon resistance Dorota Kmiec, Shilpa Iyer, Christina Stürzel, Daniel Sauter, Beatrice Hahn, Frank Kirchhoff O28 DNA repair protein Rad18 restricts HIV-1 and LINE-1 life cycle Yasuo Ariumi, Mariko Yasuda-Inoue, Koudai Kawano, Satoshi Tateishi, Priscilla Turelli O29 Natural mutations in IFITM3 allow escape from post-translational regulation and toggle antiviral specificity Alex Compton, Nicolas Roy, Françoise Porrot, Anne Billet, Nicoletta Casartelli, Jacob Yount, Chen Liang, Oliver Schwartz Session 8: Adaptive immunity & immune evasion O30 Observing evolution in HIV-1 infection: phylogenetics and mutant selection windows to infer the influence of the autologous antibody response on the viral quasispecies Carsten Magnus, Lucia Reh, Penny Moore, Therese Uhr, Jacqueline Weber, Lynn Morris, Alexandra Trkola O31 Dose and subtype specific analyses of the anti-HIV effects of IFN-alpha family members Rashel V. Grindberg, Erika Schlaepfer, Gideon Schreiber, Viviana Simon, Roberto F. Speck Session 9: Novel antiviral strategies O32 LEDGIN-mediated inhibition of the integrase-LEDGF/p75 interaction reduces reactivation of residual latent HIV Zeger Debyser, Lenard Vranckx, Jonas Demeulemeester, Suha Saleh, Eric Verdin, Anna Cereseto, Frauke Christ, Rik Gijsbers O33 NKG2D-mediated clearance of reactivated viral reservoirs by natural killer cells O34 Inhibition of HIV reactivation in brain cells by AAV-mediated delivery of CRISPR/Cas9 O35 CRISPR-Cas9 as antiviral: potent HIV-1 inhibition, but rapid virus escape and the subsequent design of escape-proof antiviral strategies Ben Berkhout, Gang Wang, Na Zhao, Atze T. Das Session 10: Recent advances in HIV vaccine development O36 Priming with a potent HIV-1 DNA vaccine frames the quality of T cell and antibody responses prior to a poxvirus and protein boost Benedikt Asbach, Josef Köstler, Beatriz Perdiguero, Mariano Esteban, Bertram L. Jacobs, David C. Montefiori, Celia C. LaBranche, Nicole L. Yates, Georgia D. Tomaras, Guido Ferrari, Kathryn E. Foulds, Mario Roederer, Gary Landucci, Donald N. Forthal, Michael S. Seaman, Natalie Hawkins, Steven G. Self, Sanjay Phogat, James Tartaglia, Susan W. Barnett, Brian Burke, Anthony D. Cristillo, Song Ding, Jonathan L. Heeney, Giuseppe Pantaleo, Ralf Wagner O37 Passive immunisation with a neutralising antibody against HIV-1 Env prevents infection of the first cells in a mucosal challenge rhesus monkey model Christiane Stahl-Hennig, Viktoria Stab, Armin Ensser, Ulrike Sauermann, Bettina Tippler, Dennis Burton, Matthias Tenbusch, Klaus Überla O38 HIV antibody Fc-glycoforms drive B cell affinity maturation Galit Alter, Giuseppe Lofano, Anne-Sophie Dugast, Viraj Kulkarni, Todd Suscovich Poster presentations Topic 1: Entry & uncoating P1 Dynein light chain is required for murine leukemia virus infection Tatiana Opazo, Felipe Barraza, Diego Herrera, Andrea Garces, Tomas Schwenke, Diego Tapia, Jorge Cancino, Gloria Arriagada P2 Peptide paratope mimics of the broadly neutralising HIV-1 antibody b12 Christina Haußner, Dominik Damm, Anette Rohrhofer, Barbara Schmidt, Jutta Eichler P3 Investigating cellular pathways involved in the transmission of HIV-1 between dendritic cells and T cells using RNAi screening techniques Rebecca Midgley, James Wheeldon, Vincent Piguet P4 Co-receptor tropism in HIV-1, HIV-2 monotypic and dual infections Priyanka Khopkar, Megha Rohamare, Smita Kulkarni P5 Characterisation of the role of CIB1 and CIB2 as HIV-1 helper factors Ana Godinho-Santos, Allan Hance, Joao Goncalves, Fabrizio Mammano P6 Buffering deleterious polymorphisms in the highly constrained C2 region of HIV-1 envelope by the flexible V3 domain Romain Gasser, Meriem Hamoudi, Martina Pellicciotta, Zhicheng Zhou, Clara Visdeloup, Philippe Colin, Martine Braibant, Bernard Lagane, Matteo Negroni P7 Entry inhibition of HERV-K(HML-2) by an Env-IgG fusion protein Jula Wamara, Norbert Bannert Topic 2: Reverse transcription & integration P8 The R263K/H51Y resistance substitutions in HIV integrase decreases levels of integrated HIV DNA over time Thibault Mesplede, Nathan Osman, Kaitlin Anstett, Jiaming Calvin Liang, Hanh Thi Pham, Mark Wainberg P9 The Retrovirus Integration Database (RID) Wei Shao, Jigui Shan, Mary Kearney, Xiaolin Wu, Frank Maldarelli, John Mellors, Brian Luke, John Coffin, Stephen Hughes P10 The small molecule 3G11 inhibits HIV-1 reverse transcription Thomas Fricke, Silvana Opp, Caitlin Shepard, Dmitri Ivanov, Baek Kim, Jose Valle-Casuso, Felipe Diaz-Griffero P11 Dual and opposite regulation of HIV-1 integration by hRAD51: impact on therapeutical approaches using homologous DNA repair modulators Vincent Parissi P12 A flexible motif essential for integration by HIV-1 integrase Marine Kanja, Pierre Cappy, Matteo Negroni, Daniela Lener P13 Interaction between HIV-1 integrase and the host protein Ku70: identification of the binding site and study of the influence on integrase-proteasome interplay Ekaterina Knyazhanskaya, Andrey Anisenko, Timofey Zatsepin, Marina Gottikh P14 Normalisation based method for