1
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Bryan C, Cepeda J, Li B, Yang K. DNA-Protein Cross-Links Derived from Abasic DNA Lesions: Recent Progress and Future Directions. Chem Res Toxicol 2025. [PMID: 40387817 DOI: 10.1021/acs.chemrestox.5c00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2025]
Abstract
Covalent DNA-protein cross-links (DPCs), if not resolved, can block DNA replication and transcription, resulting in genome instability. Compared to other types of DNA damage, how DPCs are formed and repaired is less understood. This review focuses on recent findings concerning DPCs derived from two types of abasic DNA lesions, apurinic/apyrimidinic sites and 3'-phospho-α,β-unsaturated aldehydes. It summarizes the newly reported DPCs and their identification by liquid chromatography tandem mass spectrometry. It also reviews the approaches for synthesizing stable and site-specific DPCs, and their applications for discovering the corresponding repair mechanisms. Finally, it discusses the future directions to better understand the mechanistic formation and repair of those DPCs.
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Affiliation(s)
- Cameron Bryan
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Joel Cepeda
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Bingru Li
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kun Yang
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
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2
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Porcher L, Vijayraghavan S, Patel Y, Becker S, Blouin T, McCollum J, Mieczkowski PA, Saini N. Multiple DNA repair pathways prevent acetaldehyde-induced mutagenesis in yeast. Genetics 2025; 229:iyae213. [PMID: 39707916 PMCID: PMC12005267 DOI: 10.1093/genetics/iyae213] [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: 10/23/2024] [Accepted: 12/12/2024] [Indexed: 12/23/2024] Open
Abstract
Acetaldehyde is the primary metabolite of alcohol and is present in many environmental sources, including tobacco smoke. Acetaldehyde is genotoxic, whereby it can form DNA adducts and lead to mutagenesis. Individuals with defects in acetaldehyde clearance pathways have increased susceptibility to alcohol-associated cancers. Moreover, a mutation signature specific to acetaldehyde exposure is widespread in alcohol- and smoking-associated cancers. However, the pathways that repair acetaldehyde-induced DNA damage and thus prevent mutagenesis are vaguely understood. Here, we used Saccharomyces cerevisiae to delete genes in each of the major DNA repair pathways to identify those that alter acetaldehyde-induced mutagenesis. We observed that loss of functional nucleotide excision repair had the largest effect on acetaldehyde mutagenesis. In addition, base excision repair and DNA protein crosslink repair pathways were involved in modulating acetaldehyde mutagenesis, while mismatch repair, homologous recombination, and postreplication repair are dispensable for acetaldehyde mutagenesis. Acetaldehyde-induced mutations in a nucleotide excision repair-deficient (Δrad1) background were dependent on translesion synthesis and DNA interstrand crosslink repair. Moreover, whole-genome sequencing of the mutated isolates demonstrated an increase in C→A changes coupled with an enrichment of gCn→A changes, which is diagnostic of acetaldehyde exposure in yeast and in human cancers. Finally, downregulation of the leading strand replicative polymerase Pol epsilon, but not the lagging strand polymerase, resulted in increased acetaldehyde mutagenesis, indicating that lesions are likely formed on the leading strand. Our findings demonstrate that multiple DNA repair pathways coordinate to prevent acetaldehyde-induced mutagenesis.
