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Challa S, Nandu T, Kim HB, Gong X, Renshaw CW, Li WC, Tan X, Aljardali MW, Camacho CV, Chen J, Kraus WL. A PARP14/TARG1-Regulated RACK1 MARylation Cycle Drives Stress Granule Dynamics in Ovarian Cancer Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.13.562273. [PMID: 37873085 PMCID: PMC10592810 DOI: 10.1101/2023.10.13.562273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Mono(ADP-ribosyl)ation (MARylation) is emerging as a critical regulator of ribosome function and translation. Herein, we demonstrate that RACK1, an integral component of the ribosome, is MARylated on three acidic residues by the mono(ADP-ribosyl) transferase (MART) PARP14 in ovarian cancer cells. MARylation of RACK1 is required for stress granule formation and promotes the colocalization of RACK1 in stress granules with G3BP1, eIF3η, and 40S ribosomal proteins. In parallel, we observed reduced translation of a subset of mRNAs, including those encoding key cancer regulators (e.g., AKT). Treatment with a PARP14 inhibitor or mutation of the sites of MARylation on RACK1 blocks these outcomes, as well as the growth of ovarian cancer cells in culture and in vivo. To re-set the system after prolonged stress and recovery, the ADP-ribosyl hydrolase TARG1 deMARylates RACK1, leading to the dissociation of the stress granules and the restoration of translation. Collectively, our results demonstrate a therapeutically targetable pathway that controls stress granule assembly and disassembly in ovarian cancer cells.
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Affiliation(s)
- Sridevi Challa
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Current address: Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637
| | - Tulip Nandu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hyung Bum Kim
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Graduate Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuan Gong
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Current address: Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Charles W. Renshaw
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wan-Chen Li
- Altos Labs, Bay Area Institute of Science, Redwood City, CA 94403
| | - Xinrui Tan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marwa W. Aljardali
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cristel V. Camacho
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jin Chen
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Altos Labs, Bay Area Institute of Science, Redwood City, CA 94403
| | - W. Lee Kraus
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Graduate Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Anagho HA, Mullari M, Prósz AG, Buch-Larsen SC, Cho H, Locard-Paulet M, Szallasi Z, Nielsen ML. ADP-ribosylome analysis reveals homogeneous DNA-damage-induced serine ADP-ribosylation across wild-type and BRCA-mutant breast cancer cell lines. Cell Rep 2024; 43:114433. [PMID: 38985679 DOI: 10.1016/j.celrep.2024.114433] [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: 12/15/2023] [Revised: 04/24/2024] [Accepted: 06/19/2024] [Indexed: 07/12/2024] Open
Abstract
ADP-ribosylation (ADPr) signaling plays a crucial role in DNA damage response. Inhibitors against the main enzyme catalyzing ADPr after DNA damage, poly(ADP-ribose) polymerase 1 (PARP1), are used to treat patients with breast cancer harboring BRCA1/2 mutations. However, resistance to PARP inhibitors (PARPi) is a major obstacle in treating patients. To understand the role of ADPr in PARPi sensitivity, we use liquid chromatography-tandem mass spectrometry (LC-MS/MS) to analyze ADPr in six breast cancer cell lines exhibiting different PARPi sensitivities. We identify 1,632 sites on 777 proteins across all cell lines, primarily on serine residues, with site-specific overlap of targeted residues across DNA-damage-related proteins across all cell lines, demonstrating high conservation of serine ADPr-signaling networks upon DNA damage. Furthermore, we observe site-specific differences in ADPr intensities in PARPi-sensitive BRCA mutants and unique ADPr sites in PARPi-resistant BRCA-mutant HCC1937 cells, which have low poly(ADP-ribose) glycohydrolase (PARG) levels and longer ADPr chains on PARP1.
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Affiliation(s)
- Holda Awah Anagho
- Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, 2200 Copenhagen, Denmark
| | - Meeli Mullari
- Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, 2200 Copenhagen, Denmark
| | | | - Sara Charlotte Buch-Larsen
- Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, 2200 Copenhagen, Denmark
| | - Hayoung Cho
- Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, 2200 Copenhagen, Denmark
| | - Marie Locard-Paulet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Zoltan Szallasi
- Danish Cancer Institute, Copenhagen, Denmark; Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Michael Lund Nielsen
- Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, 2200 Copenhagen, Denmark.
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Longarini EJ, Matić I. Preserving ester-linked modifications reveals glutamate and aspartate mono-ADP-ribosylation by PARP1 and its reversal by PARG. Nat Commun 2024; 15:4239. [PMID: 38762517 PMCID: PMC11102441 DOI: 10.1038/s41467-024-48314-0] [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: 01/11/2024] [Accepted: 04/26/2024] [Indexed: 05/20/2024] Open
Abstract
Ester-linked post-translational modifications, including serine and threonine ubiquitination, have gained recognition as important cellular signals. However, their detection remains a significant challenge due to the chemical lability of the ester bond. This is the case even for long-known modifications, such as ADP-ribosylation on aspartate and glutamate, whose role in PARP1 signaling has recently been questioned. Here, we present easily implementable methods for preserving ester-linked modifications. When combined with a specific and sensitive modular antibody and mass spectrometry, these approaches reveal DNA damage-induced aspartate/glutamate mono-ADP-ribosylation. This previously elusive signal represents an initial wave of PARP1 signaling, contrasting with the more enduring nature of serine mono-ADP-ribosylation. Unexpectedly, we show that the poly-ADP-ribose hydrolase PARG is capable of reversing ester-linked mono-ADP-ribosylation in cells. Our methodology enables broad investigations of various ADP-ribosylation writers and, as illustrated here for noncanonical ubiquitination, it paves the way for exploring other emerging ester-linked modifications.
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Affiliation(s)
- Edoardo José Longarini
- Research Group of Proteomics and ADP-Ribosylation Signaling, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, Cologne, 50931, Germany.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
| | - Ivan Matić
- Research Group of Proteomics and ADP-Ribosylation Signaling, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, Cologne, 50931, Germany.
- Cologne Excellence Cluster for Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany.
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Bashyal A, Brodbelt JS. Uncommon posttranslational modifications in proteomics: ADP-ribosylation, tyrosine nitration, and tyrosine sulfation. MASS SPECTROMETRY REVIEWS 2024; 43:289-326. [PMID: 36165040 PMCID: PMC10040477 DOI: 10.1002/mas.21811] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Posttranslational modifications (PTMs) are covalent modifications of proteins that modulate the structure and functions of proteins and regulate biological processes. The development of various mass spectrometry-based proteomics workflows has facilitated the identification of hundreds of PTMs and aided the understanding of biological significance in a high throughput manner. Improvements in sample preparation and PTM enrichment techniques, instrumentation for liquid chromatography-tandem mass spectrometry (LC-MS/MS), and advanced data analysis tools enhance the specificity and sensitivity of PTM identification. Highly prevalent PTMs like phosphorylation, glycosylation, acetylation, ubiquitinylation, and methylation are extensively studied. However, the functions and impact of less abundant PTMs are not as well understood and underscore the need for analytical methods that aim to characterize these PTMs. This review focuses on the advancement and analytical challenges associated with the characterization of three less common but biologically relevant PTMs, specifically, adenosine diphosphate-ribosylation, tyrosine sulfation, and tyrosine nitration. The advantages and disadvantages of various enrichment, separation, and MS/MS techniques utilized to identify and localize these PTMs are described.
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Affiliation(s)
- Aarti Bashyal
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
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Kołacz K, Robaszkiewicz A. PARP1 at the crossroad of cellular senescence and nucleolar processes. Ageing Res Rev 2024; 94:102206. [PMID: 38278370 DOI: 10.1016/j.arr.2024.102206] [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: 11/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Senescent cells that occur in response to telomere shortening, oncogenes, extracellular and intracellular stress factors are characterized by permanent cell cycle arrest, the morphological and structural changes of the cell that include the senescence-associated secretory phenotype (SASP) and nucleoli rearrangement. The associated DNA lesions induce DNA damage response (DDR), which activates the DNA repair protein - poly-ADP-ribose polymerase 1 (PARP1). This protein consumes NAD+ to synthesize ADP-ribose polymer (PAR) on its own protein chain and on other interacting proteins. The involvement of PARP1 in nucleoli processes, such as rRNA transcription and ribosome biogenesis, the maintenance of heterochromatin and nucleoli structure, as well as controlling the crucial DDR protein release from the nucleoli to nucleus, links PARP1 with cellular senescence and nucleoli functioning. In this review we describe and discuss the impact of PARP1-mediated ADP-ribosylation on early cell commitment to senescence with the possible role of senescence-induced PARP1 transcriptional repression and protein degradation on nucleoli structure and function. The cause-effect interplay between PARP1 activation/decline and nucleoli functioning during senescence needs to be studied in detail.
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Affiliation(s)
- Kinga Kołacz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, University of Lodz, Banacha 12 /16, 90-237 Lodz, Poland.
| | - Agnieszka Robaszkiewicz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research (IFBR), 600 5th Street South, St. Petersburgh, FL 33701, USA.