deep sequencing of somatic retroelement integrations in human genome Alexander Komkov, Anastasia Minervina, Gaiaz Nugmanov, Vadim Nazarov, Konstantin Khodosevich, Ilgar Mamedov, Yuri Lebedev Topic 3: Transcription and latency P15 BCA2/RABRING7 restricts HIV-1 transcription by preventing the nuclear translocation of NF-κB Marta Colomer-Lluch, Ruth Serra-Moreno P16 MATR3 post-transcriptional regulation of HIV-1 transcription during latency Ambra Sarracino, Anna Kula, Lavina Gharu, Alexander Pasternak, Carine Van Lint, Alessandro Marcello P17 HIV-1 tat intersects the SUMO pathway to regulate HIV-1 promoter activity Ann Marie McCartin, Anurag Kulkarni, Valentin Le Douce, Virginie Gautier P18 Conservation in HIV-1 Vpr guides tertiary gRNA folding and alternative splicing Ann Baeyens, Evelien Naessens, Anouk Van Nuffel, Karin Weening, Anne-Marie Reilly, Eva Claeys, Wim Trypsteen, Linos Vandekerckhove, Sven Eyckerman, Kris Gevaert, Bruno Verhasselt P19 The majority of reactivatable latent HIV are genetically distinct Hoi Ping Mok, Nicholas Norton, Axel Fun, Jack Hirst, Mark Wills, Andrew Lever P20 Do mutations in the tat exonic splice enhancer contribute to HIV-1 latency? Nicholas Norton, Hoi Ping Mok, Jack Hirst, Andrew Lever P21 Culture-to-Ct: A fast and direct RT-qPCR HIV gene reactivation screening method using primary T cell culture Valentin Le Douce, Ann Marie McCartin, Virginie Gautier P22 A novel approach to define populations of early silenced proviruses Dalibor Miklik, Filip Senigl, Jiri Hejnar Topic 4: RNA trafficking & packaging P23 Functional analysis of the structure and conformation of HIV-1 genome RNA DIS Jun-ichi Sakuragi, Sayuri Sakuragi, Masaru Yokoyama, Tatsuo Shioda, Hironori Sato P24 Regulation of foamy viral env splicing controls gag and pol expression Jochen Bodem, Rebecca Moschall, Sarah Denk, Steffen Erkelenz, Christian Schenk, Heiner Schaal Topic 5: Assembly & release P25 Transfer of HTLV-1 p8 to target T cells depends on VASP: a novel interaction partner of p8 Norbert Donhauser, Ellen Socher, Sebastian Millen, Heinrich Sticht, Andrea K. Thoma-Kress P26 COL4A1 and COL4A2 are novel HTLV-1 tax targets with a putative role in virus transmission Christine Gross, Sebastian Millen, Melanie Mann, Klaus Überla, Andrea K. Thoma-Kress P27 The C terminus of foamy virus gag protein is required for particle formation, and virus budding: starting assembly at the C terminus? Guochao Wei, Matthew J. Betts, Yang Liu, Timo Kehl, Robert B. Russell, Martin Löchelt P28 Generation of an antigen-capture ELISA and analysis of Rec and Staufen-1 effects on HERV-K(HML-2) virus particle production Oliver Hohn, Saeed Mostafa, Kirsten Hanke, Stephen Norley, Norbert Bannert P29 Antagonism of BST-2/tetherin is a conserved function of primary HIV-2 Env glycoproteins Chia-Yen Chen, Masashi Shingai, Pedro Borrego, Nuno Taveira, Klaus Strebel P30 Mutations in the packaging signal region of the HIV-1 genome cause a late domain mutant phenotype Chris Hellmund, Bo Meng, Andrew Lever P31 p6 regulates membrane association of HIV-1 gag Melanie Friedrich, Friedrich Hahn, Christian Setz, Pia Rauch, Kirsten Fraedrich, Alina Matthaei, Petra Henklein, Maximilian Traxdorf, Torgils Fossen, Ulrich Schubert Topic 6: Pathogenesis & evolution P32 Molecular and structural basis of protein evolution during viral adaptation Aya Khwaja, Meytal Galilee, Akram Alian P33 HIV-1 enhancement and neutralisation by soluble gp120 and its role for the selection of the R5-tropic “best fit” Birco Schwalbe, Heiko Hauser, Michael Schreiber P34 An insertion of seven amino acids in the Env cytoplasmic tail of Human Immunodeficiency Virus type 2 (HIV-2) selected during disease progression enhances viral replication François Dufrasne, Mara Lucchetti, Patrick Goubau, Jean Ruelle P35 Cell-associated HIV-1 unspliced to multiply spliced RNA ratio at 12 weeks ART correlates with markers of immune activation and apoptosis and predicts the CD4 T-cell count at 96 weeks ART Mirte Scherpenisse, Ben Berkhout, Alexander Pasternak P36 Faster progression in non-B subtype HIV-1-infected patients than Korean subclade of subtype B is accompanied by higher variation and no induction of gross deletion in non-B nef gene by Korean red ginseng treatment Young-Keol Cho, Jungeun Kim, Daeun Jeong P37 Aberrant expression of ERVWE1 endogenous retrovirus and overexpression of TET dioxygenases are characteristic features of seminoma Katerina Trejbalova, Martina Benesova, Dana Kucerova, Zdenka Vernerova, Rachel Amouroux, Petra Hajkova, Jiri Hejnar P38 Life history of the oldest lentivirus: characterisation of ELVgv integrations and the TRIM5 selection pattern in dermoptera Daniel Elleder, Tomas Hron, Helena Farkasova, Abinash Padhi, Jan Paces P39 Characterisation of a highly divergent endogenous retrovirus in the equine germ line Henan Zhu, Robert Gifford, Pablo Murcia P40 The emergence of pandemic retroviral infection in small ruminants Maria Luisa Carrozza, Anna-Maria Niewiadomska, Maurizio Mazzei, Mounir Abi-Said, Joseph Hughes, Stéphane