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Affiliation(s)
- Latarsha Porcher
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Sriram Vijayraghavan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Yashvi Patel
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Samuel Becker
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Thomas Blouin
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - James McCollum
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Piotr A Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie Saini
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
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3
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Leitinger M, Broggi S, Spendel M, Kalss G, Petrović I, Krainz H, Rossini F, Höfler J, Toma A, Kuchukhidze G, Mauritz M, Poppert K, Crespo‐Pimentel B, Bosque‐Varela P, Pleyers A, Ganger P, Kotzot D, Lessel D, Griessenauer CJ, Trinka E. Multiple intracerebral hematomas during SEEG recording and intradural hemorrhage after spinal tap: A case report prompting more research on collagen IV gene mutation and oral nicotine consumption as risk factors. Epilepsia Open 2025; 10:329-335. [PMID: 39579033 PMCID: PMC11803267 DOI: 10.1002/epi4.13102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 10/31/2024] [Accepted: 11/04/2024] [Indexed: 11/25/2024] Open
Abstract
Intracerebral hemorrhages (ICH) during implantation of stereo-EEG electrodes are rare. The impact of tobacco-free nicotine consumption on periprocedural bleeding is uncertain. We present a 20+ year-old man with drug-resistant epilepsy who underwent stereo-EEG with 17 depth electrodes. Within a few days after insertion, the patient developed multiple ICHs in the electrode trajectories and an intradural hemorrhage after a diagnostic spinal tap. We performed the investigation of the clotting system and whole-exome sequencing (WES). WES identified a heterozygous mutation c.4698G>T, p.(Trp1566Cys) in COL4A2 (NM_001846.4) encoding a collagen type-IV alpha-2 chain inherited from his seemingly healthy mother. As COL4A2 mutations had been identified in four adult patients with ICH we postulated that the identified variant presents a potential risk factor. Notably, mutations encoding other collagens have been linked to cerebral hemorrhages (COL4A1) and increased propensity to trigger ICH upon smoking (COL1A2). Our patient consumed at least 24 oral nicotine pouches (containing 11 mg nicotine each) per day. We consider the patient's COL4A2 mutation in combination with his substantial nicotine consumption as likely predisposition to multiple ICHs precipitated by stereo-EEG. Patients with nicotine consumption and any collagen mutation may have a substantially higher risk for hemorrhagic complications in SEEG and other neurosurgical procedures. PLAIN LANGUAGE SUMMARY: A young man with drug-resistant epilepsy experienced multiple intracerebral hemorrhages after implantation of SEEG electrodes for presurgical evaluation and concomitantly a intradural hemorrhage after a lumbar spinal tap. A collagen IV mutation of unclear significance and heavy use of oral nicotine pouches were the only potential risk factors identified. As collagen mutations were previously described risk factors and smoking in particular worsens the bleeding risk in collagen mutations, further research is warranted to prevent hemorrhages in neurosurgical procedures. Nicotine consumption in any form is a preventable risk factor.
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Affiliation(s)
- Markus Leitinger
- Department of Neurology, Neurocritical Care, and Neurorehabilitation, Center for Cognitive Neuroscience, European Reference Network EpiCARE, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
- Neuroscience Institute, Center for Cognitive Neuroscience, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Serena Broggi
- Neurology and Stroke UnitASST Sette Laghi HospitalVareseItaly
| | - Mathias Spendel
- Department of Neurosurgery, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Gudrun Kalss
- Department of Neurology, Neurocritical Care, and Neurorehabilitation, Center for Cognitive Neuroscience, European Reference Network EpiCARE, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
- Neuroscience Institute, Center for Cognitive Neuroscience, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Ivan Petrović
- Faculty of MedicineUniversity of Novi SadNovi SadSerbia
| | - Herbert Krainz
- Department of Neurosurgery, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Fabio Rossini
- Department of Neurology, Neurocritical Care, and Neurorehabilitation, Center for Cognitive Neuroscience, European Reference Network EpiCARE, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
- Neuroscience Institute, Center for Cognitive Neuroscience, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Julia Höfler
- Department of Neurology, Neurocritical Care, and Neurorehabilitation, Center for Cognitive Neuroscience, European Reference Network EpiCARE, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
- Neuroscience Institute, Center for Cognitive Neuroscience, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Andreea Toma
- Department of Neurology, Neurocritical Care, and Neurorehabilitation, Center for Cognitive Neuroscience, European Reference Network EpiCARE, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
- Neuroscience Institute, Center for Cognitive Neuroscience, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Giorgi Kuchukhidze
- Department of Neurology, Neurocritical Care, and Neurorehabilitation, Center for Cognitive Neuroscience, European Reference Network EpiCARE, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
- Neuroscience Institute, Center for Cognitive Neuroscience, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Matthias Mauritz
