1
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Cheng CY, Chen KP, Tseng TS, Hua KF, Ju TC. The therapeutic potential of (R)-carvedilol in Huntington's disease through enhancement of autophagy-lysosomal pathway via GSK-3β inhibition. Neurotherapeutics 2025; 22:e00557. [PMID: 40011132 PMCID: PMC12047517 DOI: 10.1016/j.neurot.2025.e00557] [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: 12/04/2024] [Revised: 01/22/2025] [Accepted: 02/10/2025] [Indexed: 02/28/2025] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by the abnormal expansion of CAG repeats in the huntingtin (Htt) gene, leading to the aggregation of mutant huntingtin protein (mHTT) in cells, particularly in cortical and striatal neurons. This results in involuntary movements, cognitive impairment, and emotional instability. One of the critical pathogenic mechanisms in HD is impaired autophagy, which plays a vital role in cellular homeostasis by degrading damaged organelles and misfolded proteins through the formation of autophagosomes that fuse with lysosomes. However, the aggregation of mHTT disrupts autophagic function, leading to the accumulation of mHTT and exacerbating the disease's pathogenesis. Carvedilol is an established clinical medication used to treat hypertension and congestive heart failure. It exerts protective effects by blocking both β1-and β2-adrenergic receptors, reducing sympathetic nervous activity, and promoting vasodilation through α1-adrenergic blockade. Carvedilol has been shown to possess antioxidant and anti-inflammatory properties. In this study, we demonstrate that (R)-carvedilol promotes the nuclear translocation of the transcription factor binding to IGHM enhancer 3 (TFE3) by reducing glycogen synthase-3β (GSK-3β) activation, which increases the expression of autophagy-related proteins and facilitates the autophagy-lysosomal pathway (ALP), thereby enhancing mHTT degradation. Additionally, systemic administration of (R)-carvedilol improves mHTT degradation, provides neuroprotection, and inhibits gliosis, effectively ameliorating behavioral impairments and improving disease progression. Overall, these findings indicate that (R)-carvedilol has therapeutic potential for managing HD by promoting autophagy, facilitating the clearance of mHTT aggregates, and demonstrating advantageous properties in an HD transgenic mouse model, highlighting its promise as a treatment option for neurodegenerative diseases.
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Affiliation(s)
- Chih-Yuan Cheng
- Department of Animal Science and Biotechnology, Tunghai University, Taichung 407224, Taiwan; Graduate Institute of Aerospace and Undersea Medicine, National Defense Medical Center, Taipei 114201, Taiwan
| | - Kai-Po Chen
- Department of Animal Science and Biotechnology, Tunghai University, Taichung 407224, Taiwan
| | - Tien-Sheng Tseng
- Institute of Molecular Biology, National Chung Hsing University, Taichung 402202, Taiwan
| | - Kuo-Feng Hua
- Department of Biotechnology and Animal Science, National Ilan University, Ilan 260007, Taiwan; Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
| | - Tz-Chuen Ju
- Institute of Molecular Biology, National Chung Hsing University, Taichung 402202, Taiwan; Doctoral Program in Translational Medicine, National Chung Hsing University, Taichung 402202, Taiwan.
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2
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Smolka M, Comstock W, Navarro M, Maybee D, Rho Y, Wagner M, Wang Y. Proteomic Sensors for Quantitative, Multiplexed and Spatial Monitoring of Kinase Signaling. RESEARCH SQUARE 2025:rs.3.rs-6220494. [PMID: 40196009 PMCID: PMC11975022 DOI: 10.21203/rs.3.rs-6220494/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
Abstract
Understanding kinase action requires precise quantitative measurements of their activity in vivo. In addition, the ability to capture spatial information of kinase activity is crucial to deconvolute complex signaling networks, interrogate multifaceted kinase actions, and assess drug effects or genetic perturbations. Here we developed a proteomic kinase activity sensor platform (ProKAS) for the analysis of kinase signaling using mass spectrometry. ProKAS is based on a tandem array of peptide sensors with amino acid barcodes that allow multiplexed analysis for spatial, kinetic, and screening applications. We engineered a ProKAS module to simultaneously monitor the activities of the DNA damage response kinases ATR, ATM, and CHK1 in response to genotoxic drugs, while also uncovering differences between these signaling responses in the nucleus, cytosol, and replication factories. Furthermore, we developed an in silico approach for the rational design of specific substrate peptides expandable to other kinases. Overall, ProKAS is a novel versatile system for systematically and spatially probing kinase action in cells.
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3
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Waldherr A, Fogtman A. Radiation symptoms resemble laminopathies and the physical underlying cause may sit at the lamin A C-terminus. Mol Med 2025; 31:69. [PMID: 39979866 PMCID: PMC11844092 DOI: 10.1186/s10020-025-01081-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Accepted: 01/13/2025] [Indexed: 02/22/2025] Open
Abstract
Ionizing radiation causes three divergent effects in the human body: On one side, tissue death (= deterministic effects) sets on, on the other side, mutations and cancer growth (= stochastic effects) can occur. In recent years, the additional phenomenon of accelerated aging has come to light. In the following, we argue that these seemingly contradictory radiation responses namely: (i) increased cancer growth, (ii) ablation of cancer tissue or (iii) deterministic senescence, share an underlying cause from damage at the lamin A C-terminus. In other words, besides the typically described genomic radiation impact, we propose an additional destabilization pathway via oxidation at the nuclear envelope. We propose five concrete hypotheses that draw a direct mechanistic model from radiation damage and cellular oxidative stress, to micronuclei and clinical symptoms. In conjunction with lamin B compensation, we might be able to explain why deterministic or stochastic responses dominate. If our model holds true, a novel target for radiotherapeutics and radiooncology arises, and a rationale to closer connect laminopathy and radioprotection research.
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Affiliation(s)
- Alexandra Waldherr
- Max-Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
- European Space Agency, Space Medicine Team, EAC European Astronaut Center, EAC Linder Höhe, 51147, Troisdorf, Germany.
| | - Anna Fogtman
- European Space Agency, Space Medicine Team, EAC European Astronaut Center, EAC Linder Höhe, 51147, Troisdorf, Germany
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4
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Reichlmeir M, Duecker RP, Röhrich H, Key J, Schubert R, Abell K, Possemato AP, Stokes MP, Auburger G. The ataxia-telangiectasia disease protein ATM controls vesicular protein secretion via CHGA and microtubule dynamics via CRMP5. Neurobiol Dis 2024; 203:106756. [PMID: 39615799 DOI: 10.1016/j.nbd.2024.106756] [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: 06/24/2024] [Revised: 11/25/2024] [Accepted: 11/25/2024] [Indexed: 12/16/2024] Open
Abstract
The autosomal recessive disease ataxia-telangiectasia (A-T) presents with cerebellar degeneration, immunodeficiency, radiosensitivity, capillary dilatations, and pulmonary infections. Most symptoms outside the nervous system can be explained by failures of the disease protein ATM as a Ser/Thr-kinase to coordinate DNA damage repair. However, ATM in adult neurons has cytoplasmic localization and vesicle association, where its roles remain unclear. Here, we defined novel ATM protein targets in human neuroblastoma cells, and filtered initial pathogenesis events in ATM-null mouse cerebellum. Profiles of global proteome and phosphoproteomics - both direct ATM/ATR substrates and overall phosphorylation changes - confirmed previous findings for NBN, MRE11, MDC1, CHEK1, EIF4EBP1, AP3B2, PPP2R5C, SYN1 and SLC2A1. Even stronger downregulation of ATM/ATR substrate phosphopeptides after ATM-depletion was documented for CHGA, EXPH5, NBEAL2 and CHMP6 as key factors of protein secretion and endosome dynamics, as well as for CRMP5, DISP2, PHACTR1, PLXNC1, INA and TPX2 as neurite extension factors. Prominent effects on semaphorin-CRMP5-microtubule signals and ATM association with CRMP5 were validated. As a functional consequence, microtubules were stabilized, and neurite retraction ensued. The impact of ATM on secretory granules confirms previous ATM-null cerebellar transcriptome findings. This study provides the first link of A-T neural atrophy to growth cone collapse and aberrant microtubule dynamics.
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Affiliation(s)
- Marina Reichlmeir
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany.
| | - Ruth Pia Duecker
- Division for Allergy, Pneumatology and Cystic Fibrosis, Department for Children and Adolescence, Goethe-University, Frankfurt am Main, Germany.
| | - Hanna Röhrich
- Institute for Experimental Pediatric Hematology and Oncology, Medical Faculty, Goethe-University Frankfurt, Komturstrasse 3a, 60528 Frankfurt am Main, Germany.
| | - Jana Key
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany.
| | - Ralf Schubert
- Division for Allergy, Pneumatology and Cystic Fibrosis, Department for Children and Adolescence, Goethe-University, Frankfurt am Main, Germany.
| | - Kathryn Abell
- Cell Signaling Technology, Inc., Danvers, MA 01923, USA.
| | | | | | - Georg Auburger
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany.
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5
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Lam SY, van der Lugt R, Cerutti A, Yalçin Z, Thouin AM, Simonetta M, Jacobs JJL. OTUD5 promotes end-joining of deprotected telomeres by promoting ATM-dependent phosphorylation of KAP1 S824. Nat Commun 2024; 15:8960. [PMID: 39420004 PMCID: PMC11486905 DOI: 10.1038/s41467-024-53404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 10/08/2024] [Indexed: 10/19/2024] Open
Abstract
Appropriate repair of damaged DNA and the suppression of DNA damage responses at telomeres are essential to preserve genome stability. DNA damage response (DDR) signaling consists of cascades of kinase-driven phosphorylation events, fine-tuned by proteolytic and regulatory ubiquitination. It is not fully understood how crosstalk between these two major classes of post-translational modifications impact DNA repair at deprotected telomeres. Hence, we performed a functional genetic screen to search for ubiquitin system factors that promote KAP1S824 phosphorylation, a robust DDR marker at deprotected telomeres. We identified that the OTU family deubiquitinase (DUB) OTUD5 promotes KAP1S824 phosphorylation by facilitating ATM activation, through stabilization of the ubiquitin ligase UBR5 that is required for DNA damage-induced ATM activity. Loss of OTUD5 impairs KAP1S824 phosphorylation, which suppresses end-joining mediated DNA repair at deprotected telomeres and at DNA breaks in heterochromatin. Moreover, we identified an unexpected role for the heterochromatin factor KAP1 in suppressing DNA repair at telomeres. Altogether our work reveals an important role for OTUD5 and KAP1 in relaying DDR-dependent kinase signaling to the control of DNA repair at telomeres and heterochromatin.
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Affiliation(s)
- Shiu Yeung Lam
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ruben van der Lugt
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aurora Cerutti
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Zeliha Yalçin
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alexander M Thouin
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marco Simonetta
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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6
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Torres-Diz M, Reglero C, Falkenstein CD, Castro A, Hayer KE, Radens CM, Quesnel-Vallières M, Ang Z, Sehgal P, Li MM, Barash Y, Tasian SK, Ferrando A, Thomas-Tikhonenko A. An Alternatively Spliced Gain-of-Function NT5C2 Isoform Contributes to Chemoresistance in Acute Lymphoblastic Leukemia. Cancer Res 2024; 84:3327-3336. [PMID: 39094066 PMCID: PMC11474164 DOI: 10.1158/0008-5472.can-23-3804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/11/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
Relapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL) is a major cause of pediatric cancer-related deaths. Relapse-specific mutations do not account for all chemotherapy failures in B-ALL patients, suggesting additional mechanisms of resistance. By mining RNA sequencing datasets of paired diagnostic/relapse pediatric B-ALL samples, we discovered pervasive alternative splicing (AS) patterns linked to relapse and affecting drivers of resistance to glucocorticoids, antifolates, and thiopurines. Most splicing variations represented cassette exon skipping, "poison" exon inclusion, and intron retention, phenocopying well-documented loss-of-function mutations. In contrast, relapse-associated AS of NT5C2 mRNA yielded an isoform with the functionally uncharacterized in-frame exon 6a. Incorporation of the 8-amino acid sequence SQVAVQKR into this enzyme created a putative phosphorylation site and resulted in elevated nucleosidase activity, which is a known consequence of gain-of-function mutations in NT5C2 and a common determinant of 6-mercaptopurine resistance. Consistent with this finding, NT5C2ex6a and the R238W hotspot variant conferred comparable levels of resistance to 6-mercaptopurine in B-ALL cells both in vitro and in vivo. Furthermore, both NT5C2ex6a and the R238W variant induced collateral sensitivity to the inosine monophosphate dehydrogenase inhibitor mizoribine. These results ascribe to splicing perturbations an important role in chemotherapy resistance in relapsed B-ALL and suggest that inosine monophosphate dehydrogenase inhibitors, including the commonly used immunosuppressive agent mycophenolate mofetil, could be a valuable therapeutic option for treating thiopurine-resistant leukemias. Significance: Alternative splicing is a potent mechanism of acquired drug resistance in relapsed/refractory acute lymphoblastic leukemias that has diagnostic and therapeutic implications for patients who lack mutations in known chemoresistance genes.
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Affiliation(s)
- Manuel Torres-Diz
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania.
| | - Clara Reglero
- Institute for Cancer Genetics, Columbia University, New York, New York.
| | | | - Annette Castro
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania.
| | - Katharina E. Hayer
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania.
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania.
| | - Caleb M. Radens
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania.
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Mathieu Quesnel-Vallières
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Zhiwei Ang
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania.
| | - Priyanka Sehgal
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania.
| | - Marilyn M. Li
- Division of Genomic Diagnostic, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Yoseph Barash
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania.
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Sarah K. Tasian
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania.
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University, New York, New York.
- Department of Pediatrics, Columbia University, New York, New York.
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania.
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania.