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6
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Park S, Choi C, Kim H, Shin YJ, Oh Y, Park W, Cho WK, Kim N. Olaparib enhances sensitization of BRCA-proficient breast cancer cells to x-rays and protons. Breast Cancer Res Treat 2024; 203:449-461. [PMID: 37902934 DOI: 10.1007/s10549-023-07150-4] [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: 06/08/2023] [Accepted: 09/29/2023] [Indexed: 11/01/2023]
Abstract
PURPOSE This study aimed to compare the radiosensitizing effect of the PARP inhibitor, Olaparib, between proton and X-rays irradiations in BRCA-proficient breast cancer (BC) cells. METHODS Two BRCA-proficient BC cell lines, MDA-MB-231 and T47D BC, were used. Cell proliferation was assessed using the CCK-8 assay, and radiosensitivity was determined through the clonogenic survival assay. Flow cytometry was employed to analyze cell cycle distribution and apoptosis. The kinetics of DNA damage repair were evaluated using γH2AX immunofluorescence imaging and the comet assay. Tumor spheroid assays were conducted to test radiosensitivity in a three-dimensional culture condition. RESULTS Olaparib sensitized both MDA-MB-231 and T47D cells to proton and X-ray irradiation in the clonogenic assay. MDA-MB-231 cells exhibited a higher dose enhancement factor for Olaparib than T47D cells. Olaparib increased radiation-induced G2/M cell cycle arrest and apoptosis specifically in MDA-MB-231 cells. γH2AX immunostaining and the comet assay showed Olaparib augmented radiation-induced DNA damage and apoptosis. The enhancement effect of Olaparib was more pronounced in proton irradiation than in X-ray irradiation, particularly in MDA-MB-231 cells than T47D cells. Both radiation and Olaparib dose-dependently inhibited spheroid growth in both cell lines. The synergy scores demonstrated that Olaparib interacted more strongly with protons than X-rays. The addition of an ATR inhibitor further enhanced Olaparib-induced proton radiosensitization in MDA-MB-231 cells. CONCLUSION This study found that Olaparib enhanced radiation efficacy in BRCA-proficient breast cancer cells, with a more pronounced effect observed with proton irradiation compared to X-ray irradiation. Combining Olaparib with an ATR inhibitor increased the radiosensitizing effect of protons.
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Affiliation(s)
- Sohee Park
- Department of Radiation Oncology, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Changhoon Choi
- Department of Radiation Oncology, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.
| | - Haeyoung Kim
- Department of Radiation Oncology, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.
- Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Yong Jae Shin
- Innovative Institute for Precision Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Yunjeong Oh
- Innovative Institute for Precision Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Won Park
- Department of Radiation Oncology, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Won Kyung Cho
- Department of Radiation Oncology, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Nalee Kim
- Department of Radiation Oncology, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
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7
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Jayabalan AK, Bhambhani K, Leung AKL. PARP10 is Critical for Stress Granule Initiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562236. [PMID: 37873303 PMCID: PMC10592835 DOI: 10.1101/2023.10.13.562236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Stress granules (SGs) are cytoplasmic biomolecular condensates enriched with RNA, translation factors, and other proteins. They form in response to stress and are implicated in various diseased states including viral infection, tumorigenesis, and neurodegeneration. Understanding the mechanism of SG assembly, particularly its initiation, offers potential therapeutic avenues. Although ADP-ribosylation plays a key role in SG assembly, and one of its key forms-poly(ADP-ribose) or PAR-is critical for recruiting proteins to SGs, the specific enzyme responsible remains unidentified. Here, we systematically knock down the human ADP-ribosyltransferase family and identify PARP10 as pivotal for SG assembly. Live-cell imaging reveals PARP10's crucial role in regulating initial assembly kinetics. Further, we pinpoint the core SG component, G3BP1, as a PARP10 substrate and find that PARP10 regulates SG assembly driven by both G3BP1 and its modeled mechanism. Intriguingly, while PARP10 only adds a single ADP-ribose unit to proteins, G3BP1 is PARylated, suggesting its potential role as a scaffold for protein recruitment. PARP10 knockdown alters the SG core composition, notably decreasing translation factor presence. Based on our findings, we propose a model in which ADP-ribosylation acts as a rate-limiting step, initiating the formation of this RNA-enriched condensate.
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Affiliation(s)
- Aravinth Kumar Jayabalan
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Krishna Bhambhani
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- McKusick-Nathans Department of Genetics Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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8
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Beneyton A, Nonfoux L, Gagné JP, Rodrigue A, Kothari C, Atalay N, Hendzel M, Poirier G, Masson JY. The dynamic process of covalent and non-covalent PARylation in the maintenance of genome integrity: a focus on PARP inhibitors. NAR Cancer 2023; 5:zcad043. [PMID: 37609662 PMCID: PMC10440794 DOI: 10.1093/narcan/zcad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/24/2023] Open
Abstract
Poly(ADP-ribosylation) (PARylation) by poly(ADP-ribose) polymerases (PARPs) is a highly regulated process that consists of the covalent addition of polymers of ADP-ribose (PAR) through post-translational modifications of substrate proteins or non-covalent interactions with PAR via PAR binding domains and motifs, thereby reprogramming their functions. This modification is particularly known for its central role in the maintenance of genomic stability. However, how genomic integrity is controlled by an intricate interplay of covalent PARylation and non-covalent PAR binding remains largely unknown. Of importance, PARylation has caught recent attention for providing a mechanistic basis of synthetic lethality involving PARP inhibitors (PARPi), most notably in homologous recombination (HR)-deficient breast and ovarian tumors. The molecular mechanisms responsible for the anti-cancer effect of PARPi are thought to implicate both catalytic inhibition and trapping of PARP enzymes on DNA. However, the relative contribution of each on tumor-specific cytotoxicity is still unclear. It is paramount to understand these PAR-dependent mechanisms, given that resistance to PARPi is a challenge in the clinic. Deciphering the complex interplay between covalent PARylation and non-covalent PAR binding and defining how PARP trapping and non-trapping events contribute to PARPi anti-tumour activity is essential for developing improved therapeutic strategies. With this perspective, we review the current understanding of PARylation biology in the context of the DNA damage response (DDR) and the mechanisms underlying PARPi activity and resistance.
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Affiliation(s)
- Adèle Beneyton
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
| | - Louis Nonfoux
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Jean-Philippe Gagné
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Amélie Rodrigue
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
| | - Charu Kothari
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Nurgul Atalay
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AlbertaT6G 1Z2, Canada
| | - Guy G Poirier
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Jean-Yves Masson
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
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Pei J, Zhang J, Wang XD, Kim C, Yu Y, Cong Q. Impact of Asp/Glu-ADP-ribosylation on protein-protein interaction and protein function. Proteomics 2023; 23:e2200083. [PMID: 36453556 PMCID: PMC10362910 DOI: 10.1002/pmic.202200083] [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: 07/21/2022] [Revised: 09/12/2022] [Accepted: 11/10/2022] [Indexed: 12/04/2022]
Abstract
PARylation plays critical role in regulating multiple cellular processes such as DNA damage response and repair, transcription, RNA processing, and stress response. More than 300 human proteins have been found to be modified by PARylation on acidic residues, that is, Asp (D) and Glu (E). We used the deep-learning tool AlphaFold to predict protein-protein interactions (PPIs) and their interfaces for these proteins based on coevolution signals from joint multiple sequence alignments (MSAs). AlphaFold predicted 260 confident PPIs involving PARylated proteins, and about one quarter of these PPIs have D/E-PARylation sites in their predicted PPI interfaces. AlphaFold predictions offer novel insights into the mechanisms of PARylation regulations by providing structural details of the PPI interfaces. D/E-PARylation sites have a preference to occur in coil regions and disordered regions, and PPI interfaces containing D/E-PARylation sites tend to occur between short linear sequence motifs in disordered regions and globular domains. The hub protein PCNA is predicted to interact with more than 20 proteins via the common PIP box motif and the structurally variable flanking regions. D/E-PARylation sites were found in the interfaces of key components of the RNA transcription and export complex, the SF3a spliceosome complex, and H/ACA and C/D small nucleolar ribonucleoprotein complexes, suggesting that systematic PARylation have a profound effect in regulating multiple RNA-related processes such as RNA nuclear export, splicing, and modification. Finally, PARylation of SUMO2 could modulate its interaction with CHAF1A, thereby representing a potential mechanism for the cross-talk between PARylation and SUMOylation in regulation of chromatin remodeling.
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Affiliation(s)
- Jimin Pei
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jing Zhang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xu-Dong Wang
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Chiho Kim
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Yonghao Yu
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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10
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Kejiou NS, Ilan L, Aigner S, Luo E, Tonn T, Ozadam H, Lee M, Cole G, Rabano I, Rajakulendran N, Yee BA, Najafabadi H, Moraes T, Angers S, Yeo G, Cenik C, Palazzo A. Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling. Nucleic Acids Res 2023; 51:6461-6478. [PMID: 37224531 PMCID: PMC10325899 DOI: 10.1093/nar/gkad440] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 05/01/2023] [Accepted: 05/10/2023] [Indexed: 05/26/2023] Open
Abstract
In light of the numerous studies identifying post-transcriptional regulators on the surface of the endoplasmic reticulum (ER), we asked whether there are factors that regulate compartment specific mRNA translation in human cells. Using a proteomic survey of spatially regulated polysome interacting proteins, we identified the glycolytic enzyme Pyruvate Kinase M (PKM) as a cytosolic (i.e. ER-excluded) polysome interactor and investigated how it influences mRNA translation. We discovered that the PKM-polysome interaction is directly regulated by ADP levels-providing a link between carbohydrate metabolism and mRNA translation. By performing enhanced crosslinking immunoprecipitation-sequencing (eCLIP-seq), we found that PKM crosslinks to mRNA sequences that are immediately downstream of regions that encode lysine- and glutamate-enriched tracts. Using ribosome footprint protection sequencing, we found that PKM binding to ribosomes causes translational stalling near lysine and glutamate encoding sequences. Lastly, we observed that PKM recruitment to polysomes is dependent on poly-ADP ribosylation activity (PARylation)-and may depend on co-translational PARylation of lysine and glutamate residues of nascent polypeptide chains. Overall, our study uncovers a novel role for PKM in post-transcriptional gene regulation, linking cellular metabolism and mRNA translation.
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Affiliation(s)
- Nevraj S Kejiou
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Lena Ilan
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Enching Luo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tori Tonn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Muyoung Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Gregory B Cole
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Ines Rabano
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Stephane Angers
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
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11
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Dasovich M, Leung AKL. PARPs and ADP-ribosylation: Deciphering the complexity with molecular tools. Mol Cell 2023; 83:1552-1572. [PMID: 37119811 PMCID: PMC10202152 DOI: 10.1016/j.molcel.2023.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/07/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
PARPs catalyze ADP-ribosylation-a post-translational modification that plays crucial roles in biological processes, including DNA repair, transcription, immune regulation, and condensate formation. ADP-ribosylation can be added to a wide range of amino acids with varying lengths and chemical structures, making it a complex and diverse modification. Despite this complexity, significant progress has been made in developing chemical biology methods to analyze ADP-ribosylated molecules and their binding proteins on a proteome-wide scale. Additionally, high-throughput assays have been developed to measure the activity of enzymes that add or remove ADP-ribosylation, leading to the development of inhibitors and new avenues for therapy. Real-time monitoring of ADP-ribosylation dynamics can be achieved using genetically encoded reporters, and next-generation detection reagents have improved the precision of immunoassays for specific forms of ADP-ribosylation. Further development and refinement of these tools will continue to advance our understanding of the functions and mechanisms of ADP-ribosylation in health and disease.