- Department of Neurology, Neurocritical Care, and Neurorehabilitation, Center for Cognitive Neuroscience, European Reference Network EpiCARE, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
- Neuroscience Institute, Center for Cognitive Neuroscience, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Kai‐Nicolas Poppert
- Department of Neurology, Neurocritical Care, and Neurorehabilitation, Center for Cognitive Neuroscience, European Reference Network EpiCARE, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
- Neuroscience Institute, Center for Cognitive Neuroscience, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Bernardo Crespo‐Pimentel
- Department of Neurology, Neurocritical Care, and Neurorehabilitation, Center for Cognitive Neuroscience, European Reference Network EpiCARE, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
- Neuroscience Institute, Center for Cognitive Neuroscience, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Pilar Bosque‐Varela
- Department of Neurology, Neurocritical Care, and Neurorehabilitation, Center for Cognitive Neuroscience, European Reference Network EpiCARE, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
- Neuroscience Institute, Center for Cognitive Neuroscience, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Anna Pleyers
- Department of Human Genetics, Landeskrankenhaus University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Patricia Ganger
- Department of Human Genetics, Landeskrankenhaus University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Dieter Kotzot
- Department of Human Genetics, Landeskrankenhaus University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Davor Lessel
- Department of Human Genetics, Landeskrankenhaus University HospitalParacelsus Medical UniversitySalzburgAustria
- Institute of Human GeneticsUniversity of RegensburgRegensburgGermany
- Institute of Clinical Human GeneticsUniversity Hospital RegensburgRegensburgGermany
| | - Christoph J. Griessenauer
- Department of Neurosurgery, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
| | - Eugen Trinka
- Department of Neurology, Neurocritical Care, and Neurorehabilitation, Center for Cognitive Neuroscience, European Reference Network EpiCARE, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
- Neuroscience Institute, Center for Cognitive Neuroscience, Christian Doppler University HospitalParacelsus Medical UniversitySalzburgAustria
- Medical Informatics, and TechnologyInstitute of Public Health, Medical Decision Making and Health Technology Assessment, University for Health SciencesHall in TyrolAustria
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Liu Y, Peng Y, Wang Z, Wei X, Yang K. Light-Driven Installation of Aminooxyhomolysine on Histones and Its Application for Synthesizing Stable and Site-Specific 3'-DNA-Histone Cross-Links. Bioconjug Chem 2024; 35:1883-1887. [PMID: 39547792 PMCID: PMC11818567 DOI: 10.1021/acs.bioconjchem.4c00453] [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] [Indexed: 11/17/2024]
Abstract
Histones react with various aldehyde-containing DNA modifications to form reversible but long-lived DNA-histone cross-links. The investigation of their biochemical effects and repair mechanisms has been impeded due to their reversibility and the lack of methods for synthesizing stable and structure-defined DNA-histone cross-links. Herein, we present a visible-light-driven strategy to install an aminooxyhomolysine on a histone at a defined position. Using this method, we synthesized a hydrolytically stable and site-specific 3'-DNA-histone cross-link derived from an abasic DNA lesion. Such an adduct can be efficiently repaired by proteolysis coupled with nuclease excision. This work provides a strategy that can be readily expanded to synthesize DNA-histone cross-links derived from other aldehyde-containing DNA modifications.
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Affiliation(s)
- Yangxue Liu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ying Peng
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhishuo Wang
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Xiaoying Wei
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kun Yang
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
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5
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Song W, Zhao Y, Ruggiano A, Redfield C, Newman JA, Zhu X, Cruz-Migoni A, Roddan R, McHugh P, Elliott P, Ramadan K. The dual ubiquitin binding mode of SPRTN secures rapid spatiotemporal proteolysis of DNA-protein crosslinks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.26.625361. [PMID: 39651247 PMCID: PMC11623616 DOI: 10.1101/2024.11.26.625361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2024]
Abstract
DNA-protein crosslinks (DPCs) are endogenous and chemotherapy-induced genotoxic DNA lesions and, if not repaired, lead to embryonic lethality, neurodegeneration, premature ageing, and cancer. DPCs are heavily polyubiquitinated, and the SPRTN protease and 26S proteasome emerged as two central enzymes for DPC proteolysis. The proteasome recognises its substrates by their ubiquitination status. How SPRTN protease, an essential enzyme for DPC proteolysis, achieves specificity for DPCs still needs to be discovered. We found that the N-terminal SPRTN catalytic region (SprT) possesses a ubiquitin-binding domain named the U biquitin interface of S prT D omain (USD). Using multiple biochemical, biophysical, and structural approaches, we reveal that USD binds ubiquitin chains. SPRTN binding to ubiquitin chains via USD leads to ∼ 67-fold higher activation of SPRTN proteolysis towards polyubiquitinated DPCs than the unmodified DPCs. This study reveals the ubiquitination of DPCs is the key signal for SPRTN's substrate specificity and rapid proteolysis.