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
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7
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Zhao L, Yuan J, Wang G, Jing H, Huang C, Xu L, Xu X, Sun T, Chen W, Mao X, Li G. Chromosome-level genome and population genomics of the intermediate horseshoe bat ( Rhinolophus affinis) reveal the molecular basis of virus tolerance in Rhinolophus and echolocation call frequency variation. Zool Res 2024; 45:1147-1160. [PMID: 39257377 PMCID: PMC11491789 DOI: 10.24272/j.issn.2095-8137.2024.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 05/29/2024] [Indexed: 09/12/2024] Open
Abstract
Horseshoe bats (genus Rhinolophus, family Rhinolophidae) represent an important group within chiropteran phylogeny due to their distinctive traits, including constant high-frequency echolocation, rapid karyotype evolution, and unique immune system. Advances in evolutionary biology, supported by high-quality reference genomes and comprehensive whole-genome data, have significantly enhanced our understanding of species origins, speciation mechanisms, adaptive evolutionary processes, and phenotypic diversity. However, genomic research and understanding of the evolutionary patterns of Rhinolophus are severely constrained by limited data, with only a single published genome of R. ferrumequinum currently available. In this study, we constructed a high-quality chromosome-level reference genome for the intermediate horseshoe bat ( R. affinis). Comparative genomic analyses revealed potential genetic characteristics associated with virus tolerance in Rhinolophidae. Notably, we observed expansions in several immune-related gene families and identified various genes functionally associated with the SARS-CoV-2 signaling pathway, DNA repair, and apoptosis, which displayed signs of rapid evolution. In addition, we observed an expansion of the major histocompatibility complex class II (MHC-II) region and a higher copy number of the HLA- DQB2 gene in horseshoe bats compared to other chiropteran species. Based on whole-genome resequencing and population genomic analyses, we identified multiple candidate loci (e.g., GLI3) associated with variations in echolocation call frequency across R. affinis subspecies. This research not only expands our understanding of the genetic characteristics of the Rhinolophus genus but also establishes a valuable foundation for future research.
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Affiliation(s)
- Le Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C.I.C., School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Guiqiang Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Haohao Jing
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Ting Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou, Guangdong 510070, China
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China. E-mail:
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
- Guangzhou Zoo, Guangzhou, Guangdong 510070, China. E-mail:
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8
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Li C, Fan S, Li P, Bai Y, Wang Y, Cui Y, Li M, Wang R, Shao Y, Wang Y, Zheng S, Wang R, Gao L, Li M, Zheng Y, Wang F, Gao S, Feng S, Wang J, Qu X, Li X. A sophisticated mechanism governs Pol ζ activity in response to replication stress. Nat Commun 2024; 15:7562. [PMID: 39215012 PMCID: PMC11364643 DOI: 10.1038/s41467-024-52112-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024] Open
Abstract
DNA polymerase ζ (Pol ζ) plays an essential role in replicating damaged DNA templates but contributes to mutagenesis due to its low fidelity. Therefore, ensuring tight control of Pol ζ's activity is critical for continuous and accurate DNA replication, yet the specific mechanisms remain unclear. This study reveals a regulation mechanism of Pol ζ activity in human cells. Under normal conditions, an autoinhibition mechanism keeps the catalytic subunit, REV3L, inactive. Upon encountering replication stress, however, ATR-mediated phosphorylation of REV3L's S279 cluster activates REV3L and triggers its degradation via a caspase-mediated pathway. This regulation confines the activity of Pol ζ, balancing its essential role against its mutations causing potential during replication stress. Overall, our findings elucidate a control scheme that fine tunes the low-fidelity polymerase activity of Pol ζ under challenging replication scenarios.
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Affiliation(s)
- Chun Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Shuchen Fan
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Pan Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuzhen Bai
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Ye Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yueyun Cui
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Mengdi Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Ruru Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuan Shao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yingying Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Shuo Zheng
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Rong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Lijun Gao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Miaomiao Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuanyuan Zheng
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Fengting Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Sihang Gao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Shiguo Feng
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Jianing Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xinqi Qu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xialu Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China.
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9
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Jadav R, Weiland F, Noordermeer SM, Carroll T, Gao Y, Wang J, Zhou H, Lamoliatte F, Toth R, Macartney T, Brown F, Hastie CJ, Alabert C, van Attikum H, Zenke F, Masson JY, Rouse J. Chemo-Phosphoproteomic Profiling with ATR Inhibitors Berzosertib and Gartisertib Uncovers New Biomarkers and DNA Damage Response Regulators. Mol Cell Proteomics 2024; 23:100802. [PMID: 38880245 PMCID: PMC11338954 DOI: 10.1016/j.mcpro.2024.100802] [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: 09/15/2023] [Revised: 06/04/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024] Open
Abstract
The ATR kinase protects cells against DNA damage and replication stress and represents a promising anti-cancer drug target. The ATR inhibitors (ATRi) berzosertib and gartisertib are both in clinical trials for the treatment of advanced solid tumors as monotherapy or in combination with genotoxic agents. We carried out quantitative phospho-proteomic screening for ATR biomarkers that are highly sensitive to berzosertib and gartisertib, using an optimized mass spectrometry pipeline. Screening identified a range of novel ATR-dependent phosphorylation events, which were grouped into three broad classes: (i) targets whose phosphorylation is highly sensitive to ATRi and which could be the next generation of ATR biomarkers; (ii) proteins with known genome maintenance roles not previously known to be regulated by ATR; (iii) novel targets whose cellular roles are unclear. Class iii targets represent candidate DNA damage response proteins and, with this in mind, proteins in this class were subjected to secondary screening for recruitment to DNA damage sites. We show that one of the proteins recruited, SCAF1, interacts with RNAPII in a phospho-dependent manner and recruitment requires PARP activity and interaction with RNAPII. We also show that SCAF1 deficiency partly rescues RAD51 loading in cells lacking the BRCA1 tumor suppressor. Taken together these data reveal potential new ATR biomarkers and new genome maintenance factors.
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Affiliation(s)
- Rathan Jadav
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Florian Weiland
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Sylvie M Noordermeer
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands; Department of Genetics, Oncode Institute, Utrecht, The Netherlands
| | - Thomas Carroll
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Yuandi Gao
- CHU de Quebec Research Center, Oncology Division, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec Cit, Quebec, Canada
| | - Jianming Wang
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Houjiang Zhou
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Thomas Macartney
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Fiona Brown
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - C James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Constance Alabert
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Frank Zenke
- EMD Serono, Research Unit Oncology, Billerica, Massachusetts, USA
| | - Jean-Yves Masson
- CHU de Quebec Research Center, Oncology Division, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec Cit, Quebec, Canada
| | - John Rouse
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK.
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10
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Ma R, Xu X. Deciphering the role of post-translational modifications in fanconi anemia proteins and their influence on tumorigenesis. Cancer Gene Ther 2024; 31:1113-1123. [PMID: 38879655 DOI: 10.1038/s41417-024-00797-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 08/17/2024]
Abstract
Fanconi anemia (FA) is an autosomal or X-linked human disease, characterized by bone marrow failure, cancer susceptibility and various developmental abnormalities. So far, at least 22 FA genes (FANCA-W) have been identified. Germline inactivation of any one of these FA genes causes FA symptoms. Proteins encoded by FA genes are involved in the Fanconi anemia pathway, which is known for its roles in DNA inter-strand crosslinks (ICLs) repair. Besides, its roles in genome maintenance upon replication stress has also been reported. Post-translational modifications (PTMs) of FA proteins, particularly phosphorylation and ubiquitination, emerge as critical determinants in the activation of the FA pathway during ICL repair or replication stress response. Consequent inactivation of the FA pathway engenders heightened chromosomal instability, thereby constituting a genetic susceptibility conducive to cancer predisposition and the exacerbation of tumorigenesis. In this review, we have combined recent structural analysis of FA proteins and summarized knowledge on the functions of different PTMs in regulating FA pathways, and discuss potential contributions stemming from mutations at PTMs to the genesis and progression of tumorigenesis.
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Affiliation(s)
- Rui Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xinlin Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
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11
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Torres-Diz M, Reglero C, Falkenstein CD, Castro A, Hayer KE, Radens CM, Quesnel-Vallières M, Ang Z, Sehgal P, Li MM, Barash Y, Tasian SK, Ferrando A, Thomas-Tikhonenko A. An Alternatively Spliced Gain-of-Function NT5C2 Isoform Contributes to Chemoresistance in Acute Lymphoblastic Leukemia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557413. [PMID: 39091882 PMCID: PMC11291008 DOI: 10.1101/2023.09.14.557413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Relapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL) is a major cause of pediatric cancer-related deaths. Relapse-specific mutations do not account for all chemotherapy failures in B- ALL patients, suggesting additional mechanisms of resistance. By mining RNA-seq datasets of paired diagnostic/relapse pediatric B-ALL samples, we discovered pervasive alternative splicing (AS) patterns linked to relapse and affecting drivers of resistance to glucocorticoids, anti-folates, and thiopurines. Most splicing variations represented cassette exon skipping, "poison" exon inclusion, and intron retention, phenocopying well-documented loss-of-function mutations. In contrast, relapse-associated AS of NT5C2 mRNA yielded an isoform with the functionally uncharacterized in-frame exon 6a. Incorporation of the 8-amino acid sequence SQVAVQKR into this enzyme created a putative phosphorylation site and resulted in elevated nucleosidase activity, which is a known consequence of gain-of-function mutations in NT5C2 and a common determinant of 6-mercaptopurine (6-MP) resistance. Consistent with this finding, NT5C2ex6a and the R238W hotspot variant conferred comparable levels of resistance to 6-MP in B-ALL cells both in vitro and in vivo. Furthermore, both the NT5C2ex6a and R238W variants induced collateral sensitivity to the inosine monophosphate dehydrogenase (IMPDH) inhibitor mizoribine. These results ascribe an important role for splicing perturbations in chemotherapy resistance in relapsed B-ALL and suggest that IMPDH inhibitors, including the commonly used immunosuppressive agent mycophenolate mofetil, could be a valuable therapeutic option for treating thiopurine-resistant leukemias.
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12
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Yu L, Deng Y, Wang X, Santos C, Davis IJ, Earp HS, Liu P. Co-targeting JAK1/STAT6/GAS6/TAM signaling improves chemotherapy efficacy in Ewing sarcoma. Nat Commun 2024; 15:5292. [PMID: 38906855 PMCID: PMC11192891 DOI: 10.1038/s41467-024-49667-2] [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: 09/14/2023] [Accepted: 06/14/2024] [Indexed: 06/23/2024] Open
Abstract
Ewing sarcoma is a pediatric bone and soft tissue tumor treated with chemotherapy, radiation, and surgery. Despite intensive multimodality therapy, ~50% patients eventually relapse and die of the disease due to chemoresistance. Here, using phospho-profiling, we find Ewing sarcoma cells treated with chemotherapeutic agents activate TAM (TYRO3, AXL, MERTK) kinases to augment Akt and ERK signaling facilitating chemoresistance. Mechanistically, chemotherapy-induced JAK1-SQ phosphorylation releases JAK1 pseudokinase domain inhibition allowing for JAK1 activation. This alternative JAK1 activation mechanism leads to STAT6 nuclear translocation triggering transcription and secretion of the TAM kinase ligand GAS6 with autocrine/paracrine consequences. Importantly, pharmacological inhibition of either JAK1 by filgotinib or TAM kinases by UNC2025 sensitizes Ewing sarcoma to chemotherapy in vitro and in vivo. Excitingly, the TAM kinase inhibitor MRX-2843 currently in human clinical trials to treat AML and advanced solid tumors, enhances chemotherapy efficacy to further suppress Ewing sarcoma tumor growth in vivo. Our findings reveal an Ewing sarcoma chemoresistance mechanism with an immediate translational value.
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Affiliation(s)
- Le Yu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yu Deng
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Xiaodong Wang
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Charlene Santos
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pediatrics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - H Shelton Earp
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Medicine and Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Pengda Liu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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13
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Geng A, Sun J, Tang H, Yu Y, Wang X, Zhang J, Wang X, Sun X, Zhou X, Gao N, Tan R, Xu Z, Jiang Y, Mao Z. SIRT2 promotes base excision repair by transcriptionally activating OGG1 in an ATM/ATR-dependent manner. Nucleic Acids Res 2024; 52:5107-5120. [PMID: 38554113 PMCID: PMC11109957 DOI: 10.1093/nar/gkae190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/10/2024] [Accepted: 03/11/2024] [Indexed: 04/01/2024] Open
Abstract
Sirtuin 2 (SIRT2) regulates the maintenance of genome integrity by targeting pathways of DNA damage response and homologous recombination repair. However, whether and how SIRT2 promotes base excision repair (BER) remain to be determined. Here, we found that independent of its catalytic activity SIRT2 interacted with the critical glycosylase OGG1 to promote OGG1 recruitment to its own promoter upon oxidative stress, thereby enhancing OGG1 promoter activity and increasing BER efficiency. Further studies revealed that SIRT2 was phosphorylated on S46 and S53 by ATM/ATR upon oxidative stress, and SIRT2 phosphorylation enhanced the SIRT2-OGG1 interaction and mediated the stimulatory effect of SIRT2 on OGG1 promoter activity. We also characterized 37 cancer-derived SIRT2 mutants and found that 5 exhibited the loss of the stimulatory effects on OGG1 transcription. Together, our data reveal that SIRT2 acts as a tumor suppressor by promoting OGG1 transcription and increasing BER efficiency in an ATM/ATR-dependent manner.