Hué, Robert Gifford P41 Near full-length genome (NFLG) Characterisation of HIV-1 subtype B identified in South Africa Adetayo Obasa, Graeme Jacobs, Susan Engelbrecht P42 Acquisition of Vpu-mediated tetherin antagonism by an HIV-1 group O strain Katharina Mack, Kathrin Starz, Daniel Sauter, Matthias Geyer, Frederic Bibollet-Ruche, Christina Stürzel, Marie Leoz, Jean Christophe Plantier, Beatrice H. Hahn, Frank Kirchhoff P43 The human endogenous retrovirus type K is involved in cancer stem cell markers expression and in human melanoma malignancy Ayele Argaw-Denboba, Emanuela Balestrieri, Annalucia Serafino, Ilaria Bucci, Chiara Cipriani, Corrado Spadafora, Paolo Sinibaldi-Vallebona, Claudia Matteucci P44 Natural infection of Indian non-human primates by unique lentiviruses S. Nandi Jayashree, Ujjwal Neogi, Anil K. Chhangani, Shravan Sing Rathore, Bajrang R. J. Mathur P45 Free cervical cancer screening among HIV-positive women receiving antiretroviral treatment in Nigeria Adeyemi Abati P46 Molecular evolutionary status of feline immunodeficiency virus in Turkey B. Taylan Koç, Tuba Çiğdem Oğuzoğlu Topic 7: Innate sensing & intrinsic immunity P47 Cell-to-cell contact with HTLV-1-infected T cells reduces dendritic cell immune functions and contributes to infection in trans. Takatoshi Shimauchi, Stephan Caucheteux, Jocelyn Turpin, Katja Finsterbusch, Charles Bangham, Yoshiki Tokura, Vincent Piguet P48 Deciphering the mechanisms of HIV-1 exacerbation induced by Mycobacterium tuberculosis in monocytes/macrophages Shanti Souriant, Luciana Balboa, Karine Pingris, Denise Kviatcowsky, Brigitte Raynaud-Messina, Céline Cougoule, Ingrid Mercier, Marcelo Kuroda, Pablo González-Montaner, Sandra Inwentarz, Eduardo Jose Moraña, Maria del Carmen Sasiain, Olivier Neyrolles, Isabelle Maridonneau-Parini, Geanncarlo Lugo-Villarino, Christel Vérollet P49 The SAMHD1-mediated inhibition of LINE-1 retroelements is regulated by phosphorylation Alexandra Herrmann, Sabine Wittmann, Caitlin Shepard, Dominique Thomas, Nerea Ferreirós Bouzas, Baek Kim, Thomas Gramberg P50 Activities of nuclear envelope protein SUN2 in HIV infection Xavier Lahaye, Anvita Bhargava, Takeshi Satoh, Matteo Gentili, Silvia Cerboni, Aymeric Silvin, Cécile Conrad, Hakim Ahmed-Belkacem, Elisa C. Rodriguez, Jean-François Guichou, Nathalie Bosquet, Matthieu Piel, Roger Le Grand, Megan King, Jean-Michel Pawlotsky, Nicolas Manel P51 Activation of TLR7/8 with a small molecule agonist induces a novel restriction to HIV-1 infection of monocytes Henning Hofmann, Benedicte Vanwalscappel, Nicolin Bloch, Nathaniel Landau P52 Steady state between the DNA polymerase and Rnase H domain activities of reverse transcriptases determines the sensitivity of retroviruses to inhibition by APOBEC3 proteins Stanislav Indik, Benedikt Hagen P53 HIV restriction in mature dendritic cells is related to p21 induction and p21-mediated control of the dNTP pool and SAMHD1 activity. José Carlos Valle-Casuso, Awatef Allouch, Annie David, Françoise Barré-Sinoussi, Michaela Müller-Trutwin, Monsef Benkirane, Gianfranco Pancino, Asier Saez-Cirion P54 IFITM protens restrict HIV-1 protein synthesis Wing-Yiu Lee, Chen Liang, Richard Sloan P55 Characterisation and functional analysis of the novel restriction factor Serinc5 Bianca Schulte, Silvana Opp, Felipe Diaz-Griffero P56 piRNA sequences are common in Human Endogenous Retroviral Sequences (HERVs): An antiretroviral restriction mechanism? Jonas Blomberg, Luana Vargiu, Patricia Rodriguez-Tomé, Enzo Tramontano, Göran Sperber P57 Ferroportin restricts HIV-1 infection in sickle cell disease Namita Kumari, Tatiana Ammosova, Sharmeen Diaz, Patricia Oneal, Sergei Nekhai P58 APOBEC3G modulates the response to antiretroviral drugs in humanized mice Audrey Fahrny, Gustavo Gers-Huber, Annette Audigé, Roberto F. Speck, Anitha Jayaprakash, Ravi Sachidanandam, Matt Hernandez, Marsha Dillon-White, Viviana Simon P59 High-throughput epigenetic analysis of evolutionarily young endogenous retrovirus presents in the mule deer (Odocoileus hemionus) genome Tomas Hron, Helena Farkasova, Daniel Elleder P60 Characterisation of the expression of novel endogenous retroviruses and immune interactions in a macaque model Neil Berry, Emmanuel Maze, Claire Ham, Neil Almond, Greg Towers, Robert Belshaw P61 HIV-1 restriction by orthologs of SERINC3 and SERINC5 Patrícia de Sousa-Pereira, Joana Abrantes, Massimo Pizzato, Pedro J. Esteves, Oliver T. Fackler, Oliver T. Keppler, Hanna-Mari Baldauf P62 TRIM19/PML restricts HIV infection in a cell type-dependent manner Bianca Volkmann, Tanja Kahle, Kristin Eissmann, Alexandra Herrmann, Sven Schmitt, Sabine Wittmann, Laura Merkel, Nina Reuter, Thomas Stamminger, Thomas Gramberg P63 Recent invasion of the mule deer genome by a retrovirus Helena Farkasova, Tomas Hron, Daniel Elleder P64 Does the antiviral protein SAMHD1 influence mitochondrial function? Ilaria Dalla Rosa, Kate Bishop, Antonella Spinazzola, Harriet Groom P65 cGAMP transfers intercellularly via HIV-1 Env-mediated cell–cell fusion sites and