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6
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Weickert P, Dürauer S, Götz MJ, Li HY, Stingele J. Electro-elution-based purification of covalent DNA-protein cross-links. Nat Protoc 2024; 19:2891-2914. [PMID: 38890499 DOI: 10.1038/s41596-024-01004-z] [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: 04/24/2023] [Accepted: 02/19/2024] [Indexed: 06/20/2024]
Abstract
Covalent DNA-protein cross-links (DPCs) are pervasive DNA lesions that challenge genome stability and can be induced by metabolic or chemotherapeutic cross-linking agents including reactive aldehydes, topoisomerase poisons and DNMT1 inhibitors. The purification of x-linked proteins (PxP), where DNA-cross-linked proteins are separated from soluble proteins via electro-elution, can be used to identify DPCs. Here we describe a versatile and sensitive strategy for PxP. Mammalian cells are collected following exposure to a DPC-inducing agent, embedded in low-melt agarose plugs and lysed under denaturing conditions. Following lysis, the soluble proteins are extracted from the agarose plug by electro-elution, while genomic DNA and cross-linked proteins are retained in the plug. The cross-linked proteins can then be analyzed by standard analytical techniques such as sodium dodecyl-sulfate-polyacrylamide gel electrophoresis followed by western blotting or fluorescent staining. Alternatively, quantitative mass spectrometry-based proteomics can be used for the unbiased identification of DPCs. The isolation and analysis of DPCs by PxP overcomes the limitations of alternative methods to analyze DPCs that rely on precipitation as the separating principle and can be performed by users trained in molecular or cell biology within 2-3 d. The protocol has been optimized to study DPC induction and repair in mammalian cells but may also be adapted to other sample types including bacteria, yeast and tissue samples.
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Affiliation(s)
- Pedro Weickert
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sophie Dürauer
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maximilian J Götz
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hao-Yi Li
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Julian Stingele
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.
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7
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Wojtaszek JL, Williams RS. From the TOP: Formation, recognition and resolution of topoisomerase DNA protein crosslinks. DNA Repair (Amst) 2024; 142:103751. [PMID: 39180935 PMCID: PMC11404304 DOI: 10.1016/j.dnarep.2024.103751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
Since the report of "DNA untwisting" activity in 1972, ∼50 years of research has revealed seven topoisomerases in humans (TOP1, TOP1mt, TOP2α, TOP2β, TOP3α, TOP3β and Spo11). These conserved regulators of DNA topology catalyze controlled breakage to the DNA backbone to relieve the torsional stress that accumulates during essential DNA transactions including DNA replication, transcription, and DNA repair. Each topoisomerase-catalyzed reaction involves the formation of a topoisomerase cleavage complex (TOPcc), a covalent protein-DNA reaction intermediate formed between the DNA phosphodiester backbone and a topoisomerase catalytic tyrosine residue. A variety of perturbations to topoisomerase reaction cycles can trigger failure of the enzyme to re-ligate the broken DNA strand(s), thereby generating topoisomerase DNA-protein crosslinks (TOP-DPC). TOP-DPCs pose unique threats to genomic integrity. These complex lesions are comprised of structurally diverse protein components covalently linked to genomic DNA, which are bulky DNA adducts that can directly impact progression of the transcription and DNA replication apparatus. A variety of genome maintenance pathways have evolved to recognize and resolve TOP-DPCs. Eukaryotic cells harbor tyrosyl DNA phosphodiesterases (TDPs) that directly reverse 3'-phosphotyrosyl (TDP1) and 5'-phoshotyrosyl (TDP2) protein-DNA linkages. The broad specificity Mre11-Rad50-Nbs1 and APE2 nucleases are also critical for mitigating topoisomerase-generated DNA damage. These DNA-protein crosslink metabolizing enzymes are further enabled by proteolytic degradation, with the proteasome, Spartan, GCNA, Ddi2, and FAM111A proteases implicated thus far. Strategies to target, unfold, and degrade the protein component of TOP-DPCs have evolved as well. Here we survey mechanisms for addressing Topoisomerase 1 (TOP1) and Topoisomerase 2 (TOP2) DPCs, highlighting systems for which molecular structure information has illuminated function of these critical DNA damage response pathways.
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Affiliation(s)
- Jessica L Wojtaszek
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States.
