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Mashayekhi F, Zeinali E, Ganje C, Fanta M, Li L, Godbout R, Weinfeld M, Ismail IH. CDK-Dependent Phosphorylation Regulates PNKP Function in DNA Replication. J Biol Chem 2024:107880. [PMID: 39395804 DOI: 10.1016/j.jbc.2024.107880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 09/24/2024] [Accepted: 09/27/2024] [Indexed: 10/14/2024] Open
Abstract
Okazaki fragment maturation (OFM) stands as a pivotal DNA metabolic process, crucial for genome integrity and cell viability. Dysregulation of OFM leads to DNA single-strand breaks- accumulation, which is linked to various human diseases such as cancer and neurodegenerative disorders. Recent studies have implicated LIG3-XRCC1 acting in an alternative OFM pathway to the canonical FEN1-LIG1 pathway. Here, we reveal that polynucleotide kinase-phosphatase (PNKP) is another key participant in DNA replication, akin to LIG3-XRCC1. Through functional experiments, we demonstrate PNKP's enrichment at DNA replication forks and its association with PCNA, indicating its involvement in replication processes. Cellular depletion of PNKP mirrors defects observed in OFM-related proteins, highlighting its significance in replication fork dynamics. Additionally, we identify PNKP as a substrate for cyclin-dependent kinase 1/2 (CDK1/2), which phosphorylates PNKP at multiple residues. Mutation analysis of these phosphorylation sites underscores the importance of CDK2-mediated PNKP phosphorylation in DNA replication. Our findings collectively indicate a novel role for PNKP in facilitating Okazaki fragment joining, thus shedding light on its contribution to genome stability maintenance.
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Affiliation(s)
- Fatemeh Mashayekhi
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta, Canada
| | - Elham Zeinali
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta, Canada
| | - Cassandra Ganje
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta, Canada
| | - Mesfin Fanta
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta, Canada
| | - Lei Li
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta, Canada
| | - Roseline Godbout
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta, Canada
| | - Michael Weinfeld
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta, Canada
| | - Ismail Hassan Ismail
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta, Canada; Biophysics Department, Faculty of Science, Cairo University, 12613 Giza, Egypt.
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2
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Bonnet C, Dian AL, Leriche M, Uguen P, Vagner S. Protocol to study the direct binding of proteins to RNA:DNA hybrids or RNA-DNA chimeras in living cells using cross-linking immunoprecipitation. STAR Protoc 2024; 5:103292. [PMID: 39264804 PMCID: PMC11422765 DOI: 10.1016/j.xpro.2024.103292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/16/2024] [Accepted: 08/14/2024] [Indexed: 09/14/2024] Open
Abstract
RNA-binding proteins (RBPs) are involved in many biological processes. The direct interaction between protein and RNA can be studied using cross-linking immunoprecipitation (CLIP) techniques in living cells. Here, we present a protocol to characterize the direct binding of proteins to RNA:DNA hybrids or RNA-DNA chimeras in living cells using CLIP. We describe steps for RNA-protein UV-C cross-linking in living cells, isolating RNA-protein complexes, RNA labeling, and extracting nucleic acid. We then detail procedures for nuclease treatment and nucleic acid migration.
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Affiliation(s)
- Clara Bonnet
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Ana Luisa Dian
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Mélissa Leriche
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Patricia Uguen
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France.
| | - Stéphan Vagner
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France.
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3
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Schreuder A, Wendel TJ, Dorresteijn CGV, Noordermeer SM. (Single-stranded DNA) gaps in understanding BRCAness. Trends Genet 2024; 40:757-771. [PMID: 38789375 DOI: 10.1016/j.tig.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024]
Abstract
The tumour-suppressive roles of BRCA1 and 2 have been attributed to three seemingly distinct functions - homologous recombination, replication fork protection, and single-stranded (ss)DNA gap suppression - and their relative importance is under debate. In this review, we examine the origin and resolution of ssDNA gaps and discuss the recent advances in understanding the role of BRCA1/2 in gap suppression. There are ample data showing that gap accumulation in BRCA1/2-deficient cells is linked to genomic instability and chemosensitivity. However, it remains unclear whether there is a causative role and the function of BRCA1/2 in gap suppression cannot unambiguously be dissected from their other functions. We therefore conclude that the three functions of BRCA1 and 2 are closely intertwined and not mutually exclusive.