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Affiliation(s)
- Anke Geng
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiahui Sun
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Huanyin Tang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yang Yu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiyue Wang
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Jingyuan Zhang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaona Wang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaoxiang Sun
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaofang Zhou
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Neng Gao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Rong Tan
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zhu Xu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Ying Jiang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhiyong Mao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- School of Medicine, Tongji University, Shanghai 200092, China
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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14
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Chuang CN, Liu HC, Woo TT, Chao JL, Chen CY, Hu HT, Hsueh YP, Wang TF. Noncanonical usage of stop codons in ciliates expands proteins with structurally flexible Q-rich motifs. eLife 2024; 12:RP91405. [PMID: 38393970 PMCID: PMC10942620 DOI: 10.7554/elife.91405] [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] [Indexed: 02/25/2024] Open
Abstract
Serine(S)/threonine(T)-glutamine(Q) cluster domains (SCDs), polyglutamine (polyQ) tracts and polyglutamine/asparagine (polyQ/N) tracts are Q-rich motifs found in many proteins. SCDs often are intrinsically disordered regions that mediate protein phosphorylation and protein-protein interactions. PolyQ and polyQ/N tracts are structurally flexible sequences that trigger protein aggregation. We report that due to their high percentages of STQ or STQN amino acid content, four SCDs and three prion-causing Q/N-rich motifs of yeast proteins possess autonomous protein expression-enhancing activities. Since these Q-rich motifs can endow proteins with structural and functional plasticity, we suggest that they represent useful toolkits for evolutionary novelty. Comparative Gene Ontology (GO) analyses of the near-complete proteomes of 26 representative model eukaryotes reveal that Q-rich motifs prevail in proteins involved in specialized biological processes, including Saccharomyces cerevisiae RNA-mediated transposition and pseudohyphal growth, Candida albicans filamentous growth, ciliate peptidyl-glutamic acid modification and microtubule-based movement, Tetrahymena thermophila xylan catabolism and meiosis, Dictyostelium discoideum development and sexual cycles, Plasmodium falciparum infection, and the nervous systems of Drosophila melanogaster, Mus musculus and Homo sapiens. We also show that Q-rich-motif proteins are expanded massively in 10 ciliates with reassigned TAAQ and TAGQ codons. Notably, the usage frequency of CAGQ is much lower in ciliates with reassigned TAAQ and TAGQ codons than in organisms with expanded and unstable Q runs (e.g. D. melanogaster and H. sapiens), indicating that the use of noncanonical stop codons in ciliates may have coevolved with codon usage biases to avoid triplet repeat disorders mediated by CAG/GTC replication slippage.
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Affiliation(s)
| | - Hou-Cheng Liu
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Tai-Ting Woo
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Ju-Lan Chao
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Chiung-Ya Chen
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Hisao-Tang Hu
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
- Department of Biochemical Science and Technology, National Chiayi UniversityChiayiTaiwan
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
- Department of Biochemical Science and Technology, National Chiayi UniversityChiayiTaiwan
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15
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Liu MY, Lin KR, Chien YL, Yang BZ, Tsui LY, Chu HP, Wu CSP. ATR phosphorylates DHX9 at serine 321 to suppress R-loop accumulation upon genotoxic stress. Nucleic Acids Res 2024; 52:204-222. [PMID: 37930853 PMCID: PMC10783509 DOI: 10.1093/nar/gkad973] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/19/2023] [Accepted: 10/16/2023] [Indexed: 11/08/2023] Open
Abstract
Aberrant DNA/RNA hybrids (R-loops) formed during transcription and replication disturbances pose threats to genome stability. DHX9 is an RNA helicase involved in R-loop resolution, but how DHX9 is regulated in response to genotoxic stress remains unclear. Here we report that DHX9 is phosphorylated at S321 and S688, with S321 phosphorylation primarily induced by ATR after DNA damage. Phosphorylation of DHX9 at S321 promotes its interaction with γH2AX, BRCA1 and RPA, and is required for its association with R-loops under genotoxic stress. Inhibition of ATR or expression of the non-phosphorylatable DHX9S321A prevents DHX9 from interacting with RPA and R-loops, leading to the accumulation of stress-induced R-loops. Furthermore, depletion of RPA reduces the association between DHX9 and γH2AX, and in vitro binding analysis confirms a direct interaction between DHX9 and RPA. Notably, cells with the non-phosphorylatable DHX9S321A variant exhibit hypersensitivity to genotoxic stress, while those expressing the phosphomimetic DHX9S321D variant prevent R-loop accumulation and display resistance to DNA damage agents. In summary, we uncover a new mechanism by which ATR directly regulates DHX9 through phosphorylation to eliminate stress-induced R-loops.
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Affiliation(s)
- Mei-Yin Liu
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Keng-Ru Lin
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Yuh-Ling Chien
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Bing-Ze Yang
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Li-Yu Tsui
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | | | - Ching-Shyi Peter Wu
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
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16
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Colding-Christensen CS, Kakulidis ES, Arroyo-Gomez J, Hendriks IA, Arkinson C, Fábián Z, Gambus A, Mailand N, Duxin JP, Nielsen ML. Profiling ubiquitin signalling with UBIMAX reveals DNA damage- and SCF β-Trcp1-dependent ubiquitylation of the actin-organizing protein Dbn1. Nat Commun 2023; 14:8293. [PMID: 38097601 PMCID: PMC10721886 DOI: 10.1038/s41467-023-43873-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Ubiquitin widely modifies proteins, thereby regulating most cellular functions. The complexity of ubiquitin signalling necessitates unbiased methods enabling global detection of dynamic protein ubiquitylation. Here, we describe UBIMAX (UBiquitin target Identification by Mass spectrometry in Xenopus egg extracts), which enriches ubiquitin-conjugated proteins and quantifies regulation of protein ubiquitylation under precise and adaptable conditions. We benchmark UBIMAX by investigating DNA double-strand break-responsive ubiquitylation events, identifying previously known targets and revealing the actin-organizing protein Dbn1 as a major target of DNA damage-induced ubiquitylation. We find that Dbn1 is targeted for proteasomal degradation by the SCFβ-Trcp1 ubiquitin ligase, in a conserved mechanism driven by ATM-mediated phosphorylation of a previously uncharacterized β-Trcp1 degron containing an SQ motif. We further show that this degron is sufficient to induce DNA damage-dependent protein degradation of a model substrate. Collectively, we demonstrate UBIMAX's ability to identify targets of stimulus-regulated ubiquitylation and reveal an SCFβ-Trcp1-mediated ubiquitylation mechanism controlled directly by the apical DNA damage response kinases.
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Affiliation(s)
- Camilla S Colding-Christensen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Ellen S Kakulidis
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Javier Arroyo-Gomez
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Ivo A Hendriks
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Connor Arkinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- California Institute for Quantitative Biosciences and Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Zita Fábián
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Agnieszka Gambus
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Niels Mailand
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Julien P Duxin
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.
| | - Michael L Nielsen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.
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17
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Yu Z, Kim HJ, Dernburg AF. ATM signaling modulates cohesin behavior in meiotic prophase and proliferating cells. Nat Struct Mol Biol 2023; 30:436-450. [PMID: 36879153 PMCID: PMC10113158 DOI: 10.1038/s41594-023-00929-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 01/25/2023] [Indexed: 03/08/2023]
Abstract
Cohesins are ancient and ubiquitous regulators of chromosome architecture and function, but their diverse roles and regulation remain poorly understood. During meiosis, chromosomes are reorganized as linear arrays of chromatin loops around a cohesin axis. This unique organization underlies homolog pairing, synapsis, double-stranded break induction, and recombination. We report that axis assembly in Caenorhabditis elegans is promoted by DNA-damage response (DDR) kinases that are activated at meiotic entry, even in the absence of DNA breaks. Downregulation of the cohesin-destabilizing factor WAPL-1 by ATM-1 promotes axis association of cohesins containing the meiotic kleisins COH-3 and COH-4. ECO-1 and PDS-5 also contribute to stabilizing axis-associated meiotic cohesins. Further, our data suggest that cohesin-enriched domains that promote DNA repair in mammalian cells also depend on WAPL inhibition by ATM. Thus, DDR and Wapl seem to play conserved roles in cohesin regulation in meiotic prophase and proliferating cells.
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Affiliation(s)
- Zhouliang Yu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,California Institute for Quantitative Biosciences, Berkeley, CA, USA
| | - Hyung Jun Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Abby F Dernburg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,California Institute for Quantitative Biosciences, Berkeley, CA, USA.
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18
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Choi E, Mun GI, Lee J, Lee H, Cho J, Lee YS. BRCA1 deficiency in triple-negative breast cancer: Protein stability as a basis for therapy. Biomed Pharmacother 2023; 158:114090. [PMID: 36493696 DOI: 10.1016/j.biopha.2022.114090] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/24/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Mutations in breast cancer-associated 1 (BRCA1) increase the lifetime risk of developing breast cancer by up to 51% over the risk of the general population. Many aspects of this multifunctional protein have been revealed, including its essential role in homologous recombination repair, E3 ubiquitin ligase activity, transcriptional regulation, and apoptosis. Although most studies have focused on BRCA1 deficiency due to mutations, only a minority of patients carry BRCA1 mutations. A recent study has suggested an expanded definition of BRCA1 deficiency with reduced BRCA1 levels, which accounts for almost half of all triple-negative breast cancer (TNBC) patients. Reduced BRCA1 levels can result from epigenetic modifications or increased proteasomal degradation. In this review, we discuss how this knowledge of BRCA1 function and regulation of BRCA1 protein stability can help overcome the challenges encountered in the clinic and advance current treatment strategies for BRCA1-related breast cancer patients, especially focusing on TNBC.
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Affiliation(s)
- Eun Choi
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Gil-Im Mun
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Joohyun Lee
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hanhee Lee
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jaeho Cho
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Yun-Sil Lee
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea.
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19
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Huang Y, Roig I. Genetic control of meiosis surveillance mechanisms in mammals. Front Cell Dev Biol 2023; 11:1127440. [PMID: 36910159 PMCID: PMC9996228 DOI: 10.3389/fcell.2023.1127440] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
Meiosis is a specialized cell division that generates haploid gametes and is critical for successful sexual reproduction. During the extended meiotic prophase I, homologous chromosomes progressively pair, synapse and desynapse. These chromosomal dynamics are tightly integrated with meiotic recombination (MR), during which programmed DNA double-strand breaks (DSBs) are formed and subsequently repaired. Consequently, parental chromosome arms reciprocally exchange, ultimately ensuring accurate homolog segregation and genetic diversity in the offspring. Surveillance mechanisms carefully monitor the MR and homologous chromosome synapsis during meiotic prophase I to avoid producing aberrant chromosomes and defective gametes. Errors in these critical processes would lead to aneuploidy and/or genetic instability. Studies of mutation in mouse models, coupled with advances in genomic technologies, lead us to more clearly understand how meiosis is controlled and how meiotic errors are linked to mammalian infertility. Here, we review the genetic regulations of these major meiotic events in mice and highlight our current understanding of their surveillance mechanisms. Furthermore, we summarize meiotic prophase genes, the mutations that activate the surveillance system leading to meiotic prophase arrest in mouse models, and their corresponding genetic variants identified in human infertile patients. Finally, we discuss their value for the diagnosis of causes of meiosis-based infertility in humans.
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Affiliation(s)
- Yan Huang
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Histology Unit, Department of Cell Biology, Physiology, and Immunology, Cytology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ignasi Roig
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Histology Unit, Department of Cell Biology, Physiology, and Immunology, Cytology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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20
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El Nachef L, Berthel E, Ferlazzo ML, Le Reun E, Al-Choboq J, Restier-Verlet J, Granzotto A, Sonzogni L, Bourguignon M, Foray N. Cancer and Radiosensitivity Syndromes: Is Impaired Nuclear ATM Kinase Activity the Primum Movens? Cancers (Basel) 2022; 14:cancers14246141. [PMID: 36551628 PMCID: PMC9776478 DOI: 10.3390/cancers14246141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/01/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
There are a number of genetic syndromes associated with both high cancer risk and clinical radiosensitivity. However, the link between these two notions remains unknown. Particularly, some cancer syndromes are caused by mutations in genes involved in DNA damage signaling and repair. How are the DNA sequence errors propagated and amplified to cause cell transformation? Conversely, some cancer syndromes are caused by mutations in genes involved in cell cycle checkpoint control. How is misrepaired DNA damage produced? Lastly, certain genes, considered as tumor suppressors, are not involved in DNA damage signaling and repair or in cell cycle checkpoint control. The mechanistic model based on radiation-induced nucleoshuttling of the ATM kinase (RIANS), a major actor of the response to ionizing radiation, may help in providing a unified explanation of the link between cancer proneness and radiosensitivity. In the frame of this model, a given protein may ensure its own specific function but may also play additional biological role(s) as an ATM phosphorylation substrate in cytoplasm. It appears that the mutated proteins that cause the major cancer and radiosensitivity syndromes are all ATM phosphorylation substrates, and they generally localize in the cytoplasm when mutated. The relevance of the RIANS model is discussed by considering different categories of the cancer syndromes.
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Affiliation(s)
- Laura El Nachef
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Elise Berthel
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Mélanie L. Ferlazzo
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Eymeric Le Reun
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Joelle Al-Choboq
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Juliette Restier-Verlet
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Adeline Granzotto
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Laurène Sonzogni
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Michel Bourguignon
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
- Department of Biophysics and Nuclear Medicine, Université Paris Saclay (UVSQ), 78035 Versailles, France
| | - Nicolas Foray
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
- Correspondence: ; Tel.: +33-04-7878-2828
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21
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Láscarez-Lagunas LI, Nadarajan S, Martinez-Garcia M, Quinn JN, Todisco E, Thakkar T, Berson E, Eaford D, Crawley O, Montoya A, Faull P, Ferrandiz N, Barroso C, Labella S, Koury E, Smolikove S, Zetka M, Martinez-Perez E, Colaiácovo MP. ATM/ATR kinases link the synaptonemal complex and DNA double-strand break repair pathway choice. Curr Biol 2022; 32:4719-4726.e4. [PMID: 36137547 PMCID: PMC9643613 DOI: 10.1016/j.cub.2022.08.081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/22/2022] [Accepted: 08/31/2022] [Indexed: 11/21/2022]
Abstract
DNA double-strand breaks (DSBs) are deleterious lesions, which must be repaired precisely to maintain genomic stability. During meiosis, programmed DSBs are repaired via homologous recombination (HR) while repair using the nonhomologous end joining (NHEJ) pathway is inhibited, thereby ensuring crossover formation and accurate chromosome segregation.1,2 How DSB repair pathway choice is implemented during meiosis is unknown. In C. elegans, meiotic DSB repair takes place in the context of the fully formed, highly dynamic zipper-like structure present between homologous chromosomes called the synaptonemal complex (SC).3,4,5,6,7,8,9 The SC consists of a pair of lateral elements bridged by a central region composed of the SYP proteins in C. elegans. How the structural components of the SC are regulated to maintain the architectural integrity of the assembled SC around DSB repair sites remained unclear. Here, we show that SYP-4, a central region component of the SC, is phosphorylated at Serine 447 in a manner dependent on DSBs and the ATM/ATR DNA damage response kinases. We show that this SYP-4 phosphorylation is critical for preserving the SC structure following exogenous (γ-IR-induced) DSB formation and for promoting normal DSB repair progression and crossover patterning following SPO-11-dependent and exogenous DSBs. We propose a model in which ATM/ATR-dependent phosphorylation of SYP-4 at the S447 site plays important roles both in maintaining the architectural integrity of the SC following DSB formation and in warding off repair via the NHEJ repair pathway, thereby preventing aneuploidy.