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8
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Blouin T, Saini N. Aldehyde-induced DNA-protein crosslinks- DNA damage, repair and mutagenesis. Front Oncol 2024; 14:1478373. [PMID: 39328207 PMCID: PMC11424613 DOI: 10.3389/fonc.2024.1478373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024] Open
Abstract
Aldehyde exposure has been shown to lead to the formation of DNA damage comprising of DNA-protein crosslinks (DPCs), base adducts and interstrand or intrastrand crosslinks. DPCs have recently drawn more attention because of recent advances in detection and quantification of these adducts. DPCs are highly deleterious to genome stability and have been shown to block replication forks, leading to wide-spread mutagenesis. Cellular mechanisms to prevent DPC-induced damage include excision repair pathways, homologous recombination, and specialized proteases involved in cleaving the covalently bound proteins from DNA. These pathways were first discovered in formaldehyde-treated cells, however, since then, various other aldehydes have been shown to induce formation of DPCs in cells. Defects in DPC repair or aldehyde clearance mechanisms lead to various diseases including Ruijs-Aalfs syndrome and AMeD syndrome in humans. Here, we discuss recent developments in understanding how aldehydes form DPCs, how they are repaired, and the consequences of defects in these repair pathways.
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Affiliation(s)
| | - Natalie Saini
- Department of Biochemistry and Molecular Biology, Medical University of South
Carolina, Charleston, SC, United States
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9
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Anticevic I, Otten C, Popovic M. Tyrosyl-DNA phosphodiesterase 2 (Tdp2) repairs DNA-protein crosslinks and protects against double strand breaks in vivo. Front Cell Dev Biol 2024; 12:1394531. [PMID: 39228401 PMCID: PMC11369425 DOI: 10.3389/fcell.2024.1394531] [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: 03/01/2024] [Accepted: 06/06/2024] [Indexed: 09/05/2024] Open
Abstract
DNA-protein crosslinks pose a significant challenge to genome stability and cell viability. Efficient repair of DPCs is crucial for preserving genomic integrity and preventing the accumulation of DNA damage. Despite recent advances in our understanding of DPC repair, many aspects of this process, especially at the organismal level, remain elusive. In this study, we used zebrafish as a model organism to investigate the role of TDP2 (Tyrosyl-DNA phosphodiesterase 2) in DPC repair. We characterized the two tdp2 orthologs in zebrafish using phylogenetic, syntenic and expression analysis and investigated the phenotypic consequences of tdp2 silencing in zebrafish embryos. We then quantified the effects of tdp2a and tdp2b silencing on cellular DPC levels and DSB accumulation in zebrafish embryos. Our findings revealed that tdp2b is the main ortholog during embryonic development, while both orthologs are ubiquitously present in adult tissues. Notably, the tdp2b ortholog is phylogenetically closer to human TDP2. Silencing of tdp2b, but not tdp2a, resulted in the loss of Tdp2 activity in zebrafish embryos, accompanied by the accumulation of DPCs and DSBs. Our findings contribute to a more comprehensive understanding of DPC repair at the organismal level and underscore the significance of TDP2 in maintaining genome stability.
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Affiliation(s)
| | | | - Marta Popovic
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruder Boskovic, Zagreb, Croatia
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10
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Chauhan AS, Jhujh SS, Stewart GS. E3 ligases: a ubiquitous link between DNA repair, DNA replication and human disease. Biochem J 2024; 481:923-944. [PMID: 38985307 PMCID: PMC11346458 DOI: 10.1042/bcj20240124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 07/11/2024]
Abstract
Maintenance of genome stability is of paramount importance for the survival of an organism. However, genomic integrity is constantly being challenged by various endogenous and exogenous processes that damage DNA. Therefore, cells are heavily reliant on DNA repair pathways that have evolved to deal with every type of genotoxic insult that threatens to compromise genome stability. Notably, inherited mutations in genes encoding proteins involved in these protective pathways trigger the onset of disease that is driven by chromosome instability e.g. neurodevelopmental abnormalities, neurodegeneration, premature ageing, immunodeficiency and cancer development. The ability of cells to regulate the recruitment of specific DNA repair proteins to sites of DNA damage is extremely complex but is primarily mediated by protein post-translational modifications (PTMs). Ubiquitylation is one such PTM, which controls genome stability by regulating protein localisation, protein turnover, protein-protein interactions and intra-cellular signalling. Over the past two decades, numerous ubiquitin (Ub) E3 ligases have been identified to play a crucial role not only in the initiation of DNA replication and DNA damage repair but also in the efficient termination of these processes. In this review, we discuss our current understanding of how different Ub E3 ligases (RNF168, TRAIP, HUWE1, TRIP12, FANCL, BRCA1, RFWD3) function to regulate DNA repair and replication and the pathological consequences arising from inheriting deleterious mutations that compromise the Ub-dependent DNA damage response.