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Affiliation(s)
- Morgan Dasovich
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Molecular Biology and Genetics, Department of Oncology, and Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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12
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A PARP1 PROTAC as a novel strategy against PARP inhibitor resistance via promotion of ferroptosis in p53-positive breast cancer. Biochem Pharmacol 2022; 206:115329. [PMID: 36309080 DOI: 10.1016/j.bcp.2022.115329] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/15/2022] [Accepted: 10/19/2022] [Indexed: 12/14/2022]
Abstract
Therapeutic targeting of the nuclear enzyme poly (ADP-ribose) polymerase 1 (PARP1) with PARP inhibitors (PARPis) in patients with a homologous recombination (HR)- deficient phenotype based on the mechanism of synthetic lethality has been shown tremendous success in cancer therapy. With the clinical use of various PARPis, emerging evidence has shown that some PARPis offer hope for breakthroughs in triple-negative breast cancer (TNBC) therapy, regardless of HR status. However, similar to other conventional cytotoxic drugs, PARPis are also subject to the intractable problem of drug resistance. Notably, acquired resistance to PARPis caused by point mutations in the PARP1 protein is hard to overcome with current strategies. To explore modalities to overcome resistance and identify patients who are most likely to benefit from PARP1-targeted therapy, we developed a proteolysis-targeted chimaera (PROTAC) to degrade mutant PARP1 in TNBC. Here, we investigated a PARP1 PROTAC termed "NN3″, which triggered ubiquitination and proteasome-mediated degradation of PARP1. Moreover, NN3 degraded PARP1 with resistance-related mutations. Interestingly, compared with other reported PARP1 degraders, NN3 exhibited a unique antitumor mechanism in p53-positive breast cancer cells that effectively promoted ferroptosis by downregulating the SLC7A11 pathway. Furthermore, NN3 showed potent activity and low toxicity in vivo. In conclusion, we propose PROTAC-mediated degradation of PARP1 as a novel strategy against mutation-related PARPi resistance and a paradigm for targeting breast cancer with functional p53 via ferroptosis induction.
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13
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Liu J, Wang Q, Kang Y, Xu S, Pang D. Unconventional protein post-translational modifications: the helmsmen in breast cancer. Cell Biosci 2022; 12:22. [PMID: 35216622 PMCID: PMC8881842 DOI: 10.1186/s13578-022-00756-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/07/2022] [Indexed: 01/10/2023] Open
Abstract
AbstractBreast cancer is the most prevalent malignant tumor and a leading cause of mortality among females worldwide. The tumorigenesis and progression of breast cancer involve complex pathophysiological processes, which may be mediated by post-translational modifications (PTMs) of proteins, stimulated by various genes and signaling pathways. Studies into PTMs have long been dominated by the investigation of protein phosphorylation and histone epigenetic modifications. However, with great advances in proteomic techniques, several other PTMs, such as acetylation, glycosylation, sumoylation, methylation, ubiquitination, citrullination, and palmitoylation have been confirmed in breast cancer. Nevertheless, the mechanisms, effects, and inhibitors of these unconventional PTMs (particularly, the non-histone modifications other than phosphorylation) received comparatively little attention. Therefore, in this review, we illustrate the functions of these PTMs and highlight their impact on the oncogenesis and progression of breast cancer. Identification of novel potential therapeutic drugs targeting PTMs and development of biological markers for the detection of breast cancer would be significantly valuable for the efficient selection of therapeutic regimens and prediction of disease prognosis in patients with breast cancer.
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14
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Naumenko KN, Sukhanova MV, Hamon L, Kurgina TA, Anarbaev RO, Mangerich A, Pastré D, Lavrik OI. The C-Terminal Domain of Y-Box Binding Protein 1 Exhibits Structure-Specific Binding to Poly(ADP-Ribose), Which Regulates PARP1 Activity. Front Cell Dev Biol 2022; 10:831741. [PMID: 35800891 PMCID: PMC9253770 DOI: 10.3389/fcell.2022.831741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Y-box-binding protein 1 (YB-1) is a multifunctional protein involved in the regulation of gene expression. Recent studies showed that in addition to its role in the RNA and DNA metabolism, YB-1 is involved in the regulation of PARP1 activity, which catalyzes poly(ADP-ribose) [PAR] synthesis under genotoxic stress through auto-poly(ADP-ribosyl)ation or protein trans-poly(ADP-ribosyl)ation. Nonetheless, the exact mechanism by which YB-1 regulates PAR synthesis remains to be determined. YB-1 contains a disordered Ala/Pro-rich N-terminal domain, a cold shock domain, and an intrinsically disordered C-terminal domain (CTD) carrying four clusters of positively charged amino acid residues. Here, we examined the functional role of the disordered CTD of YB-1 in PAR binding and in the regulation of PARP1-driven PAR synthesis in vitro. We demonstrated that the rate of PARP1-dependent synthesis of PAR is higher in the presence of YB-1 and is tightly controlled by the interaction between YB-1 CTD and PAR. Moreover, YB-1 acts as an effective cofactor in the PAR synthesis catalyzed by the PARP1 point mutants that generate various PAR polymeric structures, namely, short hypo- or hyperbranched polymers. We showed that either a decrease in chain length or an increase in branching frequency of PAR affect its binding affinity for YB-1 and YB-1-mediated stimulation of PARP1 enzymatic activity. These results provide important insight into the mechanism underlying the regulation of PARP1 activity by PAR-binding proteins containing disordered regions with clusters of positively charged amino acid residues, suggesting that YB-1 CTD-like domains may be considered PAR "readers" just as other known PAR-binding modules.
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Affiliation(s)
| | - Mariya V. Sukhanova
- LBCE, Institute Chemical Biology and Fundamental Medicine (ICBFM), Novosibirsk, Russia
| | - Loic Hamon
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Tatyana A. Kurgina
- LBCE, Institute Chemical Biology and Fundamental Medicine (ICBFM), Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Rashid O. Anarbaev
- LBCE, Institute Chemical Biology and Fundamental Medicine (ICBFM), Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Aswin Mangerich
- Department of Biology, Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - David Pastré
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Olga I. Lavrik
- LBCE, Institute Chemical Biology and Fundamental Medicine (ICBFM), Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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15
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Gan Y, Sha H, Zou R, Xu M, Zhang Y, Feng J, Wu J. Research Progress on Mono-ADP-Ribosyltransferases in Human Cell Biology. Front Cell Dev Biol 2022; 10:864101. [PMID: 35652091 PMCID: PMC9149570 DOI: 10.3389/fcell.2022.864101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
ADP-ribosylation is a well-established post-translational modification that is inherently connected to diverse processes, including DNA repair, transcription, and cell signaling. The crucial roles of mono-ADP-ribosyltransferases (mono-ARTs) in biological processes have been identified in recent years by the comprehensive use of genetic engineering, chemical genetics, and proteomics. This review provides an update on current methodological advances in the study of these modifiers. Furthermore, the review provides details on the function of mono ADP-ribosylation. Several mono-ARTs have been implicated in the development of cancer, and this review discusses the role and therapeutic potential of some mono-ARTs in cancer.
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Affiliation(s)
- Yujie Gan
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Huanhuan Sha
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Renrui Zou
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Miao Xu
- Nanjing Medical University, Nanjing, China
| | - Yuan Zhang
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Jifeng Feng
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
- *Correspondence: Jifeng Feng,
| | - Jianzhong Wu
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
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16
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Gai X, Xin D, Wu D, Wang X, Chen L, Wang Y, Ma K, Li Q, Li P, Yu X. Pre-ribosomal RNA reorganizes DNA damage repair factors in nucleus during meiotic prophase and DNA damage response. Cell Res 2022; 32:254-268. [PMID: 34980897 PMCID: PMC8888703 DOI: 10.1038/s41422-021-00597-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 11/11/2021] [Indexed: 11/09/2022] Open
Abstract
In response to DNA double-strand breaks (DSBs), DNA damage repair factors are recruited to DNA lesions and form nuclear foci. However, the underlying molecular mechanism remains largely elusive. Here, by analyzing the localization of DSB repair factors in the XY body and DSB foci, we demonstrate that pre-ribosomal RNA (pre-rRNA) mediates the recruitment of DSB repair factors around DNA lesions. Pre-rRNA exists in the XY body, a DSB repair hub, during meiotic prophase, and colocalizes with DSB repair factors, such as MDC1, BRCA1 and TopBP1. Moreover, pre-rRNA-associated proteins and RNAs, such as ribosomal protein subunits, RNase MRP and snoRNAs, also localize in the XY body. Similar to those in the XY body, pre-rRNA and ribosomal proteins also localize at DSB foci and associate with DSB repair factors. RNA polymerase I inhibitor treatment that transiently suppresses transcription of rDNA but does not affect global protein translation abolishes foci formation of DSB repair factors as well as DSB repair. The FHA domain and PST repeats of MDC1 recognize pre-rRNA and mediate phase separation of DSB repair factors, which may be the molecular basis for the foci formation of DSB repair factors during DSB response.