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Affiliation(s)
- Laura I Láscarez-Lagunas
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Saravanapriah Nadarajan
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Marina Martinez-Garcia
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Julianna N Quinn
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Elena Todisco
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Tanuj Thakkar
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Elizaveta Berson
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Don Eaford
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Oliver Crawley
- MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Alex Montoya
- MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Peter Faull
- MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Nuria Ferrandiz
- MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Consuelo Barroso
- MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Sara Labella
- McGill University, Biology Department, Stewart Biology Building, Room W5/24 1205 Dr. Penfield Avenue, Montreal, QC H3A1B1, Canada
| | - Emily Koury
- Department of Biology, The University of Iowa, Biology Building, Room 308, 129 E. Jefferson, Iowa City, IA 52242-1324, USA
| | - Sarit Smolikove
- Department of Biology, The University of Iowa, Biology Building, Room 308, 129 E. Jefferson, Iowa City, IA 52242-1324, USA
| | - Monique Zetka
- McGill University, Biology Department, Stewart Biology Building, Room W5/24 1205 Dr. Penfield Avenue, Montreal, QC H3A1B1, Canada
| | - Enrique Martinez-Perez
- MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Monica P Colaiácovo
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA.
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22
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Classen S, Rahlf E, Jungwirth J, Albers N, Hebestreit LP, Zielinski A, Poole L, Groth M, Koch P, Liehr T, Kankel S, Cordes N, Petersen C, Rothkamm K, Pospiech H, Borgmann K. Partial Reduction in BRCA1 Gene Dose Modulates DNA Replication Stress Level and Thereby Contributes to Sensitivity or Resistance. Int J Mol Sci 2022; 23:13363. [PMID: 36362151 PMCID: PMC9656774 DOI: 10.3390/ijms232113363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 09/08/2024] Open
Abstract
BRCA1 is a well-known breast cancer risk gene, involved in DNA damage repair via homologous recombination (HR) and replication fork protection. Therapy resistance was linked to loss and amplification of the BRCA1 gene causing inferior survival of breast cancer patients. Most studies have focused on the analysis of complete loss or mutations in functional domains of BRCA1. How mutations in non-functional domains contribute to resistance mechanisms remains elusive and was the focus of this study. Therefore, clones of the breast cancer cell line MCF7 with indels in BRCA1 exon 9 and 14 were generated using CRISPR/Cas9. Clones with successful introduced BRCA1 mutations were evaluated regarding their capacity to perform HR, how they handle DNA replication stress (RS), and the consequences on the sensitivity to MMC, PARP1 inhibition, and ionizing radiation. Unexpectedly, BRCA1 mutations resulted in both increased sensitivity and resistance to exogenous DNA damage, despite a reduction of HR capacity in all clones. Resistance was associated with improved DNA double-strand break repair and reduction in replication stress (RS). Lower RS was accompanied by increased activation and interaction of proteins essential for the S phase-specific DNA damage response consisting of HR proteins, FANCD2, and CHK1.
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Affiliation(s)
- Sandra Classen
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Elena Rahlf
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Johannes Jungwirth
- Project Group Biochemistry, Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Nina Albers
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Luca Philipp Hebestreit
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Alexandra Zielinski
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Lena Poole
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Marco Groth
- CF Next-Generation Sequencing, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Philipp Koch
- CF Life Science Computing, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07747 Jena, Germany
| | - Stefanie Kankel
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07747 Jena, Germany
| | - Nils Cordes
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstr. 74, PF 41, 01307 Dresden, Germany
- National Center for Tumor Diseases, Partner Site Dresden: German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Department of Radiotherapy and Radiation Oncology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstr. 74, PF 50, 01307 Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology-OncoRay, Bautzner Landstr. 400, 01328 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69192 Heidelberg, Germany
| | - Cordula Petersen
- Department of Radiotherapy and Radiooncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Kai Rothkamm
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Helmut Pospiech
- Project Group Biochemistry, Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Kerstin Borgmann
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
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23
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Hunter JE, Campbell AE, Hannaway NL, Kerridge S, Luli S, Butterworth JA, Sellier H, Mukherjee R, Dhillon N, Sudhindar PD, Shukla R, Brownridge PJ, Bell HL, Coxhead J, Taylor L, Leary P, Hasoon MS, Collins I, Garrett MD, Eyers CE, Perkins ND. Regulation of CHK1 inhibitor resistance by a c-Rel and USP1 dependent pathway. Biochem J 2022; 479:2063-2086. [PMID: 36240066 PMCID: PMC9704646 DOI: 10.1042/bcj20220102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/12/2022] [Accepted: 08/23/2022] [Indexed: 12/19/2022]
Abstract
Previously, we discovered that deletion of c-Rel in the Eµ-Myc mouse model of lymphoma results in earlier onset of disease, a finding that contrasted with the expected function of this NF-κB subunit in B-cell malignancies. Here we report that Eµ-Myc/cRel-/- cells have an unexpected and major defect in the CHK1 pathway. Total and phospho proteomic analysis revealed that Eµ-Myc/cRel-/- lymphomas highly resemble wild-type (WT) Eµ-Myc lymphomas treated with an acute dose of the CHK1 inhibitor (CHK1i) CCT244747. Further analysis demonstrated that this is a consequence of Eµ-Myc/cRel-/- lymphomas having lost expression of CHK1 protein itself, an effect that also results in resistance to CCT244747 treatment in vivo. Similar down-regulation of CHK1 protein levels was also seen in CHK1i resistant U2OS osteosarcoma and Huh7 hepatocellular carcinoma cells. Further investigation revealed that the deubiquitinase USP1 regulates CHK1 proteolytic degradation and that its down-regulation in our model systems is responsible, at least in part, for these effects. We demonstrate that treating WT Eµ-Myc lymphoma cells with the USP1 inhibitor ML323 was highly effective at reducing tumour burden in vivo. Targeting USP1 activity may thus be an alternative therapeutic strategy in MYC-driven tumours.
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Affiliation(s)
- Jill E. Hunter
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Amy E. Campbell
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Nicola L. Hannaway
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Scott Kerridge
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Saimir Luli
- Newcastle University Clinical and Translational Research Institute, Preclinical In Vivo Imaging (PIVI), Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Jacqueline A. Butterworth
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Helene Sellier
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Reshmi Mukherjee
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Nikita Dhillon
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Praveen D. Sudhindar
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Ruchi Shukla
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Philip J. Brownridge
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Hayden L. Bell
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Jonathan Coxhead
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Leigh Taylor
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Peter Leary
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Megan S.R. Hasoon
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Ian Collins
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sutton SM2 5NG, U.K
| | - Michelle D. Garrett
- School of Biosciences, Stacey Building, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Claire E. Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Neil D. Perkins
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
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24
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Differentiated function and localisation of SPO11-1 and PRD3 on the chromosome axis during meiotic DSB formation in Arabidopsis thaliana. PLoS Genet 2022; 18:e1010298. [PMID: 35857772 PMCID: PMC9342770 DOI: 10.1371/journal.pgen.1010298] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 08/01/2022] [Accepted: 06/16/2022] [Indexed: 11/19/2022] Open
Abstract
During meiosis, DNA double-strand breaks (DSBs) occur throughout the genome, a subset of which are repaired to form reciprocal crossovers between chromosomes. Crossovers are essential to ensure balanced chromosome segregation and to create new combinations of genetic variation. Meiotic DSBs are formed by a topoisomerase-VI-like complex, containing catalytic (e.g. SPO11) proteins and auxiliary (e.g. PRD3) proteins. Meiotic DSBs are formed in chromatin loops tethered to a linear chromosome axis, but the interrelationship between DSB-promoting factors and the axis is not fully understood. Here, we study the localisation of SPO11-1 and PRD3 during meiosis, and investigate their respective functions in relation to the chromosome axis. Using immunocytogenetics, we observed that the localisation of SPO11-1 overlaps relatively weakly with the chromosome axis and RAD51, a marker of meiotic DSBs, and that SPO11-1 recruitment to chromatin is genetically independent of the axis. In contrast, PRD3 localisation correlates more strongly with RAD51 and the chromosome axis. This indicates that PRD3 likely forms a functional link between SPO11-1 and the chromosome axis to promote meiotic DSB formation. We also uncovered a new function of SPO11-1 in the nucleation of the synaptonemal complex protein ZYP1. We demonstrate that chromosome co-alignment associated with ZYP1 deposition can occur in the absence of DSBs, and is dependent on SPO11-1, but not PRD3. Lastly, we show that the progression of meiosis is influenced by the presence of aberrant chromosomal connections, but not by the absence of DSBs or synapsis. Altogether, our study provides mechanistic insights into the control of meiotic DSB formation and reveals diverse functional interactions between SPO11-1, PRD3 and the chromosome axis. Most eukaryotes rely on the formation of gametes with half the number of chromosomes for sexual reproduction. Meiosis is a specialised type of cell division essential for the transition between a diploid and a haploid stage during gametogenesis. In early meiosis, programmed-DNA double strand breaks (DSBs) occur across the genome. These DSBs are processed by a set of proteins and the broken ends are repaired using the genetic information from the homologous chromosomes. These reciprocal exchanges of information between two chromosomes are called crossovers. Crossovers physical link chromosomes in pairs which is essential to ensure their correct segregation during the two rounds of meiotic division. Crossovers are also essential for the creation of genetic diversity as they break genetic linkages to form novel allelic blocks. The formation of DSBs is not completely understood in plants. Here we studied the function of SPO11-1 and PRD3, two proteins involved in the formation of DSBs in Arabidopsis. We discovered functional differences in their respective mode of recruitment to the chromosomes, their interactions with proteins forming the chromosome core and their roles in chromosome co-alignment. These indicate that, although SPO11-1 and PRD3 share a role in the formation of DSBs, the two proteins have additional and distinct roles beside DSB formation.
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25
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Leysen H, Walter D, Clauwaert L, Hellemans L, van Gastel J, Vasudevan L, Martin B, Maudsley S. The Relaxin-3 Receptor, RXFP3, Is a Modulator of Aging-Related Disease. Int J Mol Sci 2022; 23:4387. [PMID: 35457203 PMCID: PMC9027355 DOI: 10.3390/ijms23084387] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/12/2022] Open
Abstract
During the aging process our body becomes less well equipped to deal with cellular stress, resulting in an increase in unrepaired damage. This causes varying degrees of impaired functionality and an increased risk of mortality. One of the most effective anti-aging strategies involves interventions that combine simultaneous glucometabolic support with augmented DNA damage protection/repair. Thus, it seems prudent to develop therapeutic strategies that target this combinatorial approach. Studies have shown that the ADP-ribosylation factor (ARF) GTPase activating protein GIT2 (GIT2) acts as a keystone protein in the aging process. GIT2 can control both DNA repair and glucose metabolism. Through in vivo co-regulation analyses it was found that GIT2 forms a close coexpression-based relationship with the relaxin-3 receptor (RXFP3). Cellular RXFP3 expression is directly affected by DNA damage and oxidative stress. Overexpression or stimulation of this receptor, by its endogenous ligand relaxin 3 (RLN3), can regulate the DNA damage response and repair processes. Interestingly, RLN3 is an insulin-like peptide and has been shown to control multiple disease processes linked to aging mechanisms, e.g., anxiety, depression, memory dysfunction, appetite, and anti-apoptotic mechanisms. Here we discuss the molecular mechanisms underlying the various roles of RXFP3/RLN3 signaling in aging and age-related disorders.
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Affiliation(s)
- Hanne Leysen
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
| | - Deborah Walter
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
| | - Lore Clauwaert
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
| | - Lieselot Hellemans
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
| | - Jaana van Gastel
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
- SGS Belgium, Intercity Business Park, Generaal De Wittelaan 19-A5, 2800 Mechelen, Belgium
| | | | - Bronwen Martin
- Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium;
| | - Stuart Maudsley
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
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26
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Combemale P, Sonzogni L, Devic C, Bencokova Z, Ferlazzo ML, Granzotto A, Burlet SF, Pinson S, Amini-Adle M, Al-Choboq J, Bodgi L, Bourguignon M, Balosso J, Bachelet JT, Foray N. Individual Response to Radiation of Individuals with Neurofibromatosis Type I: Role of the ATM Protein and Influence of Statins and Bisphosphonates. Mol Neurobiol 2021; 59:556-573. [PMID: 34727321 DOI: 10.1007/s12035-021-02615-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 10/21/2021] [Indexed: 11/26/2022]
Abstract
Neurofibromatosis type 1 (NF1) is a disease characterized by high occurrence of benign and malignant brain tumours and caused by mutations of the neurofibromin protein. While there is an increasing evidence that NF1 is associated with radiosensitivity and radiosusceptibility, few studies have dealt with the molecular and cellular radiation response of cells from individuals with NF1. Here, we examined the ATM-dependent signalling and repair pathways of the DNA double-strand breaks (DSB), the key-damage induced by ionizing radiation, in skin fibroblast cell lines from 43 individuals with NF1. Ten minutes after X-rays irradiation, quiescent NF1 fibroblasts showed abnormally low rate of recognized DSB reflected by a low yield of nuclear foci formed by phosphorylated H2AX histones. Irradiated NF1 fibroblasts also presented a delayed radiation-induced nucleoshuttling of the ATM kinase (RIANS), potentially due to a specific binding of ATM to the mutated neurofibromin in cytoplasm. Lastly, NF1 fibroblasts showed abnormally high MRE11 nuclease activity suggesting a high genomic instability after irradiation. A combination of bisphosphonates and statins complemented these impairments by accelerating the RIANS, increasing the yield of recognized DSB and reducing genomic instability. Data from NF1 fibroblasts exposed to radiation in radiotherapy and CT scan conditions confirmed that NF1 belongs to the group of syndromes associated with radiosensitivity and radiosusceptibility.