triggers an innate immune response in primary target cells Shuting Xu, Aurélie Ducroux, Aparna Ponnurangam, Sergej Franz, Gabrielle Vieyres, Mathias Müsken, Thomas Zillinger, Angelina Malassa, Ellen Ewald, Veit Hornung, Winfried Barchet, Susanne Häussler, Thomas Pietschmann, Christine Goffinet P66 Pre-infection transcript levels of FAM26F in PBMCS inform about overall plasma viral load in acute and postacute phase after SIV-infection Ulrike Sauermann, Aneela Javed, Nicole Leuchte, Gabriela Salinas, Lennart Opitz, Christiane Stahl-Hennig, Sieghart Sopper P67 Sequence-function analysis of three T cell receptors targeting the HIV-1 p17 epitope SLYNTVATL Christiane Mummert, Christian Hofmann, Angela G. Hückelhoven, Silke Bergmann, Sandra M. Müller-Schmucker, Ellen G. Harrer, Jan Dörrie, Niels Schaft, Thomas Harrer P68 An immunodominant region of the envelope glycoprotein of small ruminant lentiviruses may function as decoy antigen Laure Cardinaux, M.-L. Zahno, H.-R. Vogt, R. Zanoni, G. Bertoni P69 Impact of immune activation, immune exhaustion, broadly neutralising antibodies and viral reservoirs on disease progression in HIV-infected children Maximilian Muenchhoff, Philip Goulder, Oliver Keppler Topic 9: Novel antiviral strategies P70 Identification of natural compounds as new antiviral products by bioassay-guided fractionation Alexandra Herrmann, Stephanie Rebensburg, Markus Helfer, Michael Schindler, Ruth Brack-Werner P71 The PPARG antagonism disconnects the HIV replication and effector functions in Th17 cells Yuwei Zhang, Huicheng Chen, Delphine Planas, Annie Bernier, Annie Gosselin, Jean-Pierre Routy, Petronela Ancuta P72 Characterisation of a multiresistant subtype AG reverse transcriptase: AZT resistance, sensitivity to RNase H inhibitors and inhibitor binding Birgitta Wöhrl, Anna Schneider, Angela Corona, Imke Spöring, Mareike Jordan, Bernd Buchholz, Elias Maccioni, Roberto Di Santo, Jochen Bodem, Enzo Tramontano, Kristian Schweimer P73 Insigths into the acetylation pattern of HDAC inhibitors and their potential role in HIV therapy Christian Schölz, Brian Weinert, Sebastian Wagner, Petra Beli, Yasuyuki Miyake, Jun Qi, Lars Jensen, Werner Streicher, Anna McCarthy, Nicholas Westwood, Sonia Lain, Jürgen Cox, Patrick Matthias, Matthias Mann, James Bradner, Chunaram Choudhary P74 HPV-derived and seminal amyloid peptides enhance HIV-1 infection and impair the efficacy of broadly neutralising antibodies and antiretroviral drugs Marcel Stern, Oliver T. Keppler P75 D(−)lentiginosine inhibits both proliferation and virus expression in cells infected by HTLV-1 in vitro Elena Valletta, Caterina Frezza, Claudia Matteucci, Francesca Marino-Merlo, Sandro Grelli, Anna Lucia Serafino, Antonio Mastino, Beatrice Macchi P76 HIV-1 resistance analyses of the Cape Winelands districts, South Africa Sello Mikasi, Graeme Jacobs, Susan Engelbrecht Topic 10: Recent advances in HIV vaccine development P77 Induction of complex retrovirus antigen-specific immune responses by adenovirus-based vectors depends on the order of vector administration Meike Kaulfuß, Sonja Windmann, Wibke Bayer P78 Direct impact of structural properties of HIV-1 Env on the regulation of the humoral immune response Rebecca Heß, Michael Storcksdieck gen. Bonsmann, Viktoria Stab, Carsten Kirschning, Bernd Lepenies, Matthias Tenbusch, Klaus Überla P79 Lentiviral virus-like particles mediate gerenration of T-follicular helper cells in vitro Anne Kolenbrander, Klaus Überla, Vladimir Temchura P80 Recruitment of HIV-1 Vpr to DNA damage sites and protection of proviral DNA from nuclease activity Kenta Iijima, Junya Kobayashi, Yukihito Ishizaka
Collapse
|
38
|
Wagner SA, Beli P, Serve H. Abstract 3888: Systematic characterization of aberrant signaling induced by oncogenic fusions in non-small cell lung cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-3888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent studies have greatly expanded the knowledge about genetic alterations in non-small cell lung cancer (NSCLC). Gene fusions involving the tyrosine kinases ALK, ROS and RET are found in 5 - 10% of NSCLC patients and are considered as oncogenic drivers. However, the cellular signaling activated downstream of oncogenic fusions has not been systematically investigated and it remains unclear if different fusions induce specific targetable signaling patterns.
In this study we have employed quantitative mass spectrometry (MS)-based phosphoproteomics to systematically characterize the signaling induced by oncogenic fusions frequently found in NSCLC. To this end, cDNA sequences of oncogenic fusions containing the tyrosine kinases ALK, ROS and RET and different fusion partners were constructed and ectopically expressed in HEK 293 and lung cancer cell lines. Subsequently, tyrosine phosphorylated peptides were enriched and identified by LC-MS. Stable isotope labeling with amino acids in cell culture was employed to precisely quantify the abundance of phosphorylation sites in cells expressing different oncogenic fusions.