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Affiliation(s)
- Xiaochen Gai
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Di Xin
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Duo Wu
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Xin Wang
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Linlin Chen
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Yiqing Wang
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Kai Ma
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Qilin Li
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Peng Li
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Xiaochun Yu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China. .,School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China. .,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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17
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Wang H, Wu M, Liu H, Zhou H, Zhao Y, Geng Y, Jiang B, Zhang K, Zhang B, Han Z, Du X. Comparison of the Efficacy and Safety of PARP Inhibitors as a Monotherapy for Platinum-Sensitive Recurrent Ovarian Cancer: A Network Meta-Analysis. Front Oncol 2021; 11:785102. [PMID: 34900739 PMCID: PMC8652073 DOI: 10.3389/fonc.2021.785102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/04/2021] [Indexed: 12/21/2022] Open
Abstract
Background The present COVID-19 pandemic has tended toward normality. To provide convenient, safe, and effective home treatment programs for patients with recurrent ovarian cancer (ROC), the clinical efficacy and safety of poly (ADP-ribose) polymerase inhibitor (PARPi) (including olaparib, niraparib, and rucaparib) monotherapy as a maintenance treatment for platinum-sensitive ROC were systematically evaluated. Methods Numerous electronic databases were systematically searched for randomized controlled trials (RCTs) of PARPi maintenance treatment for ROC that were published before June 2021. The primary endpoints were overall survival (OS) and progression-free survival (PFS), and the secondary endpoint was grade 3-4 adverse effects (AEs). After data extraction and the quality evaluation of the included studies, Bayesian network meta-analysis (NMA) was performed using R software. The ability of each treatment was ranked using the surface under the cumulative ranking (SUCRA) curve. Results The analysis included five studies and 1390 patients. The NMA results demonstrated that compared with the placebo, olaparib and niraparib exhibited significant benefits in the gBRCA-mutated population, and respectively reduced the risk of death by 31% (HR = 0.69, 95% CI: 0.53-0.90) and 34% (HR = 0.66, 95% CI: 0.44-0.99). Olaparib, niraparib, and rucaparib were all found to be very effective in prolonging PFS in patients with ROC. All three PARPi treatments increased the number of grade 3-4 AEs in patients with ROC as compared with the placebo. Conclusions Overall, olaparib and niraparib maintenance treatment can significantly prolong the OS of patients with gBRCA mutations. Furthermore, the three investigated PARPi monotherapy maintenance treatments can prolong PFS regardless of BRCA mutation status. Although the incidence of AEs in the treatment groups was found to be significantly higher than that in the placebo group, the patients in the treatment group tolerated the treatment. Home oral PARPi treatment can balance tumor treatment and pandemic prevention and control, and is the most convenient, safe, and effective home treatment method available against the background of the current COVID-19 pandemic. Systematic Review Registration https://inplasy.com/inplasy-2021-6-0033/.
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Affiliation(s)
- Hongmei Wang
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, China
| | - Meng Wu
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, China
| | - Haonan Liu
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, China
| | - Hang Zhou
- Department of Hematology, The First People's Hospital of Lianyungang, Jiangsu, China
| | - Yang Zhao
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, China
| | - Yifan Geng
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, China
| | - Bo Jiang
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, China
| | - Kai Zhang
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, China
| | - Bo Zhang
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, China
| | - Zhengxiang Han
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, China
| | - Xiuping Du
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, China
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18
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Wallace SR, Chihab LY, Yamasaki M, Yoshinaga BT, Torres YM, Rideaux D, Javed Z, Turumella S, Zhang M, Lawton DR, Fuller AA, Carter-O’Connell I. Rapid Analysis of ADP-Ribosylation Dynamics and Site-Specificity Using TLC-MALDI. ACS Chem Biol 2021; 16:2137-2143. [PMID: 34647721 PMCID: PMC8609518 DOI: 10.1021/acschembio.1c00542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Poly(ADP-ribose)
polymerases, PARPs, transfer ADP-ribose onto target
proteins from nicotinamide adenine dinucleotide (NAD+).
Current mass spectrometric analytical methods require proteolysis
of target proteins, limiting the study of dynamic ADP-ribosylation
on contiguous proteins. Herein, we present a matrix-assisted laser
desorption/ionization time-of-flight (MALDI-TOF) method that facilitates
multisite analysis of ADP-ribosylation. We observe divergent ADP-ribosylation
dynamics for the catalytic domains of PARPs 14 and 15, with PARP15
modifying more sites on itself (+3–4 ADP-ribose) than the closely
related PARP14 protein (+1–2 ADP-ribose)—despite similar
numbers of potential modification sites. We identify, for the first
time, a minimal peptide fragment (18 amino-acids) that is preferentially
modified by PARP14. Finally, we demonstrate through mutagenesis and
chemical treatment with hydroxylamine that PARPs 14/15 prefer acidic
residues. Our results highlight the utility of MALDI-TOF in the analysis
of PARP target modifications and in elucidating the biochemical mechanism
governing PARP target selection.
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Affiliation(s)
- Sean R. Wallace
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Leila Y. Chihab
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Miles Yamasaki
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Braden T. Yoshinaga
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Yazmin M. Torres
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Damon Rideaux
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Zeeshan Javed
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Soumya Turumella
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Michelle Zhang
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Dylan R. Lawton
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Amelia A. Fuller
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Ian Carter-O’Connell
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
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19
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Sebastian R, Aladjem MI, Oberdoerffer P. Encounters in Three Dimensions: How Nuclear Topology Shapes Genome Integrity. Front Genet 2021; 12:746380. [PMID: 34745220 PMCID: PMC8566435 DOI: 10.3389/fgene.2021.746380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Almost 25 years ago, the phosphorylation of a chromatin component, histone H2AX, was discovered as an integral part of the DNA damage response in eukaryotes. Much has been learned since then about the control of DNA repair in the context of chromatin. Recent technical and computational advances in imaging, biophysics and deep sequencing have led to unprecedented insight into nuclear organization, highlighting the impact of three-dimensional (3D) chromatin structure and nuclear topology on DNA repair. In this review, we will describe how DNA repair processes have adjusted to and in many cases adopted these organizational features to ensure accurate lesion repair. We focus on new findings that highlight the importance of chromatin context, topologically associated domains, phase separation and DNA break mobility for the establishment of repair-conducive nuclear environments. Finally, we address the consequences of aberrant 3D genome maintenance for genome instability and disease.
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Affiliation(s)
- Robin Sebastian
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Philipp Oberdoerffer
- Division of Cancer Biology, National Cancer Institute, NIH, Rockville, MD, United States
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20
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Kliza KW, Liu Q, Roosenboom LWM, Jansen PWTC, Filippov DV, Vermeulen M. Reading ADP-ribosylation signaling using chemical biology and interaction proteomics. Mol Cell 2021; 81:4552-4567.e8. [PMID: 34551281 DOI: 10.1016/j.molcel.2021.08.037] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/23/2021] [Accepted: 08/26/2021] [Indexed: 01/12/2023]
Abstract
ADP-ribose (ADPr) readers are essential components of ADP-ribosylation signaling, which regulates genome maintenance and immunity. The identification and discrimination between monoADPr (MAR) and polyADPr (PAR) readers is difficult because of a lack of suitable affinity-enrichment reagents. We synthesized well-defined ADPr probes and used these for affinity purifications combined with relative and absolute quantitative mass spectrometry to generate proteome-wide MAR and PAR interactomes, including determination of apparent binding affinities. Among the main findings, MAR and PAR readers regulate various common and distinct processes, such as the DNA-damage response, cellular metabolism, RNA trafficking, and transcription. We monitored the dynamics of PAR interactions upon induction of oxidative DNA damage and uncovered the mechanistic connections between ubiquitin signaling and ADP-ribosylation. Taken together, chemical biology enables exploration of MAR and PAR readers using interaction proteomics. Furthermore, the generated MAR and PAR interaction maps significantly expand our current understanding of ADPr signaling.
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Affiliation(s)
- Katarzyna W Kliza
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands.
| | - Qiang Liu
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, Netherlands
| | - Laura W M Roosenboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, Netherlands.
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands.
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21
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Hendriks IA, Buch-Larsen SC, Prokhorova E, Elsborg JD, Rebak AKLFS, Zhu K, Ahel D, Lukas C, Ahel I, Nielsen ML. The regulatory landscape of the human HPF1- and ARH3-dependent ADP-ribosylome. Nat Commun 2021; 12:5893. [PMID: 34625544 PMCID: PMC8501107 DOI: 10.1038/s41467-021-26172-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 09/21/2021] [Indexed: 11/08/2022] Open
Abstract
Despite the involvement of Poly(ADP-ribose) polymerase-1 (PARP1) in many important biological pathways, the target residues of PARP1-mediated ADP-ribosylation remain ambiguous. To explicate the ADP-ribosylation regulome, we analyze human cells depleted for key regulators of PARP1 activity, histone PARylation factor 1 (HPF1) and ADP-ribosylhydrolase 3 (ARH3). Using quantitative proteomics, we characterize 1,596 ADP-ribosylation sites, displaying up to 1000-fold regulation across the investigated knockout cells. We find that HPF1 and ARH3 inversely and homogenously regulate the serine ADP-ribosylome on a proteome-wide scale with consistent adherence to lysine-serine-motifs, suggesting that targeting is independent of HPF1 and ARH3. Notably, we do not detect an HPF1-dependent target residue switch from serine to glutamate/aspartate under the investigated conditions. Our data support the notion that serine ADP-ribosylation mainly exists as mono-ADP-ribosylation in cells, and reveal a remarkable degree of histone co-modification with serine ADP-ribosylation and other post-translational modifications.