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Affiliation(s)
- Patrick Combemale
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1296 Research Unit « Radiation : Defense, Health and Environment », Centre Léon-Bérard, 69008, Lyon, France
- Centre Léon-Bérard, 69008, Lyon, France
| | - Laurène Sonzogni
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1296 Research Unit « Radiation : Defense, Health and Environment », Centre Léon-Bérard, 69008, Lyon, France
| | - Clément Devic
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1296 Research Unit « Radiation : Defense, Health and Environment », Centre Léon-Bérard, 69008, Lyon, France
| | - Zuzana Bencokova
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1296 Research Unit « Radiation : Defense, Health and Environment », Centre Léon-Bérard, 69008, Lyon, France
| | - Mélanie Lydia Ferlazzo
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1296 Research Unit « Radiation : Defense, Health and Environment », Centre Léon-Bérard, 69008, Lyon, France
| | - Adeline Granzotto
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1296 Research Unit « Radiation : Defense, Health and Environment », Centre Léon-Bérard, 69008, Lyon, France
| | - Steven Franck Burlet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1296 Research Unit « Radiation : Defense, Health and Environment », Centre Léon-Bérard, 69008, Lyon, France
| | - Stéphane Pinson
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1296 Research Unit « Radiation : Defense, Health and Environment », Centre Léon-Bérard, 69008, Lyon, France
- Centre Léon-Bérard, 69008, Lyon, France
| | - Mona Amini-Adle
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1296 Research Unit « Radiation : Defense, Health and Environment », Centre Léon-Bérard, 69008, Lyon, France
- Centre Léon-Bérard, 69008, Lyon, France
| | - Joëlle Al-Choboq
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1296 Research Unit « Radiation : Defense, Health and Environment », Centre Léon-Bérard, 69008, Lyon, France
| | - Larry Bodgi
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1296 Research Unit « Radiation : Defense, Health and Environment », Centre Léon-Bérard, 69008, Lyon, France
| | - Michel Bourguignon
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1296 Research Unit « Radiation : Defense, Health and Environment », Centre Léon-Bérard, 69008, Lyon, France
- Université de Versailles-Saint Quentin en Yvelines, 78035, Versailles, France
| | - Jacques Balosso
- Service de Radiothérapie, CHU de Grenoble, 38042, Grenoble, France
| | - Jean-Thomas Bachelet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1296 Research Unit « Radiation : Defense, Health and Environment », Centre Léon-Bérard, 69008, Lyon, France
| | - Nicolas Foray
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1296 Research Unit « Radiation : Defense, Health and Environment », Centre Léon-Bérard, 69008, Lyon, France.
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27
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Hua KF, Chao AC, Lin TY, Chen WT, Lee YC, Hsu WH, Lee SL, Wang HM, Yang DI, Ju TC. Ginsenoside compound K reduces the progression of Huntington's disease via the inhibition of oxidative stress and overactivation of the ATM/AMPK pathway. J Ginseng Res 2021; 46:572-584. [PMID: 35818427 PMCID: PMC9270658 DOI: 10.1016/j.jgr.2021.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 10/16/2021] [Accepted: 11/04/2021] [Indexed: 12/12/2022] Open
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28
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Komura K, Inamoto T, Tsujino T, Matsui Y, Konuma T, Nishimura K, Uchimoto T, Tsutsumi T, Matsunaga T, Maenosono R, Yoshikawa Y, Taniguchi K, Tanaka T, Uehara H, Hirata K, Hirano H, Nomi H, Hirose Y, Ono F, Azuma H. Increased BUB1B/BUBR1 expression contributes to aberrant DNA repair activity leading to resistance to DNA-damaging agents. Oncogene 2021; 40:6210-6222. [PMID: 34545188 PMCID: PMC8553621 DOI: 10.1038/s41388-021-02021-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022]
Abstract
There has been accumulating evidence for the clinical benefit of chemoradiation therapy (CRT), whereas mechanisms in CRT-recurrent clones derived from the primary tumor are still elusive. Herein, we identified an aberrant BUB1B/BUBR1 expression in CRT-recurrent clones in bladder cancer (BC) by comprehensive proteomic analysis. CRT-recurrent BC cells exhibited a cell-cycle-independent upregulation of BUB1B/BUBR1 expression rendering an enhanced DNA repair activity in response to DNA double-strand breaks (DSBs). With DNA repair analyses employing the CRISPR/cas9 system, we revealed that cells with aberrant BUB1B/BUBR1 expression dominantly exploit mutagenic nonhomologous end joining (NHEJ). We further found that phosphorylated ATM interacts with BUB1B/BUBR1 after ionizing radiation (IR) treatment, and the resistance to DSBs by increased BUB1B/BUBR1 depends on the functional ATM. In vivo, tumor growth of CRT-resistant T24R cells was abrogated by ATM inhibition using AZD0156. A dataset analysis identified FOXM1 as a putative BUB1B/BUBR1-targeting transcription factor causing its increased expression. These data collectively suggest a redundant role of BUB1B/BUBR1 underlying mutagenic NHEJ in an ATM-dependent manner, aside from the canonical activity of BUB1B/BUBR1 on the G2/M checkpoint, and offer novel clues to overcome CRT resistance.
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Affiliation(s)
- Kazumasa Komura
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan. .,Translational Research Program, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan.
| | - Teruo Inamoto
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Takuya Tsujino
- Division of Urology, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, United States
| | - Yusuke Matsui
- Biomedical and Health Informatics Unit, Department of Integrated Health Science, Nagoya University Graduate School of Medicine, Nagoya, 461-8673, Japan.,Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 461-8673, Japan
| | - Tsuyoshi Konuma
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Kazuki Nishimura
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Taizo Uchimoto
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Takeshi Tsutsumi
- Division of Urology, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, United States
| | - Tomohisa Matsunaga
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Ryoichi Maenosono
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Yuki Yoshikawa
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Kohei Taniguchi
- Translational Research Program, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Tomohito Tanaka
- Translational Research Program, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Hirofumi Uehara
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Koichi Hirata
- Department of Pathology, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Hajime Hirano
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Hayahito Nomi
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Yoshinobu Hirose
- Department of Pathology, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Fumihito Ono
- Translational Research Program, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan.,Department of Physiology, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Haruhito Azuma
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
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29
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Arbel M, Liefshitz B, Kupiec M. DNA damage bypass pathways and their effect on mutagenesis in yeast. FEMS Microbiol Rev 2021; 45:5896953. [PMID: 32840566 DOI: 10.1093/femsre/fuaa038] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022] Open
Abstract
What is the origin of mutations? In contrast to the naïve notion that mutations are unfortunate accidents, genetic research in microorganisms has demonstrated that most mutations are created by genetically encoded error-prone repair mechanisms. However, error-free repair pathways also exist, and it is still unclear how cells decide when to use one repair method or the other. Here, we summarize what is known about the DNA damage tolerance mechanisms (also known as post-replication repair) for perhaps the best-studied organism, the yeast Saccharomyces cerevisiae. We describe the latest research, which has established the existence of at least two error-free and two error-prone inter-related mechanisms of damage tolerance that compete for the handling of spontaneous DNA damage. We explore what is known about the induction of mutations by DNA damage. We point to potential paradoxes and to open questions that still remain unanswered.
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Affiliation(s)
- Matan Arbel
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Batia Liefshitz
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
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30
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Li Z, Wang-Heaton H, Cartwright BM, Makinwa Y, Hilton BA, Musich PR, Shkriabai N, Kvaratskhelia M, Guan S, Chen Q, Yu X, Zou Y. ATR prevents Ca 2+ overload-induced necrotic cell death through phosphorylation-mediated inactivation of PARP1 without DNA damage signaling. FASEB J 2021; 35:e21373. [PMID: 33811702 PMCID: PMC8252533 DOI: 10.1096/fj.202001636rrr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 12/10/2020] [Accepted: 12/31/2020] [Indexed: 12/19/2022]
Abstract
Hyperactivation of PARP1 is known to be a major cause of necrotic cell death by depleting NAD+/ATP pools during Ca2+ overload which is associated with many ischemic diseases. However, little is known about how PARP1 hyperactivity is regulated during calcium overload. In this study we show that ATR kinase, well known for its role in DNA damage responses, suppresses ionomycin, glutamate, or quinolinic acid‐induced necrotic death of cells including SH‐SY5Y neuronal cells. We found that the inhibition of necrosis requires the kinase activity of ATR. Specifically, ATR binds to and phosphorylates PARP1 at Ser179 after the ionophore treatments. This site‐specific phosphorylation inactivates PARP1, inhibiting ionophore‐induced necrosis. Strikingly, all of this occurs in the absence of detectable DNA damage and signaling up to 8 hours after ionophore treatment. Furthermore, little AIF was released from mitochondria/cytoplasm for nuclear import, supporting the necrotic type of cell death in the early period of the treatments. Our results reveal a novel ATR‐mediated anti‐necrotic mechanism in the cellular stress response to calcium influx without DNA damage signaling.
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Affiliation(s)
- Zhengke Li
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Hui Wang-Heaton
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Brian M Cartwright
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Yetunde Makinwa
- Department of Cancer Biology, University of Toledo College of Medicine, Toledo, OH, USA
| | - Benjamin A Hilton
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Phillip R Musich
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Nikolozi Shkriabai
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Mamuka Kvaratskhelia
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Shengheng Guan
- Department of Pharmaceutical Chemistry and Mass Spectrometry Facility, University of California, San Francisco, CA, USA
| | - Qian Chen
- Department of Cancer Genetics and Epigenetics, City of Hope, Duarte, CA, USA
| | - Xiaochun Yu
- Department of Cancer Genetics and Epigenetics, City of Hope, Duarte, CA, USA
| | - Yue Zou
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA.,Department of Cancer Biology, University of Toledo College of Medicine, Toledo, OH, USA
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31
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Zhang N, Coutinho LE, Pati D. PDS5A and PDS5B in Cohesin Function and Human Disease. Int J Mol Sci 2021; 22:ijms22115868. [PMID: 34070827 PMCID: PMC8198109 DOI: 10.3390/ijms22115868] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 01/02/2023] Open
Abstract
Precocious dissociation of sisters 5 (PDS5) is an associate protein of cohesin that is conserved from yeast to humans. It acts as a regulator of the cohesin complex and plays important roles in various cellular processes, such as sister chromatid cohesion, DNA damage repair, gene transcription, and DNA replication. Vertebrates have two paralogs of PDS5, PDS5A and PDS5B, which have redundant and unique roles in regulating cohesin functions. Herein, we discuss the molecular characteristics and functions of PDS5, as well as the effects of its mutations in the development of diseases and their relevance for novel therapeutic strategies.
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Affiliation(s)
| | | | - Debananda Pati
- Correspondence: ; Tel.: +1-832-824-4575; Fax: +1-832-825-4651
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32
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Agelidis A, Suryawanshi RK, Patil CD, Campeau A, Gonzalez DJ, Shukla D. Dissociation of DNA damage sensing by endoglycosidase HPSE. iScience 2021; 24:102242. [PMID: 33748723 PMCID: PMC7957091 DOI: 10.1016/j.isci.2021.102242] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/09/2021] [Accepted: 02/24/2021] [Indexed: 12/25/2022] Open
Abstract
Balance between cell proliferation and elimination is critical in handling threats both exogenous and of internal dysfunction. Recent work has implicated a conserved but poorly understood endoglycosidase heparanase (HPSE) in the restriction of innate defense responses, yet biochemical mediators of these key functions remained unclear. Here, an unbiased immunopurification proteomics strategy is employed to identify and rank uncharacterized interactions between HPSE and mediators of canonical signaling pathways linking cell cycle and stress responses. We demonstrate with models of genotoxic stress including herpes simplex virus infection and chemotherapeutic treatment that HPSE dampens innate responses to double-stranded DNA breakage by interfering with signal transduction between initial sensors and downstream mediators. Given the long-standing recognition of HPSE in driving late-stage inflammatory disease exemplified by tissue destruction and cancer metastasis, modulation of this protein with control over the DNA damage response imparts a unique strategy in the development of unconventional multivalent therapy. HPSE binds key proteins at interface of DNA damage signaling and IFN responses Nuclear translocation of DNA damage transducer ATM is enhanced in absence of HPSE Cells lacking HPSE display enhanced sensitivity to DNA damage-induced death HPSE interfaces with regulators of DNA damage response to influence cell fate
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Affiliation(s)
- Alex Agelidis
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Rahul K. Suryawanshi
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Chandrashekhar D. Patil
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Anaamika Campeau
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J. Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy, University of California, San Diego, La Jolla, CA 92093, USA
| | - Deepak Shukla
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
- Corresponding author
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33
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Campbell AE, Ferraz Franco C, Su LI, Corbin EK, Perkins S, Kalyuzhnyy A, Jones AR, Brownridge PJ, Perkins ND, Eyers CE. Temporal modulation of the NF-κB RelA network in response to different types of DNA damage. Biochem J 2021; 478:533-551. [PMID: 33438746 PMCID: PMC7886319 DOI: 10.1042/bcj20200627] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/30/2022]
Abstract
Different types of DNA damage can initiate phosphorylation-mediated signalling cascades that result in stimulus specific pro- or anti-apoptotic cellular responses. Amongst its many roles, the NF-κB transcription factor RelA is central to these DNA damage response pathways. However, we still lack understanding of the co-ordinated signalling mechanisms that permit different DNA damaging agents to induce distinct cellular outcomes through RelA. Here, we use label-free quantitative phosphoproteomics to examine the temporal effects of exposure of U2OS cells to either etoposide (ETO) or hydroxyurea (HU) by monitoring the phosphorylation status of RelA and its protein binding partners. Although few stimulus-specific differences were identified in the constituents of phosphorylated RelA interactome after exposure to these DNA damaging agents, we observed subtle, but significant, changes in their phosphorylation states, as a function of both type and duration of treatment. The DNA double strand break (DSB)-inducing ETO invoked more rapid, sustained responses than HU, with regulated targets primarily involved in transcription, cell division and canonical DSB repair. Kinase substrate prediction of ETO-regulated phosphosites suggest abrogation of CDK and ERK1 signalling, in addition to the known induction of ATM/ATR. In contrast, HU-induced replicative stress mediated temporally dynamic regulation, with phosphorylated RelA binding partners having roles in rRNA/mRNA processing and translational initiation, many of which contained a 14-3-3ε binding motif, and were putative substrates of the dual specificity kinase CLK1. Our data thus point to differential regulation of key cellular processes and the involvement of distinct signalling pathways in modulating DNA damage-specific functions of RelA.