Our data demonstrate that all investigated oncogenic fusions induce massive tyrosine phosphorylation of proteins and lead to increased phosphorylation of the majority of all quantified phospho-tyrosine sites. For instance, we quantified ∼1300 unique phosphotyrosine sites from HEK 293 cells expressing EML4-ALK. Of those, 952 increased more than 4-fold in abundance. Comparative analyses of the signaling patterns allowed defining kinase-specific phosphorylation signatures. In addition, comparison of signaling patterns induced by different fusions permitted us to investigate the contribution of the non-kinase fusion partner to the downstream signaling. We were able to identify several phosphorylation events that were associated with specific non-kinase fusion partners. For example, kinase fusions containing the kinesin-1 heavy chain (KIF5B) specifically led to phosphorylation of cytoskeletal proteins, including cytoskeleton-associated protein 5 (CKAP5). We are currently investigating the functional role of these phosphorylation events for the oncogenic transformation.
In summary, we demonstrate that MS-based phosphoproteomics is a powerful tool to investigate aberrant signaling induced by oncogenic fusions in non-small cell lung cancer. Importantly, we find that the kinases involved in the oncogenic fusions largely define the downstream signaling and that the investigated fusion partners only exhibited a minor effect on the downstream signaling.
Citation Format: Sebastian A. Wagner, Petra Beli, Hubert Serve. Systematic characterization of aberrant signaling induced by oncogenic fusions in non-small cell lung cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3888.
Collapse
Affiliation(s)
| | - Petra Beli
- 2Insitute of Molecular Biology (IMB), Mainz, Germany
| | - Hubert Serve
- 1Goethe University Frankfurt, Frankfurt, Germany
| |
Collapse
|
39
|
Wagner SA, Satpathy S, Beli P, Choudhary C. SPATA2 links CYLD to the TNF-α receptor signaling complex and modulates the receptor signaling outcomes. EMBO J 2016; 35:1868-84. [PMID: 27307491 DOI: 10.15252/embj.201694300] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/31/2016] [Indexed: 11/09/2022] Open
Abstract
TNF-α is a key regulator of innate immune and proinflammatory responses. However, the composition of the TNF-α receptor-associated signaling complexes (TNF-RSC) and the architecture of the downstream signaling networks are incompletely understood. We employed quantitative mass spectrometry to demonstrate that TNF-α stimulation induces widespread protein phosphorylation and that the scope of phosphorylation expands in a temporal manner. TNF-α stimulation also induces rapid ubiquitylation of components of the TNF-RSC Temporal analysis of the TNF-RSC composition identified SPATA2 as a novel component of the TNF-RSC The predicted PUB domain in the N-terminus of SPATA2 interacts with the USP domain of CYLD, whereas the C-terminus of SPATA2 interacts with HOIP SPATA2 is required for recruitment of CYLD to the TNF-RSC Downregulation of SPATA2 augments transcriptional activation of NF-κB and inhibits TNF-α-induced necroptosis, pointing to an important function of SPATA2 in modulating the outcomes of TNF-α signaling. Taken together, our study draws a detailed map of TNF-α signaling, identifies SPATA2 as a novel component of TNF-α signaling, and provides a rich resource for further functional investigations.
Collapse
Affiliation(s)
- Sebastian A Wagner
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark Department of Medicine, Hematology/Oncology, Goethe University School of Medicine, Frankfurt, Germany German Cancer Consortium (DKTK), Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Shankha Satpathy
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Petra Beli
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark Institute of Molecular Biology (IMB), Mainz, Germany
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
40
|
Heidelberger JB, Wagner SA, Beli P. Mass Spectrometry-Based Proteomics for Investigating DNA Damage-Associated Protein Ubiquitylation. Front Genet 2016; 7:109. [PMID: 27379159 PMCID: PMC4905943 DOI: 10.3389/fgene.2016.00109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/30/2016] [Indexed: 11/13/2022] Open
Abstract
Modification of proteins with the 76 amino acid protein ubiquitin plays essential roles in cellular signaling. Development of methods for specific enrichment of ubiquitin remnant peptides and advances in high-resolution mass spectrometry have enabled proteome-wide identification of endogenous ubiquitylation sites. Moreover, ubiquitin remnant profiling has emerged as a powerful approach for investigating changes in protein ubiquitylation in response to cellular perturbations, such as DNA damage, as well as for identification of substrates of ubiquitin-modifying enzymes. Despite these advances, interrogation of ubiquitin chain topologies on substrate proteins remains a challenging task. Here, we describe mass spectrometry-based approaches for quantitative analyses of site-specific protein ubiquitylation and highlight recent studies that employed these methods for investigation of ubiquitylation in the context of the cellular DNA damage response. Furthermore, we provide an overview of experimental strategies for probing ubiquitin chain topologies on proteins and discuss how these methods can be applied to analyze functions of ubiquitylation in the DNA damage response.
Collapse
Affiliation(s)
| | - Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Germany
| | - Petra Beli
- Institute of Molecular Biology Mainz, Germany
| |
Collapse
|
41
|
Yang J, Wagner SA, Beli P. Illuminating Spatial and Temporal Organization of Protein Interaction Networks by Mass Spectrometry-Based Proteomics. Front Genet 2015; 6:344. [PMID: 26648978 PMCID: PMC4665136 DOI: 10.3389/fgene.2015.00344] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/20/2015] [Indexed: 11/13/2022] Open
Abstract
Protein–protein interactions are at the core of all cellular functions and dynamic alterations in protein interactions regulate cellular signaling. In the last decade, mass spectrometry (MS)-based proteomics has delivered unprecedented insights into human protein interaction networks. Affinity purification-MS (AP-MS) has been extensively employed for focused and high-throughput studies of steady state protein–protein interactions. Future challenges remain in mapping transient protein interactions after cellular perturbations as well as in resolving the spatial organization of protein interaction networks. AP-MS can be combined with quantitative proteomics approaches to determine the relative abundance of purified proteins in different conditions, thereby enabling the identification of transient protein interactions. In addition to affinity purification, methods based on protein co-fractionation have been combined with quantitative MS to map transient protein interactions during cellular signaling. More recently, approaches based on proximity tagging that preserve the spatial dimension of protein interaction networks have been introduced. Here, we provide an overview of MS-based methods for analyzing protein–protein interactions with a focus on approaches that aim to dissect the temporal and spatial aspects of protein interaction networks.