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Affiliation(s)
- Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Sara C Buch-Larsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Jonas D Elsborg
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Alexandra K L F S Rebak
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Claudia Lukas
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
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22
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Gadad SS, Camacho CV, Malladi V, Hutti CR, Nagari A, Kraus WL. PARP-1 Regulates Estrogen-Dependent Gene Expression in Estrogen Receptor α-Positive Breast Cancer Cells. Mol Cancer Res 2021; 19:1688-1698. [PMID: 34158394 PMCID: PMC8492518 DOI: 10.1158/1541-7786.mcr-21-0103] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/01/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) has gained considerable attention as a target for therapeutic inhibitors in breast cancers. Previously we showed that PARP-1 localizes to active gene promoters to regulate histone methylation and RNA polymerase II activity (Pol II), altering the expression of various tumor-related genes. Here we report a role for PARP-1 in estrogen-dependent transcription in estrogen receptor alpha (ERα)-positive (ER+) breast cancers. Global nuclear run-on and sequencing analyses functionally linked PARP-1 to the direct control of estrogen-regulated gene expression in ER+ MCF-7 breast cancer cells by promoting transcriptional elongation by Pol II. Furthermore, chromatin immunoprecipitation sequencing analyses revealed that PARP-1 regulates the estrogen-dependent binding of ERα and FoxA1 to a subset of genomic ERα binding sites, promoting active enhancer formation. Moreover, we found that the expression levels of the PARP-1- and estrogen-coregulated gene set are enriched in the luminal subtype of breast cancer, and high PARP-1 expression in ER+ cases correlates with poor survival. Finally, treatment with a PARP inhibitor or a transcriptional elongation inhibitor attenuated estrogen-dependent growth of multiple ER+ breast cancer cell lines. Taken together, our results show that PARP-1 regulates critical molecular pathways that control the estrogen-dependent gene expression program underlying the proliferation of ER+ breast cancer cells. IMPLICATIONS: PARP-1 regulates the estrogen-dependent genomic binding of ERα and FoxA1 to regulate critical gene expression programs by RNA Pol II that underlie the proliferation of ER+ breast cancers, providing a potential therapeutic opportunity for PARP inhibitors in estrogen-responsive breast cancers.
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Affiliation(s)
- Shrikanth S Gadad
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, Texas
| | - Cristel V Camacho
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Venkat Malladi
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Charles R Hutti
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Anusha Nagari
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas
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23
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Liu X, Xie R, Yu LL, Chen SH, Yang X, Singh AK, Li H, Wu C, Yu X. AI26 inhibits the ADP-ribosylhydrolase ARH3 and suppresses DNA damage repair. J Biol Chem 2020; 295:13838-13849. [PMID: 32753484 DOI: 10.1074/jbc.ra120.012801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 08/01/2020] [Indexed: 01/21/2023] Open
Abstract
The ADP-ribosylhydrolase ARH3 plays a key role in DNA damage repair, digesting poly(ADP-ribose) and removing ADP-ribose from serine residues of the substrates. Specific inhibitors that selectively target ARH3 would be a useful tool to examine DNA damage repair, as well as a possible strategy for tumor suppression. However, efforts to date have not identified any suitable compounds. Here, we used in silico and biochemistry screening to search for ARH3 inhibitors. We discovered a small molecule compound named ARH3 inhibitor 26 (AI26) as, to our knowledge, the first ARH3 inhibitor. AI26 binds to the catalytic pocket of ARH3 and inhibits the enzymatic activity of ARH3 with an estimated IC50 of ∼2.41 μm in vitro Moreover, hydrolysis of DNA damage-induced ADP-ribosylation was clearly inhibited when cells were pretreated with AI26, leading to defects in DNA damage repair. In addition, tumor cells with DNA damage repair defects were hypersensitive to AI26 treatment, as well as combinations of AI26 and other DNA-damaging agents such as camptothecin and doxorubicin. Collectively, these results reveal not only a chemical probe to study ARH3-mediated DNA damage repair but also a chemotherapeutic strategy for tumor suppression.
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Affiliation(s)
- Xiuhua Liu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Rong Xie
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Lily L Yu
- Westridge School, Pasadena, California, USA
| | - Shih-Hsun Chen
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Xiaoyun Yang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Anup K Singh
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Hongzhi Li
- Drug Discovery and Structural Biology Core Facility, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Chen Wu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
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24
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Murphy MR, Kleiman FE. Connections between 3' end processing and DNA damage response: Ten years later. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1571. [PMID: 31657151 PMCID: PMC7295566 DOI: 10.1002/wrna.1571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022]
Abstract
Ten years ago we reviewed how the cellular DNA damage response (DDR) is controlled by changes in the functional and structural properties of nuclear proteins, resulting in a timely coordinated control of gene expression that allows DNA repair. Expression of genes that play a role in DDR is regulated not only at transcriptional level during mRNA biosynthesis but also by changing steady-state levels due to turnover of the transcripts. The 3' end processing machinery, which is important in the regulation of mRNA stability, is involved in these gene-specific responses to DNA damage. Here, we review the latest mechanistic connections described between 3' end processing and DDR, with a special emphasis on alternative polyadenylation, microRNA and RNA binding proteins-mediated deadenylation, and discuss the implications of deregulation of these steps in DDR and human disease. This article is categorized under: RNA Processing > 3' End Processing RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Michael Robert Murphy
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
| | - Frida Esther Kleiman
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
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25
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Kim DS, Challa S, Jones A, Kraus WL. PARPs and ADP-ribosylation in RNA biology: from RNA expression and processing to protein translation and proteostasis. Genes Dev 2020; 34:302-320. [PMID: 32029452 PMCID: PMC7050490 DOI: 10.1101/gad.334433.119] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this review, Kim et al. discuss the importance of PARP family members and ADPRylation in gene regulation, mRNA processing, and protein abundance. ADP-ribosylation (ADPRylation) is a posttranslational modification of proteins discovered nearly six decades ago, but many important questions remain regarding its molecular functions and biological roles, as well as the activity of the ADP-ribose (ADPR) transferase enzymes (PARP family members) that catalyze it. Growing evidence indicates that PARP-mediated ADPRylation events are key regulators of the protein biosynthetic pathway, leading from rDNA transcription and ribosome biogenesis to mRNA synthesis, processing, and translation. In this review we describe the role of PARP proteins and ADPRylation in all facets of this pathway. PARP-1 and its enzymatic activity are key regulators of rDNA transcription, which is a critical step in ribosome biogenesis. An emerging role of PARPs in alternative splicing of mRNAs, as well as direct ADPRylation of mRNAs, highlight the role of PARP members in RNA processing. Furthermore, PARP activity, stimulated by cellular stresses, such as viral infections and ER stress, leads to the regulation of mRNA stability and protein synthesis through posttranscriptional mechanisms. Dysregulation of PARP activity in these processes can promote disease states. Collectively, these results highlight the importance of PARP family members and ADPRylation in gene regulation, mRNA processing, and protein abundance. Future studies in these areas will yield new insights into the fundamental mechanisms and a broader utility for PARP-targeted therapeutic agents.
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Affiliation(s)
- Dae-Seok Kim
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Sridevi Challa
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Aarin Jones
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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26
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Larsen SC, Hendriks IA, Lyon D, Jensen LJ, Nielsen ML. Systems-wide Analysis of Serine ADP-Ribosylation Reveals Widespread Occurrence and Site-Specific Overlap with Phosphorylation. Cell Rep 2020; 24:2493-2505.e4. [PMID: 30157440 DOI: 10.1016/j.celrep.2018.07.083] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/31/2018] [Accepted: 07/25/2018] [Indexed: 01/02/2023] Open
Abstract
ADP-ribosylation (ADPr) is a reversible posttranslational modification involved in a range of cellular processes. Here, we report system-wide identification of serine ADPr in human cells upon oxidative stress. High-resolution mass spectrometry and unrestricted data processing confirm that serine residues are the major target of ADPr in HeLa cells. Proteome-wide analysis identifies 3,090 serine ADPr sites, with 97% of acceptor sites modulating more than 2-fold upon oxidative stress, while treatment with the poly (ADP-ribose) polymerase (PARP) inhibitor olaparib abrogates this induction. Serine ADPr predominantly targets nuclear proteins, while structural-predictive analyses reveal that serine ADPr preferentially targets disordered protein regions. The identified ADP-ribosylated serines significantly overlap with known phosphorylated serines, and large-scale phosphoproteomics analysis provides evidence for site-specific crosstalk between serine ADPr and phosphorylation. Collectively, we demonstrate that serine ADPr is a widespread modification and a major nuclear signaling response to oxidative stress, with a regulatory scope comparable to other extensive posttranslational modifications.
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Affiliation(s)
- Sara C Larsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - David Lyon
- Disease Systems Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Lars J Jensen
- Disease Systems Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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27
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McPherson RL, Ong SE, Leung AKL. Ion-Pairing with Triethylammonium Acetate Improves Solid-Phase Extraction of ADP-Ribosylated Peptides. J Proteome Res 2020; 19:984-990. [PMID: 31859514 DOI: 10.1021/acs.jproteome.9b00696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
ADP-ribosylation refers to the post-translational modification of protein substrates with monomers or polymers of the small molecule ADP-ribose. ADP-ribosylation is enzymatically regulated and plays roles in cellular processes including DNA repair, nucleic acid metabolism, cell death, cellular stress responses, and antiviral immunity. Recent advances in the field of ADP-ribosylation have led to the development of proteomics approaches to enrich and identify endogenous ADP-ribosylated peptides by liquid chromatography tandem mass spectrometry (LC-MS/MS). A number of these methods rely on reverse-phase solid-phase extraction as a critical step in preparing cellular peptides for further enrichment steps in proteomics workflows. The anionic ion-pairing reagent trifluoroacetic acid (TFA) is typically used during reverse-phase solid-phase extraction to promote retention of tryptic peptides. Here we report that TFA and other carboxylate ion-pairing reagents are inefficient for reverse-phase solid-phase extraction of ADP-ribosylated peptides. Substitution of TFA with cationic ion-pairing reagents, such as triethylammonium acetate (TEAA), improves recovery of ADP-ribosylated peptides. We further demonstrate that substitution of TFA with TEAA in a proteomics workflow specific for identifying ADP-ribosylated peptides increases identification rates of ADP-ribosylated peptides by LC-MS/MS.