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Affiliation(s)
- Amy E. Campbell
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Catarina Ferraz Franco
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Ling-I Su
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Emma K. Corbin
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Simon Perkins
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Anton Kalyuzhnyy
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Andrew R. Jones
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Philip J. Brownridge
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Neil D. Perkins
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
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34
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Locke AJ, Hossain L, McCrostie G, Ronato DA, Fitieh A, Rafique T, Mashayekhi F, Motamedi M, Masson JY, Ismail I. SUMOylation mediates CtIP's functions in DNA end resection and replication fork protection. Nucleic Acids Res 2021; 49:928-953. [PMID: 33406258 PMCID: PMC7826263 DOI: 10.1093/nar/gkaa1232] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
Double-strand breaks and stalled replication forks are a significant threat to genomic stability that can lead to chromosomal rearrangements or cell death. The protein CtIP promotes DNA end resection, an early step in homologous recombination repair, and has been found to protect perturbed forks from excessive nucleolytic degradation. However, it remains unknown how CtIP's function in fork protection is regulated. Here, we show that CtIP recruitment to sites of DNA damage and replication stress is impaired upon global inhibition of SUMOylation. We demonstrate that CtIP is a target for modification by SUMO-2 and that this occurs constitutively during S phase. The modification is dependent on the activities of cyclin-dependent kinases and the PI-3-kinase-related kinase ATR on CtIP's carboxyl-terminal region, an interaction with the replication factor PCNA, and the E3 SUMO ligase PIAS4. We also identify residue K578 as a key residue that contributes to CtIP SUMOylation. Functionally, a CtIP mutant where K578 is substituted with a non-SUMOylatable arginine residue is defective in promoting DNA end resection, homologous recombination, and in protecting stalled replication forks from excessive nucleolytic degradation. Our results shed further light on the tightly coordinated regulation of CtIP by SUMOylation in the maintenance of genome stability.
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Affiliation(s)
- Andrew J Locke
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
| | - Lazina Hossain
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
| | - Glynnis McCrostie
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
| | - Daryl A Ronato
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec City, Québec, G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine; Laval University Cancer Research Center, Université Laval, Québec City, Québec, G1V 0A6, Canada
| | - Amira Fitieh
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Tanzeem Ahmed Rafique
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
| | - Fatemeh Mashayekhi
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
| | - Mobina Motamedi
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
| | - Jean-Yves Masson
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec City, Québec, G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine; Laval University Cancer Research Center, Université Laval, Québec City, Québec, G1V 0A6, Canada
| | - Ismail Hassan Ismail
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta; Cross Cancer Institute, Edmonton, Alberta, T6G 1Z2, Canada
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
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35
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Woo TT, Chuang CN, Wang TF. Budding yeast Rad51: a paradigm for how phosphorylation and intrinsic structural disorder regulate homologous recombination and protein homeostasis. Curr Genet 2021; 67:389-396. [PMID: 33433732 PMCID: PMC8139929 DOI: 10.1007/s00294-020-01151-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/08/2020] [Accepted: 12/22/2020] [Indexed: 11/26/2022]
Abstract
The RecA-family recombinase Rad51 is the central player in homologous recombination (HR), the faithful pathway for repairing DNA double-strand breaks (DSBs) during both mitosis and meiosis. The behavior of Rad51 protein in vivo is fine-tuned via posttranslational modifications conducted by multiple protein kinases in response to cell cycle cues and DNA lesions. Unrepaired DSBs and ssDNA also activate Mec1ATR and Tel1ATM family kinases to initiate the DNA damage response (DDR) that safeguards genomic integrity. Defects in HR and DDR trigger genome instability and result in cancer predisposition, infertility, developmental defects, neurological diseases or premature aging. Intriguingly, yeast Mec1ATR- and Tel1ATM-dependent phosphorylation promotes Rad51 protein stability during DDR, revealing how Mec1ATR can alleviate proteotoxic stress. Moreover, Mec1ATR- and Tel1ATM-dependent phosphorylation also occurs on DDR-unrelated proteins, suggesting that Mec1ATR and Tel1ATM have a DDR-independent function in protein homeostasis. In this minireview, we first describe how human and budding yeast Rad51 are phosphorylated by multiple protein kinases at different positions to promote homology-directed DNA repair and recombination (HDRR). Then, we discuss recent findings showing that intrinsic structural disorder and Mec1ATR/Tel1ATM-dependent phosphorylation are coordinated in yeast Rad51 to regulate both HR and protein homeostasis.
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Affiliation(s)
- Tai-Ting Woo
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chi-Ning Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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36
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Tang LY, Thomas A, Zhou M, Zhang YE. Phosphorylation of SMURF2 by ATM exerts a negative feedback control of DNA damage response. J Biol Chem 2020; 295:18485-18493. [PMID: 33097595 PMCID: PMC9350827 DOI: 10.1074/jbc.ra120.014179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 10/22/2020] [Indexed: 11/29/2022] Open
Abstract
Timely repair of DNA double-strand breaks (DSBs) is essential to maintaining genomic integrity and preventing illnesses induced by genetic abnormalities. We previously demonstrated that the E3 ubiquitin ligase SMURF2 plays a critical tumor suppressing role via its interaction with RNF20 (ring finger protein 20) in shaping chromatin landscape and preserving genomic stability. However, the mechanism that mobilizes SMURF2 in response to DNA damage remains unclear. Using biochemical approaches and MS analysis, we show that upon the onset of the DNA-damage response, SMURF2 becomes phosphorylated at Ser384 by ataxia telangiectasia mutated (ATM) serine/threonine kinase, and this phosphorylation is required for its interaction with RNF20. We demonstrate that a SMURF2 mutant with an S384A substitution has reduced capacity to ubiquitinate RNF20 while promoting Smad3 ubiquitination unabatedly. More importantly, mouse embryonic fibroblasts expressing the SMURF2 S384A mutant show a weakened ability to sustain the DSB response compared with those expressing WT SMURF2 following etoposide treatment. These data indicate that SMURF2-mediated RNF20 ubiquitination and degradation controlled by ataxia telangiectasia mutated-induced phosphorylation at Ser384 constitutes a negative feedback loop that regulates DSB repair.
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Affiliation(s)
- Liu-Ya Tang
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Adam Thomas
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ming Zhou
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Ying E Zhang
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.
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Fujii A, Sunatani Y, Furuichi K, Fujimoto K, Adachi H, Iwabuchi K, Yokoyama H. DNA damage in human glomerular endothelial cells induces nodular glomerulosclerosis via an ATR and ANXA2 pathway. Sci Rep 2020; 10:22206. [PMID: 33335142 PMCID: PMC7747722 DOI: 10.1038/s41598-020-79106-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 11/18/2020] [Indexed: 01/15/2023] Open
Abstract
Collagen type VI (COL6) deposition occurs in various glomerular diseases, causing serious pathological damage like nodular lesions. However, the mechanisms underlying the deposition of COL6 remain unclear. In renal biopsy samples, immunohistochemical analyses revealed that COL6 and phosphorylated histone H2AX (γ-H2AX), a DNA damage marker, were detected mainly in diabetic nodular glomerulosclerosis, in which the γ-H2AX-positive area was identified as the independent factor significantly associated with the COL6-positive area (β: 0.539, t = 2.668). In in vitro studies, COL6 secretion from human renal glomerular endothelial cells (HRGECs) was assessed by measuring the decrease in the cytoplasmic COL6-positive cells and an increase in the amount of COL6 in the culture medium. Mitomycin C (MMc) treatment of HRGECs increased the number of γ-H2AX-positive cells and COL6 secretion, which were suppressed by a specific inhibitor of ataxia telangiectasia and Rad3-related (ATR). MMc-induced COL6 secretion was also suppressed by Annexin A2 (ANXA2) siRNA transfection. Moreover, the inhibition of ATR activity did not induce any extra suppression in the MMc-induced COL6 secretion by ANXA2 siRNA transfected cells. These results confirm that nodular glomerulosclerosis partially results from DNA damage in the glomerulus and that DNA damage-induced COL6 secretion from HRGECs occurs through an ATR and ANXA2-mediated pathway.
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Affiliation(s)
- Ai Fujii
- Department of Nephrology, School of Medicine, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Ishikawa, 920-0293, Japan
| | - Yumi Sunatani
- Department of Biochemistry I, School of Medicine, Kanazawa Medical University, Uchinada, Japan
| | - Kengo Furuichi
- Department of Nephrology, School of Medicine, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Ishikawa, 920-0293, Japan
| | - Keiji Fujimoto
- Department of Nephrology, School of Medicine, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Ishikawa, 920-0293, Japan
| | - Hiroki Adachi
- Department of Nephrology, School of Medicine, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Ishikawa, 920-0293, Japan
| | - Kuniyoshi Iwabuchi
- Department of Biochemistry I, School of Medicine, Kanazawa Medical University, Uchinada, Japan
| | - Hitoshi Yokoyama
- Department of Nephrology, School of Medicine, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Ishikawa, 920-0293, Japan.
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Woo TT, Chuang CN, Higashide M, Shinohara A, Wang TF. Dual roles of yeast Rad51 N-terminal domain in repairing DNA double-strand breaks. Nucleic Acids Res 2020; 48:8474-8489. [PMID: 32652040 PMCID: PMC7470947 DOI: 10.1093/nar/gkaa587] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 06/24/2020] [Accepted: 07/03/2020] [Indexed: 01/17/2023] Open
Abstract
Highly toxic DNA double-strand breaks (DSBs) readily trigger the DNA damage response (DDR) in cells, which delays cell cycle progression to ensure proper DSB repair. In Saccharomyces cerevisiae, mitotic S phase (20–30 min) is lengthened upon DNA damage. During meiosis, Spo11-induced DSB onset and repair lasts up to 5 h. We report that the NH2-terminal domain (NTD; residues 1–66) of Rad51 has dual functions for repairing DSBs during vegetative growth and meiosis. Firstly, Rad51-NTD exhibits autonomous expression-enhancing activity for high-level production of native Rad51 and when fused to exogenous β-galactosidase in vivo. Secondly, Rad51-NTD is an S/T-Q cluster domain (SCD) harboring three putative Mec1/Tel1 target sites. Mec1/Tel1-dependent phosphorylation antagonizes the proteasomal degradation pathway, increasing the half-life of Rad51 from ∼30 min to ≥180 min. Our results evidence a direct link between homologous recombination and DDR modulated by Rad51 homeostasis.
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Affiliation(s)
- Tai-Ting Woo
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Ning Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Mika Higashide
- Laboratory of Genome-Chromosome Functions, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Japan
| | - Akira Shinohara
- Laboratory of Genome-Chromosome Functions, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Japan
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
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Katarkar A, Bottoni G, Clocchiatti A, Goruppi S, Bordignon P, Lazzaroni F, Gregnanin I, Ostano P, Neel V, Dotto GP. NOTCH1 gene amplification promotes expansion of Cancer Associated Fibroblast populations in human skin. Nat Commun 2020; 11:5126. [PMID: 33046701 PMCID: PMC7550609 DOI: 10.1038/s41467-020-18919-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 09/09/2020] [Indexed: 12/23/2022] Open
Abstract
Cancer associated fibroblasts (CAFs) are a key component of the tumor microenvironment. Genomic alterations in these cells remain a point of contention. We report that CAFs from skin squamous cell carcinomas (SCCs) display chromosomal alterations, with heterogeneous NOTCH1 gene amplification and overexpression that also occur, to a lesser extent, in dermal fibroblasts of apparently unaffected skin. The fraction of the latter cells harboring NOTCH1 amplification is expanded by chronic UVA exposure, to which CAFs are resistant. The advantage conferred by NOTCH1 amplification and overexpression can be explained by NOTCH1 ability to block the DNA damage response (DDR) and ensuing growth arrest through suppression of ATM-FOXO3a association and downstream signaling cascade. In an orthotopic model of skin SCC, genetic or pharmacological inhibition of NOTCH1 activity suppresses cancer/stromal cells expansion. Here we show that NOTCH1 gene amplification and increased expression in CAFs are an attractive target for stroma-focused anti-cancer intervention.