Collapse
Affiliation(s)
- Jiwen Yang
- Institute of Molecular Biology , Mainz, Germany
| | - Sebastian A Wagner
- Department of Medicine, Hematology and Oncology, Goethe University , Frankfurt, Germany
| | - Petra Beli
- Institute of Molecular Biology , Mainz, Germany
| |
Collapse
|
42
|
Tollenaere MAX, Villumsen BH, Blasius M, Nielsen JC, Wagner SA, Bartek J, Beli P, Mailand N, Bekker-Jensen S. p38- and MK2-dependent signalling promotes stress-induced centriolar satellite remodelling via 14-3-3-dependent sequestration of CEP131/AZI1. Nat Commun 2015; 6:10075. [PMID: 26616734 PMCID: PMC4674683 DOI: 10.1038/ncomms10075] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/30/2015] [Indexed: 12/26/2022] Open
Abstract
Centriolar satellites (CS) are small granular structures that cluster in the vicinity of centrosomes. CS are highly susceptible to stress stimuli, triggering abrupt displacement of key CS factors. Here we discover a linear p38-MK2-14-3-3 signalling pathway that specifically targets CEP131 to trigger CS remodelling after cell stress. We identify CEP131 as a substrate of the p38 effector kinase MK2 and pinpoint S47 and S78 as critical MK2 phosphorylation sites in CEP131. Ultraviolet-induced phosphorylation of these residues generates direct binding sites for 14-3-3 proteins, which sequester CEP131 in the cytoplasm to block formation of new CS, thereby leading to rapid depletion of these structures. Mutating S47 and S78 in CEP131 is sufficient to abolish stress-induced CS reorganization, demonstrating that CEP131 is the key regulatory target of MK2 and 14-3-3 in these structures. Our findings reveal the molecular mechanism underlying dynamic CS remodelling to modulate centrosome functions on cell stress. Centriolar satellites (CS) dynamically remodel in response to cellular stress. Here the authors describe a mechanism for stress-mediated remodelling, whereby CEP131 is phosphorylated downstream of p38, creating binding sites for 14-3-3 that lead to the sequestration of CEP131 in the cytoplasm and disassembly of CS.
Collapse
Affiliation(s)
- Maxim A X Tollenaere
- Ubiquitin Signaling Group, Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark
| | - Bine H Villumsen
- Ubiquitin Signaling Group, Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark
| | - Melanie Blasius
- Danish Cancer Society Research Center, Strandboulevarden 49, Copenhagen DK-2100, Denmark
| | - Julie C Nielsen
- Ubiquitin Signaling Group, Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark
| | - Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University Medical School, Theodor-Stern-Kai 7, Frankfurt DE-60590, Germany
| | - Jiri Bartek
- Danish Cancer Society Research Center, Strandboulevarden 49, Copenhagen DK-2100, Denmark.,Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm SE-17176, Sweden
| | - Petra Beli
- Institute of Molecular Biology, Ackermannweg 4, Mainz DE-55128, Germany
| | - Niels Mailand
- Ubiquitin Signaling Group, Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark
| | - Simon Bekker-Jensen
- Ubiquitin Signaling Group, Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark
| |
Collapse
|
43
|
Schmidt CK, Galanty Y, Sczaniecka-Clift M, Coates J, Jhujh S, Demir M, Cornwell M, Beli P, Jackson SP. Systematic E2 screening reveals a UBE2D-RNF138-CtIP axis promoting DNA repair. Nat Cell Biol 2015; 17:1458-1470. [PMID: 26502057 PMCID: PMC4894550 DOI: 10.1038/ncb3260] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 09/22/2015] [Indexed: 12/27/2022]
Abstract
Ubiquitylation is crucial for proper cellular responses to DNA double-strand breaks (DSBs). If unrepaired, these highly cytotoxic lesions cause genome instability, tumorigenesis, neurodegeneration or premature ageing. Here, we conduct a comprehensive, multilayered screen to systematically profile all human ubiquitin E2 enzymes for impacts on cellular DSB responses. With a widely applicable approach, we use an exemplary E2 family, UBE2Ds, to identify ubiquitylation-cascade components downstream of E2s. Thus, we uncover the nuclear E3 ligase RNF138 as a key homologous recombination (HR)-promoting factor that functions with UBE2Ds in cells. Mechanistically, UBE2Ds and RNF138 accumulate at DNA-damage sites and act at early resection stages by promoting CtIP ubiquitylation and accrual. This work supplies insights into regulation of DSB repair by HR. Moreover, it provides a rich information resource on E2s that can be exploited by follow-on studies.