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Affiliation(s)
- Robert Lyle McPherson
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health , Johns Hopkins University , Baltimore , Maryland 21205 , United States
| | - Shao-En Ong
- Department of Pharmacology , University of Washington , Seattle , Washington 98195 , United States
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health , Johns Hopkins University , Baltimore , Maryland 21205 , United States.,Department of Molecular Biology and Genetics, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States.,Department of Oncology, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
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28
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Uncoupling of PARP1 trapping and inhibition using selective PARP1 degradation. Nat Chem Biol 2019; 15:1223-1231. [PMID: 31659317 PMCID: PMC6864272 DOI: 10.1038/s41589-019-0379-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 09/05/2019] [Indexed: 12/02/2022]
Abstract
PARP1 inhibitors (PARPi) are known to kill tumor cells via two mechanisms (i.e., PARP1 catalytic inhibition vs. PARP1 trapping). The relative contribution of these two pathways in mediating the cytotoxicity of PARPi, however, is incompletely understood. Here we designed a series of small molecule PARP degraders. Treatment with one such compound iRucaparib results in highly efficient and specific PARP1 degradation. iRucaparib blocks the enzymatic activity of PARP1 in vitro, and PARP1-mediated PARylation signaling in intact cells. This strategy mimics PARP1 genetic depletion, which enables the pharmacological decoupling of PARP1 inhibition from PARP1 trapping. Finally, by depleting PARP1, iRucaparib protects muscle cells and primary cardiomyocytes from DNA damage-induced energy crisis and cell death. In summary, these compounds represent “non-trapping” PARP1 degraders that block both the catalytic activity and scaffolding effects of PARP1, providing an ideal approach for the amelioration of the various pathological conditions caused by PARP1 hyperactivation.
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29
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Yamashita S, Tanaka M, Nodono H, Hamada A, Hamada T, Hasegawa M, Nishi Y, Moss J, Miwa M. Human alcohol dehydrogenase 1 is an acceptor protein for polyADP-ribosylation. Biochem Pharmacol 2019; 167:27-32. [PMID: 30936015 PMCID: PMC9872671 DOI: 10.1016/j.bcp.2019.03.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 03/19/2019] [Indexed: 01/26/2023]
Abstract
Alcohol dehydrogenase (ADH) is important for preventing alcohol toxicity and developmental disorders, and may be involved in other diseases including neurodegenerative diseases. We found that the major acceptor protein of polyADP-ribosylation in a model organism of neurodegeneration using a Drosophila melanogaster mutant lacking poly(ADP-ribose) glycohydrolase, was ADH. Thus we postulated that human ADH activity might be regulated by polyADP-ribosylation, a post-translational modification. The radioactivity of [32P]NAD+ was incorporated into human ADH1 by human poly(ADP-ribose) polymerase 1 in vitro, but was not incorporated when heat-inactivated PARP1 or a PARP inhibitor, 3-aminobenzamide, was used. The incorporated radioactivity was not released from ADH1 protein in the presence of excess amount of ADP-ribose or poly(ADP-ribose) as competitors. However, it was released by incubation with 1 M neutral NH2OH or 0.1 N NaOH, but was not with 0.1 N HCl, suggesting the bond between ADH1 and poly(ADP-ribose) is an ester linkage. When HepG2 cells, a human hepatoma cell line, were cultured in the presence of another PARP inhibitor, olaparib, ADH activity of the cell was significantly increased. These results suggest that polyADP-ribosylation could regulate ADH activity in vivo and might be involved in neurodegeneration.
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Affiliation(s)
- Sachiko Yamashita
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan,Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1590, USA
| | - Masakazu Tanaka
- Department of Microbiology, Kansai Medical University, Hirakata, Osaka 573-1010, Japan,Division of Molecular Pathology, Center for Chronic Viral Diseases, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Hiroto Nodono
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Akiko Hamada
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Takashi Hamada
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Makoto Hasegawa
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Yoshisuke Nishi
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Joel Moss
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1590, USA
| | - Masanao Miwa
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan,Corresponding author. (M. Miwa)
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30
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Li P, Zhen Y, Yu Y. Site-specific analysis of the Asp- and Glu-ADP-ribosylated proteome by quantitative mass spectrometry. Methods Enzymol 2019; 626:301-321. [PMID: 31606080 DOI: 10.1016/bs.mie.2019.06.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
ADP-ribosylation is a protein post-translational modification that is critically involved in a wide array of biological processes connected to cell stress responses. Enzymes known as poly-ADP-ribose polymerases (PARPs) catalyze the addition of the ADP-ribose units to amino acids with various side chain chemistries. In particular, the PARP family member PARP1 is responsible for the modification of a large number of proteins and is involved in initiation of the DNA damage response, although the mechanisms through which PARP1 functions are still incompletely understood. The analysis of protein ADP-ribosylation is challenging because PARylation is a low-abundance, labile and heterogeneous protein modification. Recently, we developed an integrative proteomic platform for the site-specific analysis of protein ADP-ribosylation on Asp and Glu residues. Herein, we describe the method, and demonstrate its utility in quantitative characterization of the human Asp- and Glu-ADP-ribosylated proteome.
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Affiliation(s)
- Peng Li
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Yuanli Zhen
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Yonghao Yu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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31
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Activation of PARP-1 by snoRNAs Controls Ribosome Biogenesis and Cell Growth via the RNA Helicase DDX21. Mol Cell 2019; 75:1270-1285.e14. [PMID: 31351877 DOI: 10.1016/j.molcel.2019.06.020] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 04/16/2019] [Accepted: 06/17/2019] [Indexed: 12/23/2022]
Abstract
PARP inhibitors (PARPi) prevent cancer cell growth by inducing synthetic lethality with DNA repair defects (e.g., in BRCA1/2 mutant cells). We have identified an alternative pathway for PARPi-mediated growth control in BRCA1/2-intact breast cancer cells involving rDNA transcription and ribosome biogenesis. PARP-1 binds to snoRNAs, which stimulate PARP-1 catalytic activity in the nucleolus independent of DNA damage. Activated PARP-1 ADP-ribosylates DDX21, an RNA helicase that localizes to nucleoli and promotes rDNA transcription when ADP-ribosylated. Treatment with PARPi or mutation of the ADP-ribosylation sites reduces DDX21 nucleolar localization, rDNA transcription, ribosome biogenesis, protein translation, and cell growth. The salient features of this pathway are evident in xenografts in mice and human breast cancer patient samples. Elevated levels of PARP-1 and nucleolar DDX21 are associated with cancer-related outcomes. Our studies provide a mechanistic rationale for efficacy of PARPi in cancer cells lacking defects in DNA repair whose growth is inhibited by PARPi.
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32
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Islas-Robles A, Yedlapudi D, Lau SS, Monks TJ. Toxicoproteomic Analysis of Poly(ADP-ribose)-associated Proteins Induced by Oxidative Stress in Human Proximal Tubule Cells. Toxicol Sci 2019; 171:117-131. [PMID: 31165168 DOI: 10.1093/toxsci/kfz131] [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: 02/20/2019] [Revised: 04/28/2019] [Accepted: 05/26/2019] [Indexed: 11/14/2022] Open
Abstract
2,3,5-Tris-(glutathion-S-yl)hydroquinone (TGHQ) is a nephrotoxic and nephrocarcinogenic metabolite of hydroquinone. TGHQ generates ROS, causing DNA strand breaks, hyperactivation of PARP-1, increases in intracellular calcium ([Ca2+]i), and cell death. PARP-1 catalyzes the attachment of ADP-ribose polymers (PAR) to target proteins. In human kidney proximal tubule cells (HK-2), ROS-mediated PARP-1 hyperactivation and elevations in [Ca2+]i are reciprocally coupled. The molecular mechanism of this interaction is unclear. The aim of the present study was to identify ROS-induced PAR-associated proteins to further understand their potential role in cell death. PAR-associated proteins were enriched by immunoprecipitation, identified by LC-MS/MS, and relative abundance was obtained by spectral counting. 356 proteins were PAR-modified following TGHQ treatment. 13 proteins exhibited gene ontology annotations related to calcium. Among these proteins, the general transcription factor II-I (TFII-I) is directly involved in the modulation of [Ca2+]i. TFII-I binding to phospholipase C (PLC) leads to calcium influx via the TRPC3 channel. However, inhibition of TRPC3 or PLC had no effect on TGHQ-mediated cell death, suggesting that their loss of function may be necessary but insufficient to cause cell death. Nevertheless, TGHQ promoted a time-dependent translocation of TFII-I from the nucleus to the cytosol concomitant with a decrease in tyrosine phosphorylation in α/β-TFII-I. Therefore it is likely that ROS have an important impact on the function of TFII-I, such as regulation of transcription, and DNA translesion synthesis. Our data also sheds light on PAR mediated signaling during oxidative stress, and contributes to the development of strategies to prevent PAR-dependent cell death.
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Affiliation(s)
- Argel Islas-Robles
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721.,Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Wayne State University, MI 48201
| | - Deepthi Yedlapudi
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Wayne State University, MI 48201
| | - Serrine S Lau
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Wayne State University, MI 48201
| | - Terrence J Monks
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Wayne State University, MI 48201
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33
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Singatulina AS, Hamon L, Sukhanova MV, Desforges B, Joshi V, Bouhss A, Lavrik OI, Pastré D. PARP-1 Activation Directs FUS to DNA Damage Sites to Form PARG-Reversible Compartments Enriched in Damaged DNA. Cell Rep 2019; 27:1809-1821.e5. [DOI: 10.1016/j.celrep.2019.04.031] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 09/21/2018] [Accepted: 04/04/2019] [Indexed: 12/19/2022] Open
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Higashi H, Maejima T, Lee LH, Yamazaki Y, Hottiger MO, Singh SA, Aikawa M. A Study into the ADP-Ribosylome of IFN-γ-Stimulated THP-1 Human Macrophage-like Cells Identifies ARTD8/PARP14 and ARTD9/PARP9 ADP-Ribosylation. J Proteome Res 2019; 18:1607-1622. [PMID: 30848916 PMCID: PMC6456868 DOI: 10.1021/acs.jproteome.8b00895] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
ADP-ribosylation is a post-translational modification that, until recently, has remained elusive to study at the cellular level. Previously dependent on radioactive tracers to identify ADP-ribosylation targets, several advances in mass spectrometric workflows now permit global identification of ADP-ribosylated substrates. In this study, we capitalized on two ADP-ribosylation enrichment strategies, and multiple activation methods performed on the Orbitrap Fusion Lumos, to identify IFN-γ-induced ADP-ribosylation substrates in macrophages. The ADP-ribosyl binding protein, Af1521, was used to enrich ADP-ribosylated peptides, and the antipoly-ADP-ribosyl antibody, 10H, was used to enrich ADP-ribosylated proteins. ADP-ribosyl-specific mass spectra were further enriched by an ADP-ribose product ion triggered EThcD and HCD activation strategy, in combination with multiple acquisitions that segmented the survey scan into smaller ranges. HCD and EThcD resulted in overlapping and unique ADP-ribosyl peptide identifications, with HCD providing more peptide identifications but EThcD providing more reliable ADP-ribosyl acceptor sites. Our acquisition strategies also resulted in the first ever characterization of ADP-ribosyl on three poly-ADP-ribose polymerases, ARTD9/PARP9, ARTD10/PARP10, and ARTD8/PARP14. IFN-γ increased the ADP-ribosylation status of ARTD9/PARP9, ARTD8/PARP14, and proteins involved in RNA processes. This study therefore summarizes specific molecular pathways at the intersection of IFN-γ and ADP-ribosylation signaling pathways.