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Affiliation(s)
- Atul Katarkar
- Department of Biochemistry, University of Lausanne, 1066, Epalinges, Switzerland
| | - Giulia Bottoni
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, MA, 02129, USA.,Department of Dermatology, Harvard Medical School, Boston, MA, 02125, USA
| | - Andrea Clocchiatti
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, MA, 02129, USA.,Department of Dermatology, Harvard Medical School, Boston, MA, 02125, USA
| | - Sandro Goruppi
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, MA, 02129, USA.,Department of Dermatology, Harvard Medical School, Boston, MA, 02125, USA
| | - Pino Bordignon
- Department of Biochemistry, University of Lausanne, 1066, Epalinges, Switzerland
| | - Francesca Lazzaroni
- Department of Biochemistry, University of Lausanne, 1066, Epalinges, Switzerland
| | - Ilaria Gregnanin
- Cancer Genomics Laboratory, Edo and Elvo Tempia Valenta Foundation, Biella, 13900, Italy
| | - Paola Ostano
- Cancer Genomics Laboratory, Edo and Elvo Tempia Valenta Foundation, Biella, 13900, Italy
| | - Victor Neel
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - G Paolo Dotto
- Department of Biochemistry, University of Lausanne, 1066, Epalinges, Switzerland. .,Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, MA, 02129, USA. .,Department of Dermatology, Harvard Medical School, Boston, MA, 02125, USA. .,International Cancer Prevention Institute, 1066, Epalinges, Switzerland.
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40
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Villoria MT, Gutiérrez-Escribano P, Alonso-Rodríguez E, Ramos F, Merino E, Campos A, Montoya A, Kramer H, Aragón L, Clemente-Blanco A. PP4 phosphatase cooperates in recombinational DNA repair by enhancing double-strand break end resection. Nucleic Acids Res 2020; 47:10706-10727. [PMID: 31544936 PMCID: PMC6846210 DOI: 10.1093/nar/gkz794] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/30/2019] [Accepted: 09/11/2019] [Indexed: 12/30/2022] Open
Abstract
The role of Rad53 in response to a DNA lesion is central for the accurate orchestration of the DNA damage response. Rad53 activation relies on its phosphorylation by Mec1 and its own autophosphorylation in a manner dependent on the adaptor Rad9. While the mechanism behind Rad53 activation has been well documented, less is known about the processes that counteract its activity along the repair of a DNA adduct. Here, we describe that PP4 phosphatase is required to avoid Rad53 hyper-phosphorylation during the repair of a double-strand break, a process that impacts on the phosphorylation status of multiple factors involved in the DNA damage response. PP4-dependent Rad53 dephosphorylation stimulates DNA end resection by relieving the negative effect that Rad9 exerts over the Sgs1/Dna2 exonuclease complex. Consequently, elimination of PP4 activity affects resection and repair by single-strand annealing, defects that are bypassed by reducing Rad53 hyperphosphorylation. These results confirm that Rad53 phosphorylation is controlled by PP4 during the repair of a DNA lesion and demonstrate that the attenuation of its kinase activity during the initial steps of the repair process is essential to efficiently enhance recombinational DNA repair pathways that depend on long-range resection for their success.
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Affiliation(s)
- María Teresa Villoria
- Cell Cycle and Genome Stability Group, Institute of Functional Biology and Genomics (IBFG), Spanish National Research Council (CSIC). University of Salamanca (USAL), C/ Zacarías González 2, Salamanca 37007, Spain
| | - Pilar Gutiérrez-Escribano
- Cell Cycle Group. Medical Research Council, London Institute of Medical Science, Du Cane Road, London W12 0NN, UK
| | - Esmeralda Alonso-Rodríguez
- Cell Cycle and Genome Stability Group, Institute of Functional Biology and Genomics (IBFG), Spanish National Research Council (CSIC). University of Salamanca (USAL), C/ Zacarías González 2, Salamanca 37007, Spain
| | - Facundo Ramos
- Cell Cycle and Genome Stability Group, Institute of Functional Biology and Genomics (IBFG), Spanish National Research Council (CSIC). University of Salamanca (USAL), C/ Zacarías González 2, Salamanca 37007, Spain
| | - Eva Merino
- Cell Cycle and Genome Stability Group, Institute of Functional Biology and Genomics (IBFG), Spanish National Research Council (CSIC). University of Salamanca (USAL), C/ Zacarías González 2, Salamanca 37007, Spain
| | - Adrián Campos
- Cell Cycle and Genome Stability Group, Institute of Functional Biology and Genomics (IBFG), Spanish National Research Council (CSIC). University of Salamanca (USAL), C/ Zacarías González 2, Salamanca 37007, Spain
| | - Alex Montoya
- Biological Mass Spectrometry and Proteomics Laboratory, Medical Research Council, London Institute of Medical Science, Du Cane Road, London W12 0NN, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Laboratory, Medical Research Council, London Institute of Medical Science, Du Cane Road, London W12 0NN, UK
| | - Luis Aragón
- Cell Cycle Group. Medical Research Council, London Institute of Medical Science, Du Cane Road, London W12 0NN, UK
| | - Andrés Clemente-Blanco
- Cell Cycle and Genome Stability Group, Institute of Functional Biology and Genomics (IBFG), Spanish National Research Council (CSIC). University of Salamanca (USAL), C/ Zacarías González 2, Salamanca 37007, Spain
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41
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Lee MS, Joo JW, Choi H, Kang HA, Kim K. Mec1 Modulates Interhomolog Crossover and Interplays with Tel1 at Post Double-Strand Break Stages. J Microbiol Biotechnol 2020; 30:469-475. [PMID: 31847509 PMCID: PMC9728206 DOI: 10.4014/jmb.1909.09020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/27/2019] [Accepted: 12/01/2019] [Indexed: 12/15/2022]
Abstract
During meiosis I, programmed DNA double-strand breaks (DSBs) occur to promote chromosome pairing and recombination between homologs. In Saccharomyces cerevisiae, Mec1 and Tel1, the orthologs of human ATR and ATM, respectively, regulate events upstream of the cell cycle checkpoint to initiate DNA repair. Tel1ATM and Mec1ATR are required for phosphorylating various meiotic proteins during recombination. This study aimed to investigate the role of Tel1ATM and Mec1ATR in meiotic prophase via physical analysis of recombination. Tel1ATM cooperated with Mec1ATR to mediate DSB-to-single end invasion transition, but negatively regulated DSB formation. Furthermore, Mec1ATR was required for the formation of interhomolog joint molecules from early prophase, thus establishing a recombination partner choice. Moreover, Mec1ATR specifically promoted crossover-fated DSB repair. Together, these results suggest that Tel1ATM and Mec1ATR function redundantly or independently in all post-DSB stages.
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Affiliation(s)
- Min-Su Lee
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jung Whan Joo
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyungseok Choi
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Ah Kang
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Keunpil Kim
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
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42
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Tian M, Loidl J. An MCM family protein promotes interhomolog recombination by preventing precocious intersister repair of meiotic DSBs. PLoS Genet 2019; 15:e1008514. [PMID: 31815942 PMCID: PMC6922451 DOI: 10.1371/journal.pgen.1008514] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/19/2019] [Accepted: 11/11/2019] [Indexed: 12/02/2022] Open
Abstract
Recombinational repair of meiotic DNA double-strand breaks (DSBs) uses the homologous chromosome as a template, although the sister chromatid offers itself as a spatially more convenient substrate. In many organisms, this choice is reinforced by the recombination protein Dmc1. In Tetrahymena, the repair of DSBs, which are formed early in prophase, is postponed to late prophase when homologous chromosomes and sister chromatids become juxtaposed owing to tight parallel packing in the thread-shaped nucleus, and thus become equally suitable for use as repair templates. The delay in DSB repair is achieved by rejection of the invading strand by the Sgs1 helicase in early meiotic prophase. In the absence of Mcmd1, a meiosis-specific minichromosome maintenance (MCM)-like protein (and its partner Pamd1), Dmc1 is prematurely lost from chromatin and DNA synthesis (as monitored by BrdU incorporation) takes place in early prophase. In mcmd1Δ and pamd1Δ mutants, only a few crossovers are formed. In a mcmd1Δ hop2Δ double mutant, normal timing of Dmc1 loss and DNA synthesis is restored. Because Tetrahymena Hop2 is believed to enable homologous strand invasion, we conclude that Dmc1 loss in the absence of Mcmd1 affects only post-invasion recombination intermediates. Therefore, we propose that the Dmc1 nucleofilament becomes dismantled immediately after forming a heteroduplex with a template strand. As a consequence, repair synthesis and D-loop extension starts in early prophase intermediates and prevents strand rejection before the completion of homologous pairing. In this case, DSB repair may primarily use the sister chromatid. We conclude that Mcmd1‒Pamd1 protects the Dmc1 nucleofilament from premature dismantling, thereby suppressing precocious repair synthesis and excessive intersister strand exchange at the cost of homologous recombination. Minichromosome maintenance (MCM) proteins are mainly known for their involvement in DNA replication. However, distant members of this protein family have recently been shown to promote interhomolog over intersister recombination in meiosis. They achieve this by enforcing or stabilizing the invasion of a double-stranded DNA by a filament consisting of a homologous single-stranded DNA molecule coated with a strand exchange protein. This interaction then would lead to the exchange of DNA strands and, ultimately, crossing over. Here, we study a member of the MCM protein family in the protist Tetrahymena thermophila. Meiosis in this organism has several unusual features: A synaptonemal complex is not formed, and homologous prealignment occurs during the close parallel arrangement of chromosomes in the extremely elongated, threadlike meiotic prophase nucleus. This noncanonical pairing has come along with altered mechanisms for recombination partner choice. Thus, we find that the Tetrahymena meiotic MCM protein promotes crossovers in an unprecedented way: It suppresses the formation of recombination intermediates between sister DNA molecules early in meiosis, thereby increasing the chance of competing interhomolog recombination events. Thus, members of the same protein family have been harnessed by different organisms to achieve the same result via completely different mechanisms.
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Affiliation(s)
- Miao Tian
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Josef Loidl
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- * E-mail:
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Martín-Guerrero SM, Casado P, Muñoz-Gámez JA, Carrasco MC, Navascués J, Cuadros MA, López-Giménez JF, Cutillas PR, Martín-Oliva D. Poly(ADP-Ribose) Polymerase-1 inhibition potentiates cell death and phosphorylation of DNA damage response proteins in oxidative stressed retinal cells. Exp Eye Res 2019; 188:107790. [DOI: 10.1016/j.exer.2019.107790] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/24/2019] [Accepted: 09/02/2019] [Indexed: 10/26/2022]
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Zhang W, Chen Z, Zhang D, Zhao B, Liu L, Xie Z, Yao Y, Zheng P. KHDC3L mutation causes recurrent pregnancy loss by inducing genomic instability of human early embryonic cells. PLoS Biol 2019; 17:e3000468. [PMID: 31609975 PMCID: PMC6812846 DOI: 10.1371/journal.pbio.3000468] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 10/24/2019] [Accepted: 09/26/2019] [Indexed: 12/28/2022] Open
Abstract
Recurrent pregnancy loss (RPL) is an important complication in reproductive health. About 50% of RPL cases are unexplained, and understanding the genetic basis is essential for its diagnosis and prognosis. Herein, we report causal KH domain containing 3 like (KHDC3L) mutations in RPL. KHDC3L is expressed in human epiblast cells and ensures their genome stability and viability. Mechanistically, KHDC3L binds to poly(ADP-ribose) polymerase 1 (PARP1) to stimulate its activity. In response to DNA damage, KHDC3L also localizes to DNA damage sites and facilitates homologous recombination (HR)-mediated DNA repair. KHDC3L dysfunction causes PARP1 inhibition and HR repair deficiency, which is synthetically lethal. Notably, we identified two critical residues, Thr145 and Thr156, whose phosphorylation by Ataxia-telangiectasia mutated (ATM) is essential for KHDC3L’s functions. Importantly, two deletions of KHDC3L (p.E150_V160del and p.E150_V172del) were detected in female RPL patients, both of which harbor a common loss of Thr156 and are impaired in PARP1 activation and HR repair. In summary, our study reveals both KHDC3L as a new RPL risk gene and its critical function in DNA damage repair pathways. Recurrent pregnancy loss is an important complication in reproductive health, and about 50% of cases remain unexplained. This study shows that KHDC3L safeguards the genomic stability of human early embryonic cells, and damaging mutations in its gene cause recurrent pregnancy loss in humans.
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Affiliation(s)
- Weidao Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zhongliang Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Dengfeng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - Bo Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lu Liu
- Department of Obstetrics and Gynaecology, Yan An Hospital, Kunming Medical University, Kunming, China
| | - Zhengyuan Xie
- Yunnan Key Laboratory for Fertility Regulation and Birth Health of Minority Nationalities, Key Laboratory of Preconception Health in Western China, NHFPC, Population and Family Planning Institute of Yunnan Province, Kunming, China
| | - Yonggang Yao
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- * E-mail:
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A pathway linking translation stress to checkpoint kinase 2 signaling in Neurospora crassa. Proc Natl Acad Sci U S A 2019; 116:17271-17279. [PMID: 31413202 PMCID: PMC6717302 DOI: 10.1073/pnas.1815396116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Checkpoint kinase 2 (CHK-2) is a key component of the DNA damage response (DDR) pathway and its activation mechanism is evolutionarily conserved. We show that PERIOD-4 (PRD-4), the CHK-2 ortholog of Neurospora crassa, is part of an additional signaling pathway that is activated when protein translation is compromised. Translation stress induces phosphorylation of PRD-4 by an upstream kinase distinct from those of the DDR pathway. We present evidence that the activating kinase is mTOR. Translation stress is sensed via a decrease in levels of an unstable inhibitor that antagonizes phosphorylation of PRD-4. Checkpoint kinase 2 (CHK-2) is a key component of the DNA damage response (DDR). CHK-2 is activated by the PIP3-kinase-like kinases (PI3KKs) ataxia telangiectasia mutated (ATM) and ataxia telangiectasia and Rad3-related protein (ATR), and in metazoan also by DNA-dependent protein kinase catalytic subunit (DNA-PKcs). These DNA damage-dependent activation pathways are conserved and additional activation pathways of CHK-2 are not known. Here we show that PERIOD-4 (PRD-4), the CHK-2 ortholog of Neurospora crassa, is part of a signaling pathway that is activated when protein translation is compromised. Translation stress induces phosphorylation of PRD-4 by a PI3KK distinct from ATM and ATR. Our data indicate that the activating PI3KK is mechanistic target of rapamycin (mTOR). We provide evidence that translation stress is sensed by unbalancing the expression levels of an unstable protein phosphatase that antagonizes phosphorylation of PRD-4 by mTOR complex 1 (TORC1). Hence, Neurospora mTOR and PRD-4 appear to coordinate metabolic state and cell cycle progression.