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Affiliation(s)
- Anoop S. Chauhan
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Satpal S. Jhujh
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Grant S. Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
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11
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Noireterre A, Stutz F. Cdc48/p97 segregase: Spotlight on DNA-protein crosslinks. DNA Repair (Amst) 2024; 139:103691. [PMID: 38744091 DOI: 10.1016/j.dnarep.2024.103691] [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: 12/22/2023] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024]
Abstract
The ATP-dependent molecular chaperone Cdc48 (in yeast) and its human counterpart p97 (also known as VCP), are essential for a variety of cellular processes, including the removal of DNA-protein crosslinks (DPCs) from the DNA. Growing evidence demonstrates in the last years that Cdc48/p97 is pivotal in targeting ubiquitinated and SUMOylated substrates on chromatin, thereby supporting the DNA damage response. Along with its cofactors, notably Ufd1-Npl4, Cdc48/p97 has emerged as a central player in the unfolding and processing of DPCs. This review introduces the detailed structure, mechanism and cellular functions of Cdc48/p97 with an emphasis on the current knowledge of DNA-protein crosslink repair pathways across several organisms. The review concludes by discussing the potential therapeutic relevance of targeting p97 in DPC repair.
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Affiliation(s)
- Audrey Noireterre
- Department of Molecular and Cellular Biology, University of Geneva, Geneva 4 1211, Switzerland
| | - Françoise Stutz
- Department of Molecular and Cellular Biology, University of Geneva, Geneva 4 1211, Switzerland.
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12
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Hurben AK, Zhang Q, Galligan JJ, Tretyakova N, Erber L. Endogenous Cellular Metabolite Methylglyoxal Induces DNA-Protein Cross-Links in Living Cells. ACS Chem Biol 2024; 19:1291-1302. [PMID: 38752800 PMCID: PMC11353540 DOI: 10.1021/acschembio.4c00100] [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] [Indexed: 06/22/2024]
Abstract
Methylglyoxal (MGO) is an electrophilic α-oxoaldehyde generated endogenously through metabolism of carbohydrates and exogenously due to autoxidation of sugars, degradation of lipids, and fermentation during food and drink processing. MGO can react with nucleophilic sites within proteins and DNA to form covalent adducts. MGO-induced advanced glycation end-products such as protein and DNA adducts are thought to be involved in oxidative stress, inflammation, diabetes, cancer, renal failure, and neurodegenerative diseases. Additionally, MGO has been hypothesized to form toxic DNA-protein cross-links (DPC), but the identities of proteins participating in such cross-linking in cells have not been determined. In the present work, we quantified DPC formation in human cells exposed to MGO and identified proteins trapped on DNA upon MGO exposure using mass spectrometry-based proteomics. A total of 265 proteins were found to participate in MGO-derived DPC formation including gene products engaged in telomere organization, nucleosome assembly, and gene expression. In vitro experiments confirmed DPC formation between DNA and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), as well as histone proteins H3.1 and H4. Collectively, our study provides the first evidence for MGO-mediated DNA-protein cross-linking in living cells, prompting future studies regarding the relevance of these toxic lesions in cancer, diabetes, and other diseases linked to elevated MGO levels.
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Affiliation(s)
- Alexander K. Hurben
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States; Present Address: Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Qi Zhang
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - James J. Galligan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Luke Erber
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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13
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Benedict B, Kristensen SM, Duxin JP. What are the DNA lesions underlying formaldehyde toxicity? DNA Repair (Amst) 2024; 138:103667. [PMID: 38554505 DOI: 10.1016/j.dnarep.2024.103667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 04/01/2024]
Abstract
Formaldehyde is a highly reactive organic compound. Humans can be exposed to exogenous sources of formaldehyde, but formaldehyde is also produced endogenously as a byproduct of cellular metabolism. Because formaldehyde can react with DNA, it is considered a major endogenous source of DNA damage. However, the nature of the lesions underlying formaldehyde toxicity in cells remains vastly unknown. Here, we review the current knowledge of the different types of nucleic acid lesions that are induced by formaldehyde and describe the repair pathways known to counteract formaldehyde toxicity. Taking this knowledge together, we discuss and speculate on the predominant lesions generated by formaldehyde, which underly its natural toxicity.