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Affiliation(s)
- Hideyuki Higashi
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Takashi Maejima
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Lang Ho Lee
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Yukiyoshi Yamazaki
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease , University of Zurich , 8057 Zurich , Switzerland
| | - Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States.,Center for Excellence in Vascular Biology, Cardiovascular Division , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States.,Channing Division of Network Medicine, Department of Medicine , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States
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35
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O'Sullivan J, Tedim Ferreira M, Gagné JP, Sharma AK, Hendzel MJ, Masson JY, Poirier GG. Emerging roles of eraser enzymes in the dynamic control of protein ADP-ribosylation. Nat Commun 2019; 10:1182. [PMID: 30862789 PMCID: PMC6414514 DOI: 10.1038/s41467-019-08859-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 02/02/2019] [Indexed: 12/21/2022] Open
Abstract
Protein ADP-ribosylation is essential for the regulation of several cellular pathways, enabling dynamic responses to diverse pathophysiological conditions. It is modulated through a dynamic interplay between ADP-ribose readers, writers and erasers. While ADP-ribose synthesis has been studied and reviewed extensively, ADP-ribose processing by erasing enzymes has received comparably less attention. However, major progress in the mass spectrometric identification of ADP-ribosylated residues and the biochemical characterization of ADP-ribose erasers has substantially expanded our knowledge of ADP-ribosylation dynamics. Herein, we describe recent insights into the biology of ADP-ribose erasers and discuss the intricately orchestrated cellular processes to switch off ADP-ribose-dependent mechanisms. ADP-ribose erasing enzymes are increasingly recognized as critical regulators of protein ADP-ribosylation dynamics in living systems. Here, the authors review recent advances in the discovery and characterization of ADP-ribose erasers and discuss their role within the cellular ADP-ribosylation machinery.
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Affiliation(s)
- Julia O'Sullivan
- Genome Stability Laboratory, Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, HDQ Pavilion, Oncology Division, Québec, G1R 2J6, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, G1V 0A6, Canada
| | - Maria Tedim Ferreira
- Genome Stability Laboratory, Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, HDQ Pavilion, Oncology Division, Québec, G1R 2J6, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, G1V 0A6, Canada.,Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, CHUL Pavilion, Oncology division, Québec, G1V 4G2, Canada
| | - Jean-Philippe Gagné
- Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, G1V 0A6, Canada.,Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, CHUL Pavilion, Oncology division, Québec, G1V 4G2, Canada
| | - Ajit K Sharma
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G 1Z2, Canada
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G 1Z2, Canada.,Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G 2H7, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, HDQ Pavilion, Oncology Division, Québec, G1R 2J6, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, G1V 0A6, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Québec, G1R 3S3, Canada
| | - Guy G Poirier
- Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, G1V 0A6, Canada. .,Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, CHUL Pavilion, Oncology division, Québec, G1V 4G2, Canada. .,Centre de Recherche sur le Cancer de l'Université Laval, Québec, G1R 3S3, Canada.
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36
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Ando Y, Elkayam E, McPherson RL, Dasovich M, Cheng SJ, Voorneveld J, Filippov DV, Ong SE, Joshua-Tor L, Leung AKL. ELTA: Enzymatic Labeling of Terminal ADP-Ribose. Mol Cell 2019; 73:845-856.e5. [PMID: 30712989 PMCID: PMC6629254 DOI: 10.1016/j.molcel.2018.12.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/22/2018] [Accepted: 12/21/2018] [Indexed: 12/14/2022]
Abstract
ADP-ribosylation refers to the addition of one or more ADP-ribose groups onto proteins. The attached ADP-ribose monomers or polymers, commonly known as poly(ADP-ribose) (PAR), modulate the activities of the modified substrates or their binding affinities to other proteins. However, progress in this area is hindered by a lack of tools to investigate this protein modification. Here, we describe a new method named ELTA (enzymatic labeling of terminal ADP-ribose) for labeling free or protein-conjugated ADP-ribose monomers and polymers at their 2'-OH termini using the enzyme OAS1 and dATP. When coupled with various dATP analogs (e.g., radioactive, fluorescent, affinity tags), ELTA can be used to explore PAR biology with techniques routinely used to investigate DNA or RNA function. We demonstrate that ELTA enables the biophysical measurements of protein binding to PAR of a defined length, detection of PAR length from proteins and cells, and enrichment of sub-femtomole amounts of ADP-ribosylated peptides from cell lysates.
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Affiliation(s)
- Yoshinari Ando
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Elad Elkayam
- Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Robert Lyle McPherson
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Morgan Dasovich
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Shang-Jung Cheng
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jim Voorneveld
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Dmitri V Filippov
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Leemor Joshua-Tor
- Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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37
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Kassab MA, Yu X. The role of dePARylation in DNA damage repair and cancer suppression. DNA Repair (Amst) 2019; 76:20-29. [PMID: 30807923 DOI: 10.1016/j.dnarep.2019.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/03/2019] [Indexed: 12/19/2022]
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a reversible post-translational modification regulating various biological pathways including DNA damage repair (DDR). Rapid turnover of PARylation is critically important for an optimal DNA damage response and maintaining genomic stability. Recent studies show that PARylation is tightly regulated by a group of enzymes that can erase the ADP-ribose (ADPR) groups from target proteins. The aim of this review is to present a comprehensive understanding of dePARylation enzymes, their substrates and roles in DDR. Special attention will be laid on the role of these proteins in the development of cancer and their feasibility in anticancer therapeutics.
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Affiliation(s)
- Muzaffer Ahmad Kassab
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010, USA
| | - Xiaochun Yu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010, USA.
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38
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Drown BS, Shirai T, Rack JGM, Ahel I, Hergenrother PJ. Monitoring Poly(ADP-ribosyl)glycohydrolase Activity with a Continuous Fluorescent Substrate. Cell Chem Biol 2018; 25:1562-1570.e19. [PMID: 30318463 PMCID: PMC6309520 DOI: 10.1016/j.chembiol.2018.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/17/2018] [Accepted: 09/12/2018] [Indexed: 11/30/2022]
Abstract
The post-translational modification (PTM) and signaling molecule poly(ADP-ribose) (PAR) has an impact on diverse biological processes. This PTM is regulated by a series of ADP-ribosyl glycohydrolases (PARG enzymes) that cleave polymers and/or liberate monomers from their protein targets. Existing methods for monitoring these hydrolases rely on detection of the natural substrate, PAR, commonly achieved via radioisotopic labeling. Here we disclose a general substrate for monitoring PARG activity, TFMU-ADPr, which directly reports on total PAR hydrolase activity via release of a fluorophore; this substrate has excellent reactivity, generality (processed by the major PARG enzymes), stability, and usability. A second substrate, TFMU-IDPr, selectively reports on PARG activity only from the enzyme ARH3. Use of these probes in whole-cell lysate experiments has revealed a mechanism by which ARH3 is inhibited by cholera toxin. TFMU-ADPr and TFMU-IDPr are versatile tools for assessing small-molecule inhibitors in vitro and probing the regulation of ADP-ribosyl catabolic enzymes.
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Affiliation(s)
- Bryon S Drown
- Department of Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 261 Roger Adams Lab Box 36-5, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Tomohiro Shirai
- Department of Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 261 Roger Adams Lab Box 36-5, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | | | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Paul J Hergenrother
- Department of Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 261 Roger Adams Lab Box 36-5, 600 S. Mathews Avenue, Urbana, IL 61801, USA.
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39
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Palazzo L, Ahel I. PARPs in genome stability and signal transduction: implications for cancer therapy. Biochem Soc Trans 2018; 46:1681-1695. [PMID: 30420415 PMCID: PMC6299239 DOI: 10.1042/bst20180418] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/15/2018] [Accepted: 09/21/2018] [Indexed: 01/03/2023]
Abstract
The poly(ADP-ribose) polymerase (PARP) superfamily of enzymes catalyses the ADP-ribosylation (ADPr) of target proteins by using nicotinamide adenine dinucleotide (NAD+) as a donor. ADPr reactions occur either in the form of attachment of a single ADP-ribose nucleotide unit on target proteins or in the form of ADP-ribose chains, with the latter called poly(ADP-ribosyl)ation. PARPs regulate many cellular processes, including the maintenance of genome stability and signal transduction. In this review, we focus on the PARP family members that possess the ability to modify proteins by poly(ADP-ribosyl)ation, namely PARP1, PARP2, Tankyrase-1, and Tankyrase-2. Here, we detail the cellular functions of PARP1 and PARP2 in the regulation of DNA damage response and describe the function of Tankyrases in Wnt-mediated signal transduction. Furthermore, we discuss how the understanding of these pathways has provided some major breakthroughs in the treatment of human cancer.
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Affiliation(s)
- Luca Palazzo
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, U.K.