Collapse
Affiliation(s)
- Christine K Schmidt
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN Cambridge, UK
| | - Yaron Galanty
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN Cambridge, UK
| | - Matylda Sczaniecka-Clift
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN Cambridge, UK
| | - Julia Coates
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN Cambridge, UK
| | - Satpal Jhujh
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN Cambridge, UK
| | - Mukerrem Demir
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN Cambridge, UK
| | - Matthew Cornwell
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN Cambridge, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Stephen P Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN Cambridge, UK
- The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA Cambridge, UK
| |
Collapse
|
44
|
Affiliation(s)
- Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| |
Collapse
|
45
|
Satpathy S, Wagner SA, Beli P, Gupta R, Kristiansen TA, Malinova D, Francavilla C, Tolar P, Bishop GA, Hostager BS, Choudhary C. Systems-wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation. Mol Syst Biol 2015; 11:810. [PMID: 26038114 PMCID: PMC4501846 DOI: 10.15252/msb.20145880] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 04/30/2015] [Accepted: 05/06/2015] [Indexed: 12/02/2022] Open
Abstract
B-cell receptor (BCR) signaling is essential for the development and function of B cells; however, the spectrum of proteins involved in BCR signaling is not fully known. Here we used quantitative mass spectrometry-based proteomics to monitor the dynamics of BCR signaling complexes (signalosomes) and to investigate the dynamics of downstream phosphorylation and ubiquitylation signaling. We identify most of the previously known components of BCR signaling, as well as many proteins that have not yet been implicated in this system. BCR activation leads to rapid tyrosine phosphorylation and ubiquitylation of the receptor-proximal signaling components, many of which are co-regulated by both the modifications. We illustrate the power of multilayered proteomic analyses for discovering novel BCR signaling components by demonstrating that BCR-induced phosphorylation of RAB7A at S72 prevents its association with effector proteins and with endo-lysosomal compartments. In addition, we show that BCL10 is modified by LUBAC-mediated linear ubiquitylation, and demonstrate an important function of LUBAC in BCR-induced NF-κB signaling. Our results offer a global and integrated view of BCR signaling, and the provided datasets can serve as a valuable resource for further understanding BCR signaling networks.
Collapse
Affiliation(s)
- Shankha Satpathy
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sebastian A Wagner
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Petra Beli
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajat Gupta
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Trine A Kristiansen
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dessislava Malinova
- Division of Immune Cell Biology, MRC National Institute for Medical Research, Mill Hill, London, UK
| | - Chiara Francavilla
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pavel Tolar
- Division of Immune Cell Biology, MRC National Institute for Medical Research, Mill Hill, London, UK
| | - Gail A Bishop
- Department of Microbiology, Graduate Program in Immunology and Department of Internal Medicine, University of Iowa, Iowa City, IA, USA VAMC, Iowa City, IA, USA
| | - Bruce S Hostager
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
46
|
Brown JS, Lukashchuk N, Sczaniecka-Clift M, Britton S, le Sage C, Calsou P, Beli P, Galanty Y, Jackson SP. Neddylation promotes ubiquitylation and release of Ku from DNA-damage sites. Cell Rep 2015; 11:704-14. [PMID: 25921528 PMCID: PMC4431666 DOI: 10.1016/j.celrep.2015.03.058] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 11/12/2014] [Accepted: 03/25/2015] [Indexed: 11/24/2022] Open
Abstract
The activities of many DNA-repair proteins are controlled through reversible covalent modification by ubiquitin and ubiquitin-like molecules. Nonhomologous end-joining (NHEJ) is the predominant DNA double-strand break (DSB) repair pathway in mammalian cells and is initiated by DSB ends being recognized by the Ku70/Ku80 (Ku) heterodimer. By using MLN4924, an anti-cancer drug in clinical trials that specifically inhibits conjugation of the ubiquitin-like protein, NEDD8, to target proteins, we demonstrate that NEDD8 accumulation at DNA-damage sites is a highly dynamic process. In addition, we show that depleting cells of the NEDD8 E2-conjugating enzyme, UBE2M, yields ionizing radiation hypersensitivity and reduced cell survival following NHEJ. Finally, we demonstrate that neddylation promotes Ku ubiquitylation after DNA damage and release of Ku and Ku-associated proteins from damage sites following repair. These studies provide insights into how the NHEJ core complex dissociates from repair sites and highlight its importance for cell survival following DSB induction.
Collapse
Affiliation(s)
- Jessica S Brown
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK
| | - Natalia Lukashchuk
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK
| | - Matylda Sczaniecka-Clift
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK
| | - Sébastien Britton
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université de Toulouse-Université Paul Sabatier, Equipe Labellisée Ligue contre le Cancer, 31077 Toulouse, France
| | - Carlos le Sage
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK
| | - Patrick Calsou
- Institut de Pharmacologie et de Biologie Structurale, CNRS, Université de Toulouse-Université Paul Sabatier, Equipe Labellisée Ligue contre le Cancer, 31077 Toulouse, France
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany.
| | - Yaron Galanty
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK.
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK.
| |
Collapse
|
47
|
Gallina I, Colding C, Henriksen P, Beli P, Nakamura K, Offman J, Mathiasen DP, Silva S, Hoffmann E, Groth A, Choudhary C, Lisby M. Cmr1/WDR76 defines a nuclear genotoxic stress body linking genome integrity and protein quality control. Nat Commun 2015; 6:6533. [PMID: 25817432 PMCID: PMC4389229 DOI: 10.1038/ncomms7533] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 02/05/2015] [Indexed: 11/09/2022] Open
Abstract
DNA replication stress is a source of genomic instability. Here we identify changed mutation rate 1 (Cmr1) as a factor involved in the response to DNA replication stress in Saccharomyces cerevisiae and show that Cmr1--together with Mrc1/Claspin, Pph3, the chaperonin containing TCP1 (CCT) and 25 other proteins--define a novel intranuclear quality control compartment (INQ) that sequesters misfolded, ubiquitylated and sumoylated proteins in response to genotoxic stress. The diversity of proteins that localize to INQ indicates that other biological processes such as cell cycle progression, chromatin and mitotic spindle organization may also be regulated through INQ. Similar to Cmr1, its human orthologue WDR76 responds to proteasome inhibition and DNA damage by relocalizing to nuclear foci and physically associating with CCT, suggesting an evolutionarily conserved biological function. We propose that Cmr1/WDR76 plays a role in the recovery from genotoxic stress through regulation of the turnover of sumoylated and phosphorylated proteins.