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46
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Tian M, Loidl J. A chromatin-associated protein required for inducing and limiting meiotic DNA double-strand break formation. Nucleic Acids Res 2019; 46:11822-11834. [PMID: 30357385 PMCID: PMC6294514 DOI: 10.1093/nar/gky968] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/05/2018] [Indexed: 11/13/2022] Open
Abstract
Programmed DNA double-strand breaks (DSBs) are required for meiotic recombination, but the number is strictly controlled because they are potentially harmful. Here we report a novel protein, Pars11, which is required for Spo11-dependent DSB formation in the protist Tetrahymena. Pars11 localizes to chromatin early in meiotic prophase in a Spo11-independent manner and is removed before the end of prophase. Pars11 removal depends on DSB formation and ATR-dependent phosphorylation. In the absence of the DNA damage sensor kinase ATR, Pars11 is retained on chromatin and excess DSBs are generated. Similar levels of Pars11 persistence and DSB overproduction occur in a non-phosphorylatable pars11 mutant. We conclude that Pars11 supports DSB formation by Spo11 until enough DSBs are formed; thereafter, DSB production stops in response to ATR-dependent degradation of Pars11 or its removal from chromatin. A similar DSB control mechanism involving a Rec114-Tel1/ATM-dependent negative feedback loop regulates DSB formation in budding yeast. However, there is no detectable sequence homology between Pars11 and Rec114, and DSB numbers are more tightly controlled by Pars11 than by Rec114. The discovery of this mechanism for DSB regulation in the evolutionarily distant protist and fungal lineages suggests that it is conserved across eukaryotes.
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Affiliation(s)
- Miao Tian
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Josef Loidl
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
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47
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Rodríguez A, Naveja JJ, Torres L, García de Teresa B, Juárez-Figueroa U, Ayala-Zambrano C, Azpeitia E, Mendoza L, Frías S. WIP1 Contributes to the Adaptation of Fanconi Anemia Cells to DNA Damage as Determined by the Regulatory Network of the Fanconi Anemia and Checkpoint Recovery Pathways. Front Genet 2019; 10:411. [PMID: 31130988 PMCID: PMC6509935 DOI: 10.3389/fgene.2019.00411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/15/2019] [Indexed: 02/01/2023] Open
Abstract
DNA damage adaptation (DDA) allows the division of cells with unrepaired DNA damage. DNA repair deficient cells might take advantage of DDA to survive. The Fanconi anemia (FA) pathway repairs DNA interstrand crosslinks (ICLs), and deficiencies in this pathway cause a fraction of breast and ovarian cancers as well as FA, a chromosome instability syndrome characterized by bone marrow failure and cancer predisposition. FA cells are hypersensitive to ICLs; however, DDA might promote their survival. We present the FA-CHKREC Boolean Network Model, which explores how FA cells might use DDA. The model integrates the FA pathway with the G2 checkpoint and the checkpoint recovery (CHKREC) processes. The G2 checkpoint mediates cell-cycle arrest (CCA) and the CHKREC activates cell-cycle progression (CCP) after resolution of DNA damage. Analysis of the FA-CHKREC network indicates that CHKREC drives DDA in FA cells, ignoring the presence of unrepaired DNA damage and allowing their division. Experimental inhibition of WIP1, a CHKREC component, in FA lymphoblast and cancer cell lines prevented division of FA cells, in agreement with the prediction of the model.
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Affiliation(s)
- Alfredo Rodríguez
- Laboratorio de Citogenética, Departamento de Investigación en Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - J Jesús Naveja
- PECEM, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Leda Torres
- Laboratorio de Citogenética, Departamento de Investigación en Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Benilde García de Teresa
- Laboratorio de Citogenética, Departamento de Investigación en Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Ulises Juárez-Figueroa
- Laboratorio de Citogenética, Departamento de Investigación en Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Cecilia Ayala-Zambrano
- Laboratorio de Citogenética, Departamento de Investigación en Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Eugenio Azpeitia
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sara Frías
- Laboratorio de Citogenética, Departamento de Investigación en Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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48
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Sonego M, Pellarin I, Costa A, Vinciguerra GLR, Coan M, Kraut A, D’Andrea S, Dall’Acqua A, Castillo-Tong DC, Califano D, Losito S, Spizzo R, Couté Y, Vecchione A, Belletti B, Schiappacassi M, Baldassarre G. USP1 links platinum resistance to cancer cell dissemination by regulating Snail stability. SCIENCE ADVANCES 2019; 5:eaav3235. [PMID: 31086816 PMCID: PMC6506239 DOI: 10.1126/sciadv.aav3235] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 04/01/2019] [Indexed: 06/01/2023]
Abstract
Resistance to platinum-based chemotherapy is a common event in patients with cancer, generally associated with tumor dissemination and metastasis. Whether platinum treatment per se activates molecular pathways linked to tumor spreading is not known. Here, we report that the ubiquitin-specific protease 1 (USP1) mediates ovarian cancer cell resistance to platinum, by regulating the stability of Snail, which, in turn, promotes tumor dissemination. At the molecular level, we observed that upon platinum treatment, USP1 is phosphorylated by ATM and ATR and binds to Snail. Then, USP1 de-ubiquitinates and stabilizes Snail expression, conferring resistance to platinum, increased stem cell-like features, and metastatic ability. Consistently, knockout or pharmacological inhibition of USP1 increased platinum sensitivity and decreased metastatic dissemination in a Snail-dependent manner. Our findings identify Snail as a USP1 target and open the way to a novel strategy to overcome platinum resistance and more successfully treat patients with ovarian cancer.
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Affiliation(s)
- Maura Sonego
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano, Italy
| | - Ilenia Pellarin
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano, Italy
| | - Alice Costa
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano, Italy
| | - Gian Luca Rampioni Vinciguerra
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano, Italy
- Faculty of Medicine and Psychology, Department of Clinical and Molecular Medicine, University of Rome “La Sapienza,” Santo Andrea Hospital, 00189 Rome, Italy
| | - Michela Coan
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano, Italy
| | - Alexandra Kraut
- University of Grenoble Alpes, CEA, INSERM, BIG-BGE, F-38000 Grenoble, France
| | - Sara D’Andrea
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano, Italy
| | - Alessandra Dall’Acqua
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano, Italy
| | - Dan Cacsire Castillo-Tong
- Translational Gynecology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Wien, 1090 Vienna, Austria
| | - Daniela Califano
- Genomica Funzionale, Fondazione G. Pascale, IRCCS, National Cancer Institute, 80100 Naples, Italy
| | - Simona Losito
- Anatomia Patologica, Fondazione G. Pascale, IRCCS, National Cancer Institute, 80100 Naples, Italy
| | - Riccardo Spizzo
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano, Italy
| | - Yohann Couté
- University of Grenoble Alpes, CEA, INSERM, BIG-BGE, F-38000 Grenoble, France
| | - Andrea Vecchione
- Faculty of Medicine and Psychology, Department of Clinical and Molecular Medicine, University of Rome “La Sapienza,” Santo Andrea Hospital, 00189 Rome, Italy
| | - Barbara Belletti
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano, Italy
| | - Monica Schiappacassi
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano, Italy
| | - Gustavo Baldassarre
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano, Italy
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49
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Wu Z, Qiu M, Guo Y, Zhao J, Liu Z, Wang H, Meng M, Yuan Z, Mi Z. OTU deubiquitinase 4 is silenced and radiosensitizes non-small cell lung cancer cells via inhibiting DNA repair. Cancer Cell Int 2019; 19:99. [PMID: 31011293 PMCID: PMC6466656 DOI: 10.1186/s12935-019-0816-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/05/2019] [Indexed: 12/25/2022] Open
Abstract
Background Radiotherapy is becoming one major therapeutics for non-small cell lung cancer (NSCLC). Identifying novel radiosensitizers will greatly increase the efficacy of radiotherapy and benefit more patients. OTU deubiquitinase 4 (OTUD4) has been reported involved in DNA damage repair pathways and could be a potential target for chemotherapy therapy. This study aimed to investigate the roles of OTUD4 in regulation of radiosensitivity of NSCLC via modulating DNA repair. Methods The expression of OTUD4, γ-H2Ax and ATM/CHK2/p53 pathway-related signaling molecules were detected by Western blotting and QRT-PCR. The methylation of OTUD4 promoter was investigated by 5-aza-deoxycytidine treatment, methylation-specific PCR and bisulfite genomic sequencing assays. Radiosensitivity was assessed by the clonogenic formation assay. Cell cycle, cell apoptosis were analyzed by flow cytometry. DNA damage and repair were determined by comet assay, γ-H2Ax foci staining and flow cytometry. Results OTUD4 is dramatically downregulated in NSCLC and its downregulation significantly correlates with poor prognosis of NSCLC patients. Promoter hypermethylation is responsible for the loss of OTUD4 expression in NSCLC cells. Overexpression of OTUD4 increases radiosensitivity of NSCLC cells exhibiting as impaired clonogenic formation ability, enhanced cell cycle arrest and increased cell apoptosis. Moreover, molecular mechanism study reveals that OTUD4 radiosensitizs NSCLC cells via ATM/CHK2/P53 signaling and inhibiting homology-directed repair of DNA double strand breaks induced by ionizing radiation. Conclusions This study uncovers a tumor-suppressing role of OTUD4 and that OTUD4 is a potential radiosensitizer for NSCLC. Electronic supplementary material The online version of this article (10.1186/s12935-019-0816-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhiqiang Wu
- 1Department of Radiation Oncology, Tianjin Medical University Cancer Institute & Hospital, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060 China
| | - Minghan Qiu
- 1Department of Radiation Oncology, Tianjin Medical University Cancer Institute & Hospital, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060 China
| | - Yu Guo
- 2Department of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Jinlin Zhao
- 1Department of Radiation Oncology, Tianjin Medical University Cancer Institute & Hospital, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060 China
| | - Zhuang Liu
- 1Department of Radiation Oncology, Tianjin Medical University Cancer Institute & Hospital, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060 China
| | - Hui Wang
- 1Department of Radiation Oncology, Tianjin Medical University Cancer Institute & Hospital, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060 China
| | - Maobin Meng
- 1Department of Radiation Oncology, Tianjin Medical University Cancer Institute & Hospital, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060 China
| | - Zhiyong Yuan
- 1Department of Radiation Oncology, Tianjin Medical University Cancer Institute & Hospital, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060 China
| | - Zeyun Mi
- 3Department of Biochemistry and Molecular Biology, College of Basic Medical Science, Tianjin Medical University, Tianjin, 300070 China
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50
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Wang J, Zhang H, Al Shibar M, Willard B, Ray A, Runge KW. Rif1 phosphorylation site analysis in telomere length regulation and the response to damaged telomeres. DNA Repair (Amst) 2018; 65:26-33. [PMID: 29544213 PMCID: PMC5911405 DOI: 10.1016/j.dnarep.2018.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/02/2018] [Accepted: 03/05/2018] [Indexed: 12/11/2022]
Abstract
Telomeres, the ends of eukaryotic chromosomes, consist of repetitive DNA sequences and their bound proteins that protect the end from the DNA damage response. Short telomeres with fewer repeats are preferentially elongated by telomerase. Tel1, the yeast homolog of human ATM kinase, is preferentially recruited to short telomeres and Tel1 kinase activity is required for telomere elongation. Rif1, a telomere-binding protein, negatively regulates telomere length by forming a complex with two other telomere binding proteins, Rap1 and Rif2, to block telomerase recruitment. Rif1 has 14 SQ/TQ consensus phosphorylation sites for ATM kinases, including 6 in a SQ/TQ Cluster Domain (SCD) similar to other DNA damage response proteins. These 14 sites were analyzed as N-terminal, SCD and C-terminal domains. Mutating some sites to non-phosphorylatable residues increased telomere length in cells lacking Tel1 while a different set of phosphomimetic mutants increased telomere length in cells lacking Rif2, suggesting that Rif1 phosphorylation has both positive and negative effects on length regulation. While these mutations did not alter the sensitivity to DNA damaging agents, inducing telomere-specific damage by growing cells lacking YKU70 at high temperature revealed a role for the SCD. Mass spectrometry of Rif1 from wild type cells or those induced for telomere-specific DNA damage revealed increased phosphorylation in cells with telomere damage at an ATM consensus site in the SCD, S1351, and non-ATM sites S181 and S1637. A phosphomimetic rif1-S1351E mutation caused an increase in telomere length at synthetic telomeres but not natural telomeres. These results indicate that the Rif1 SCD can modulate Rif1 function. As all Rif1 orthologs have one or more SCD domains, these results for yeast Rif1 have implications for the regulation of Rif1 function in humans and other organisms.
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Affiliation(s)
- Jinyu Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, United States; Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, United States; Department of Immunology, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, United States
| | - Haitao Zhang
- Department of Immunology, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, United States
| | - Mohammed Al Shibar
- Department of Immunology, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, United States
| | - Belinda Willard
- Lerner Research Institute Proteomics and Metabolomics Core, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, United States
| | - Alo Ray
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, United States
| | - Kurt W Runge
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, United States; Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, United States; Department of Immunology, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, United States.
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