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Affiliation(s)
- Anne Schreuder
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Tiemen J Wendel
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Carlo G V Dorresteijn
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
| | - Sylvie M Noordermeer
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
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4
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Machour FE, R Abu-Zhayia E, Kamar J, Barisaac AS, Simon I, Ayoub N. Harnessing DNA replication stress to target RBM10 deficiency in lung adenocarcinoma. Nat Commun 2024; 15:6417. [PMID: 39080280 PMCID: PMC11289143 DOI: 10.1038/s41467-024-50882-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/23/2024] [Indexed: 08/02/2024] Open
Abstract
The splicing factor RNA-binding motif protein 10 (RBM10) is frequently mutated in lung adenocarcinoma (LUAD) (9-25%). Most RBM10 cancer mutations are loss-of-function, correlating with increased tumorigenesis and limiting the efficacy of current LUAD targeted therapies. Remarkably, therapeutic strategies leveraging RBM10 deficiency remain unexplored. Here, we conduct a CRISPR-Cas9 synthetic lethality (SL) screen and identify ~60 RBM10 SL genes, including WEE1 kinase. WEE1 inhibition sensitizes RBM10-deficient LUAD cells in-vitro and in-vivo. Mechanistically, we identify a splicing-independent role of RBM10 in regulating DNA replication fork progression and replication stress response, which underpins RBM10-WEE1 SL. Additionally, RBM10 interacts with active DNA replication forks, relying on DNA Primase Subunit 1 (PRIM1) that synthesizes Okazaki RNA primers. Functionally, we demonstrate that RBM10 serves as an anchor for recruiting Histone Deacetylase 1 (HDAC1) to facilitate H4K16 deacetylation and R-loop homeostasis to maintain replication fork stability. Collectively, our data reveal a role of RBM10 in fine-tuning DNA replication and provide therapeutic arsenal for targeting RBM10-deficient tumors.
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Affiliation(s)
- Feras E Machour
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Enas R Abu-Zhayia
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Joyce Kamar
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | | | - Itamar Simon
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Nabieh Ayoub
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
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Ellison V, Polotskaia A, Xiao G, Leybengrub P, Qiu W, Lee R, Hendrickson R, Hu W, Bargonetti J. A CANCER PERSISTENT DNA REPAIR CIRCUIT DRIVEN BY MDM2, MDM4 (MDMX), AND MUTANT P53 FOR RECRUITMENT OF MDC1 AND 53BP1 TO CHROMATIN. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576487. [PMID: 38328189 PMCID: PMC10849484 DOI: 10.1101/2024.01.20.576487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The influence of the metastasis promoting proteins mutant p53 (mtp53) and MDM2 on Cancer Persistent Repair (CPR) to promote cancer cell survival is understudied. Interactions between the DNA repair choice protein 53BP1 and wild type tumor suppressor protein p53 (wtp53) regulates cell cycle control. Cancer cells often express elevated levels of transcriptionally inactive missense mutant p53 (mtp53) that interacts with MDM2 and MDM4/MDMX (herein called MDMX). The ability of mtp53 to maintain a 53BP1 interaction while in the context of interactions with MDM2 and MDMX has not been described. We asked if MDM2 regulates chromatin-based phosphorylation events in the context of mtp53 by comparing the chromatin of T47D breast cancer cells with and without MDM2 in a phospho-peptide stable isotope labeling in cell culture (SILAC) screen. We found reduced phospho-53BP1 chromatin association, which we confirmed by chromatin fractionation and immunofluorescence in multiple breast cancer cell lines. We used the Proximity Ligation Assay (PLA) in breast cancer cell lines and detected 53BP1 in close proximity to mtp53, MDM2, and the DNA repair protein MDC1. Through disruption of the mtp53-MDM2 interaction, by either Nutlin 3a or a mtp53 R273H C-terminal deletion, we uncovered that mtp53 was required for MDM2-53BP1 interaction foci. Our data suggests that mtp53 works with MDM2 and 53BP1 to promote CPR and cell survival.
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Affiliation(s)
- Viola Ellison
- Hunter College, The Department of Biological Sciences, Belfer Research Building, New York, NY
| | - Alla Polotskaia
- Hunter College, The Department of Biological Sciences, Belfer Research Building, New York, NY
| | - Gu Xiao
- Hunter College, The Department of Biological Sciences, Belfer Research Building, New York, NY
| | - Pamella Leybengrub
- Hunter College, The Department of Biological Sciences, Belfer Research Building, New York, NY
| | - Weigang Qiu
- Hunter College, The Department of Biological Sciences, Belfer Research Building, New York, NY
| | - Rusia Lee
- Hunter College, The Department of Biological Sciences, Belfer Research Building, New York, NY
- The Graduate Center City University of New York, Departments of Biology and Biochemistry, New York, NY
| | | | - Wenwei Hu
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ
| | - Jill Bargonetti
- Hunter College, The Department of Biological Sciences, Belfer Research Building, New York, NY
- The Graduate Center City University of New York, Departments of Biology and Biochemistry, New York, NY
- Weill Cornell Medical College, Department of Cell and Developmental Biology, New York, NY
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