Collapse
Affiliation(s)
- Irene Gallina
- Department of Biology, University of Copenhagen, Room 4.1.07, Copenhagen N DK-2200, Denmark
| | - Camilla Colding
- Department of Biology, University of Copenhagen, Room 4.1.07, Copenhagen N DK-2200, Denmark
| | - Peter Henriksen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Petra Beli
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Kyosuke Nakamura
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Judith Offman
- MRC, Centre for Genome Damage and Stability, School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
| | - David P Mathiasen
- Department of Biology, University of Copenhagen, Room 4.1.07, Copenhagen N DK-2200, Denmark
| | - Sonia Silva
- Department of Biology, University of Copenhagen, Room 4.1.07, Copenhagen N DK-2200, Denmark
| | - Eva Hoffmann
- MRC, Centre for Genome Damage and Stability, School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Chunaram Choudhary
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Room 4.1.07, Copenhagen N DK-2200, Denmark
| |
Collapse
|
48
|
Oka Y, Varmark H, Vitting‐Seerup K, Beli P, Waage J, Hakobyan A, Mistrik M, Choudhary C, Rohde M, Bekker‐Jensen S, Mailand N. UBL5 is essential for pre‐
mRNA
splicing and sister chromatid cohesion in human cells. EMBO Rep 2014. [DOI: 10.15252/embr.201439478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
|
49
|
Bursomanno S, Beli P, Khan AM, Minocherhomji S, Wagner SA, Bekker-Jensen S, Mailand N, Choudhary C, Hickson ID, Liu Y. Proteome-wide analysis of SUMO2 targets in response to pathological DNA replication stress in human cells. DNA Repair (Amst) 2014; 25:84-96. [PMID: 25497329 DOI: 10.1016/j.dnarep.2014.10.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/26/2014] [Accepted: 10/28/2014] [Indexed: 02/04/2023]
Abstract
SUMOylation is a form of post-translational modification involving covalent attachment of SUMO (Small Ubiquitin-like Modifier) polypeptides to specific lysine residues in the target protein. In human cells, there are four SUMO proteins, SUMO1-4, with SUMO2 and SUMO3 forming a closely related subfamily. SUMO2/3, in contrast to SUMO1, are predominantly involved in the cellular response to certain stresses, including heat shock. Substantial evidence from studies in yeast has shown that SUMOylation plays an important role in the regulation of DNA replication and repair. Here, we report a proteomic analysis of proteins modified by SUMO2 in response to DNA replication stress in S phase in human cells. We have identified a panel of 22 SUMO2 targets with increased SUMOylation during DNA replication stress, many of which play key functions within the DNA replication machinery and/or in the cellular response to DNA damage. Interestingly, POLD3 was found modified most significantly in response to a low dose aphidicolin treatment protocol that promotes common fragile site (CFS) breakage. POLD3 is the human ortholog of POL32 in budding yeast, and has been shown to act during break-induced recombinational repair. We have also shown that deficiency of POLD3 leads to an increase in RPA-bound ssDNA when cells are under replication stress, suggesting that POLD3 plays a role in the cellular response to DNA replication stress. Considering that DNA replication stress is a source of genome instability, and that excessive replication stress is a hallmark of pre-neoplastic and tumor cells, our characterization of SUMO2 targets during a perturbed S-phase should provide a valuable resource for future functional studies in the fields of DNA metabolism and cancer biology.
Collapse
Affiliation(s)
- Sara Bursomanno
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, DK-2200 Copenhagen, Denmark
| | - Petra Beli
- Department of Proteomics, The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Panum Institute, DK-2200 Copenhagen, Denmark; Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Asif M Khan
- Molecular Oncology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sheroy Minocherhomji
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, DK-2200 Copenhagen, Denmark
| | - Sebastian A Wagner
- Department of Proteomics, The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Panum Institute, DK-2200 Copenhagen, Denmark
| | - Simon Bekker-Jensen
- Department of Disease Biology, The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Panum Institute, DK-2200 Copenhagen, Denmark
| | - Niels Mailand
- Department of Disease Biology, The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Panum Institute, DK-2200 Copenhagen, Denmark
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Panum Institute, DK-2200 Copenhagen, Denmark
| | - Ian D Hickson
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, DK-2200 Copenhagen, Denmark; Molecular Oncology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Ying Liu
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, DK-2200 Copenhagen, Denmark; Molecular Oncology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| |
Collapse
|
50
|
Oka Y, Varmark H, Vitting-Seerup K, Beli P, Waage J, Hakobyan A, Mistrik M, Choudhary C, Rohde M, Bekker-Jensen S, Mailand N. UBL5 is essential for pre-mRNA splicing and sister chromatid cohesion in human cells. EMBO Rep 2014; 15:956-64. [PMID: 25092792 DOI: 10.15252/embr.201438679] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
UBL5 is an atypical ubiquitin-like protein, whose function in metazoans remains largely unexplored. We show that UBL5 is required for sister chromatid cohesion maintenance in human cells. UBL5 primarily associates with spliceosomal proteins, and UBL5 depletion decreases pre-mRNA splicing efficiency, leading to globally enhanced intron retention. Defective sister chromatid cohesion is a general consequence of dysfunctional pre-mRNA splicing, resulting from the selective downregulation of the cohesion protection factor Sororin. As the UBL5 yeast orthologue, Hub1, also promotes spliceosome functions, our results show that UBL5 plays an evolutionary conserved role in pre-mRNA splicing, the integrity of which is essential for the fidelity of chromosome segregation.
Collapse
Affiliation(s)
- Yasuyoshi Oka
- Ubiquitin Signaling Group, Department of Disease Biology, The Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
| | - Hanne Varmark
- Ubiquitin Signaling Group, Department of Disease Biology, The Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer Vitting-Seerup
- Bioinformatics Centre, Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Petra Beli
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark Institute of Molecular Biology (IMB), Mainz, Germany
| | - Johannes Waage
- Bioinformatics Centre, Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Anna Hakobyan
- Department of Cell Death and Metabolism, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Martin Mistrik
- Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Rohde
- Department of Cell Death and Metabolism, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Simon Bekker-Jensen
- Ubiquitin Signaling Group, Department of Disease Biology, The Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
| | - Niels Mailand
- Ubiquitin Signaling Group, Department of Disease Biology, The Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|