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40
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Ding L, Chen X, Xu X, Qian Y, Liang G, Yao F, Yao Z, Wu H, Zhang J, He Q, Yang B. PARP1 Suppresses the Transcription of PD-L1 by Poly(ADP-Ribosyl)ating STAT3. Cancer Immunol Res 2018; 7:136-149. [PMID: 30401677 DOI: 10.1158/2326-6066.cir-18-0071] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 08/10/2018] [Accepted: 11/01/2018] [Indexed: 11/16/2022]
Abstract
Studies have pointed to a role of PARP1 in regulating gene expression through poly(ADP-ribosyl)ating, sequence-specific, DNA-binding transcription factors. However, few examples exist that link this role of PARP1 to the immunogenicity of cancer cells. Here, we report that PARP1 poly(ADP-ribosyl)ates STAT3 and subsequently promotes STAT3 dephosphorylation, resulting in reduced transcriptional activity of STAT3 and expression of PD-L1. In this study, we showed that PARP1 silencing or pharmacologic inhibition enhanced the transcription of PD-L1 in cancer cells, which was accompanied by the upregulation of PD-L1 protein expression, both in the cytoplasm and on the cell surface. This induction of PD-L1 was attenuated in the absence of the transcription factor STAT3. Cell-based studies indicated that PARP1 interacted directly with STAT3 and caused STAT3 poly(ADP-ribosyl)ation. STAT3's activation of PD-L1 transcription was abolished by the overexpression of wild-type PARP1 but not mutant PARP1, which lacks catalytic activity. PARP1 downregulation or catalytic inhibition enhanced the phosphorylation of STAT3, which was reversed by the ectopic expression of wild-type PARP1 but not by mutated PARP1. An inverse correlation between PARP1 and PD-L1 was also observed in clinical ovarian cancer samples. Overall, our study revealed PARP1-mediated poly(ADP-ribosyl)ation of STAT3 as a key step in inhibiting the transcription of PD-L1, and this mechanism exists in a variety of cancer cells.
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Affiliation(s)
- Ling Ding
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xi Chen
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaqing Xu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yuli Qian
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Guikai Liang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Fengqi Yao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhangting Yao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Honghai Wu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Jieqiong Zhang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
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41
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Gagné JP, Langelier MF, Pascal JM, Poirier GG. Hydrofluoric Acid-Based Derivatization Strategy To Profile PARP-1 ADP-Ribosylation by LC-MS/MS. J Proteome Res 2018; 17:2542-2551. [PMID: 29812941 DOI: 10.1021/acs.jproteome.8b00146] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite significant advances in the development of mass spectrometry-based methods for the identification of protein ADP-ribosylation, current protocols suffer from several drawbacks that preclude their widespread applicability. Given the intrinsic heterogeneous nature of poly(ADP-ribose), a number of strategies have been developed to generate simple derivatives for effective interrogation of protein databases and site-specific localization of the modified residues. Currently, the generation of spectral signatures indicative of ADP-ribosylation rely on chemical or enzymatic conversion of the modification to a single mass increment. Still, limitations arise from the lability of the poly(ADP-ribose) remnant during tandem mass spectrometry, the varying susceptibilities of different ADP-ribose-protein bonds to chemical hydrolysis, or the context dependence of enzyme-catalyzed reactions. Here, we present a chemical-based derivatization method applicable to the confident identification of site-specific ADP-ribosylation by conventional mass spectrometry on any targeted amino acid residue. Using PARP-1 as a model protein, we report that treatment of ADP-ribosylated peptides with hydrofluoric acid generates a specific +132 Da mass signature that corresponds to the decomposition of mono- and poly(ADP-ribosylated) peptides into ribose adducts as a consequence of the cleavage of the phosphorus-oxygen bonds.
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Affiliation(s)
- Jean-Philippe Gagné
- Centre de Recherche du CHU de Québec - Pavillon CHUL, Faculté de Médecine , Université Laval , Québec G1V 4G2 Canada
| | - Marie-France Langelier
- Department of Biochemistry and Molecular Medicine , Université de Montréal , 2900 Boulevard Edouard-Montpetit , Montréal H3T 1J4 , Canada
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine , Université de Montréal , 2900 Boulevard Edouard-Montpetit , Montréal H3T 1J4 , Canada
| | - Guy G Poirier
- Centre de Recherche du CHU de Québec - Pavillon CHUL, Faculté de Médecine , Université Laval , Québec G1V 4G2 Canada
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Bütepage M, Preisinger C, von Kriegsheim A, Scheufen A, Lausberg E, Li J, Kappes F, Feederle R, Ernst S, Eckei L, Krieg S, Müller-Newen G, Rossetti G, Feijs KLH, Verheugd P, Lüscher B. Nucleolar-nucleoplasmic shuttling of TARG1 and its control by DNA damage-induced poly-ADP-ribosylation and by nucleolar transcription. Sci Rep 2018; 8:6748. [PMID: 29712969 PMCID: PMC5928194 DOI: 10.1038/s41598-018-25137-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/09/2018] [Indexed: 02/06/2023] Open
Abstract
Macrodomains are conserved protein folds associated with ADP-ribose binding and turnover. ADP-ribosylation is a posttranslational modification catalyzed primarily by ARTD (aka PARP) enzymes in cells. ARTDs transfer either single or multiple ADP-ribose units to substrates, resulting in mono- or poly-ADP-ribosylation. TARG1/C6orf130 is a macrodomain protein that hydrolyzes mono-ADP-ribosylation and interacts with poly-ADP-ribose chains. Interactome analyses revealed that TARG1 binds strongly to ribosomes and proteins associated with rRNA processing and ribosomal assembly factors. TARG1 localized to transcriptionally active nucleoli, which occurred independently of ADP-ribose binding. TARG1 shuttled continuously between nucleoli and nucleoplasm. In response to DNA damage, which activates ARTD1/2 (PARP1/2) and promotes synthesis of poly-ADP-ribose chains, TARG1 re-localized to the nucleoplasm. This was dependent on the ability of TARG1 to bind to poly-ADP-ribose. These findings are consistent with the observed ability of TARG1 to competitively interact with RNA and PAR chains. We propose a nucleolar role of TARG1 in ribosome assembly or quality control that is stalled when TARG1 is re-located to sites of DNA damage.
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Affiliation(s)
- Mareike Bütepage
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Christian Preisinger
- Proteomics Facility, Interdisciplinary Centre for Clinical Research (IZKF), Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Alexander von Kriegsheim
- Systems Biology Ireland, Conway Institute, University College Dublin, Dublin 4, Ireland.,Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Anja Scheufen
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Eva Lausberg
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.,Institute of Human Genetics, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Jinyu Li
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.,College of Chemistry, Fuzhou University, 350116, Fuzhou, China
| | - Ferdinand Kappes
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.,Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, No 111, Ren Ai Road, Dushu Lake Higher Education Town, Suzhou Industrial Park, Suzhou, 215123, P.R. China
| | - Regina Feederle
- Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Neuherberg, Germany
| | - Sabrina Ernst
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.,Immunohistochemistry and Confocal Microscopy Facility, Interdisciplinary Centre for Clinical Research (IZKF), Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Laura Eckei
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Sarah Krieg
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Gerhard Müller-Newen
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.,Immunohistochemistry and Confocal Microscopy Facility, Interdisciplinary Centre for Clinical Research (IZKF), Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425, Jülich, Germany.,Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425, Jülich, Germany.,Department of Oncology, Hematology and Stem Cell Transplantation, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Karla L H Feijs
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Patricia Verheugd
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
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Palazzo L, Leidecker O, Prokhorova E, Dauben H, Matic I, Ahel I. Serine is the major residue for ADP-ribosylation upon DNA damage. eLife 2018; 7:e34334. [PMID: 29480802 PMCID: PMC5837557 DOI: 10.7554/elife.34334] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/23/2018] [Indexed: 12/18/2022] Open
Abstract
Poly(ADP-ribose) polymerases (PARPs) are a family of enzymes that synthesise ADP-ribosylation (ADPr), a reversible modification of proteins that regulates many different cellular processes. Several mammalian PARPs are known to regulate the DNA damage response, but it is not clear which amino acids in proteins are the primary ADPr targets. Previously, we reported that ARH3 reverses the newly discovered type of ADPr (ADPr on serine residues; Ser-ADPr) and developed tools to analyse this modification (Fontana et al., 2017). Here, we show that Ser-ADPr represents the major fraction of ADPr synthesised after DNA damage in mammalian cells and that globally Ser-ADPr is dependent on HPF1, PARP1 and ARH3. In the absence of HPF1, glutamate/aspartate becomes the main target residues for ADPr. Furthermore, we describe a method for site-specific validation of serine ADP-ribosylated substrates in cells. Our study establishes serine as the primary form of ADPr in DNA damage signalling.
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Affiliation(s)
- Luca Palazzo
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUnited Kingdom
| | | | - Evgeniia Prokhorova
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUnited Kingdom
| | - Helen Dauben
- Max Planck Institute for Biology of AgeingCologneGermany
| | - Ivan Matic
- Max Planck Institute for Biology of AgeingCologneGermany
| | - Ivan Ahel
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUnited Kingdom
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Zhen Y, Yu Y. Proteomic Analysis of the Downstream Signaling Network of PARP1. Biochemistry 2018; 57:429-440. [PMID: 29327913 DOI: 10.1021/acs.biochem.7b01022] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Poly-ADP-ribosylation (PARylation) is a protein posttranslational modification (PTM) that is critically involved in many biological processes that are linked to cell stress responses. It is catalyzed by a class of enzymes known as poly-ADP-ribose polymerases (PARPs). In particular, PARP1 is a nuclear protein that is activated upon sensing nicked DNA. Once activated, PARP1 is responsible for the synthesis of a large number of PARylated proteins and initiation of the DNA damage response mechanisms. This observation provided the rationale for developing PARP1 inhibitors for the treatment of human malignancies. Indeed, three PARP1 inhibitors (Olaparib, Rucaparib, and Niraparib) have recently been approved by the Food and Drug Administration for the treatment of ovarian cancer. Moreover, in 2017, both Olaparib and Niraparib have also been approved for the treatment of fallopian tube cancer and primary peritoneal cancer. Despite this very exciting progress in the clinic, the basic signaling mechanism that connects PARP1 to a diverse array of biological processes is still poorly understood. This is, in large part, due to the inherent technical difficulty associated with the analysis of protein PARylation, which is a low-abundance, labile, and heterogeneous PTM. The study of PARylation has been greatly facilitated by the recent advances in mass spectrometry-based proteomic technologies tailored to the analysis of this modification. In this Perspective, we discuss these breakthroughs, including their technical development, and applications that provide a global view of the many biological processes regulated by this important protein modification.
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Affiliation(s)
- Yuanli Zhen
- Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Yonghao Yu
- Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
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