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Affiliation(s)
- Bente Benedict
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Stella Munkholm Kristensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Julien P Duxin
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark.
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14
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Herr LM, Schaffer ED, Fuchs KF, Datta A, Brosh RM. Replication stress as a driver of cellular senescence and aging. Commun Biol 2024; 7:616. [PMID: 38777831 PMCID: PMC11111458 DOI: 10.1038/s42003-024-06263-w] [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: 12/13/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Replication stress refers to slowing or stalling of replication fork progression during DNA synthesis that disrupts faithful copying of the genome. While long considered a nexus for DNA damage, the role of replication stress in aging is under-appreciated. The consequential role of replication stress in promotion of organismal aging phenotypes is evidenced by an extensive list of hereditary accelerated aging disorders marked by molecular defects in factors that promote replication fork progression and operate uniquely in the replication stress response. Additionally, recent studies have revealed cellular pathways and phenotypes elicited by replication stress that align with designated hallmarks of aging. Here we review recent advances demonstrating the role of replication stress as an ultimate driver of cellular senescence and aging. We discuss clinical implications of the intriguing links between cellular senescence and aging including application of senotherapeutic approaches in the context of replication stress.
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Affiliation(s)
- Lauren M Herr
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Ethan D Schaffer
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kathleen F Fuchs
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Arindam Datta
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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15
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Wen T, Zhao S, Stingele J, Ravanat JL, Greenberg MM. Quantification of Intracellular DNA-Protein Cross-Links with N7-Methyl-2'-Deoxyguanosine and Their Contribution to Cytotoxicity. Chem Res Toxicol 2024; 37:814-823. [PMID: 38652696 PMCID: PMC11105979 DOI: 10.1021/acs.chemrestox.4c00076] [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] [Indexed: 04/25/2024]
Abstract
The major product of DNA-methylating agents, N7-methyl-2'-deoxyguanosine (MdG), is a persistent lesion in vivo, but it is not believed to have a large direct physiological impact. However, MdG reacts with histone proteins to form reversible DNA-protein cross-links (DPCMdG), a family of DNA lesions that can significantly threaten cell survival. In this paper, we developed a tandem mass spectrometry method for quantifying the amounts of MdG and DPCMdG in nuclear DNA by taking advantage of their chemical lability and the concurrent release of N7-methylguanine. Using this method, we determined that DPCMdG is formed in less than 1% yield based upon the levels of MdG in methyl methanesulfonate (MMS)-treated HeLa cells. Despite its low chemical yield, DPCMdG contributes to MMS cytotoxicity. Consequently, cells that lack efficient DPC repair by the DPC protease SPRTN are hypersensitive to MMS. This investigation shows that the downstream chemical and biochemical effects of initially formed DNA damage can have significant biological consequences. With respect to MdG formation, the initial DNA lesion is only the beginning.
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Affiliation(s)
- Tingyu Wen
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Shubo Zhao
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Jean-Luc Ravanat
- Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, 38000 Grenoble, France
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
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16
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Oka Y, Nakazawa Y, Shimada M, Ogi T. Endogenous aldehyde-induced DNA-protein crosslinks are resolved by transcription-coupled repair. Nat Cell Biol 2024; 26:784-796. [PMID: 38600234 PMCID: PMC11098742 DOI: 10.1038/s41556-024-01401-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
DNA-protein crosslinks (DPCs) induced by aldehydes interfere with replication and transcription. Hereditary deficiencies in DPC repair and aldehyde clearance processes cause progeria, including Ruijs-Aalfs syndrome (RJALS) and AMeD syndrome (AMeDS) in humans. Although the elimination of DPC during replication has been well established, how cells overcome DPC lesions in transcription remains elusive. Here we show that endogenous aldehyde-induced DPC roadblocks are efficiently resolved by transcription-coupled repair (TCR). We develop a high-throughput sequencing technique to measure the genome-wide distribution of DPCs (DPC-seq). Using proteomics and DPC-seq, we demonstrate that the conventional TCR complex as well as VCP/p97 and the proteasome are required for the removal of formaldehyde-induced DPCs. TFIIS-dependent cleavage of RNAPII transcripts protects against transcription obstacles. Finally, a mouse model lacking both aldehyde clearance and TCR confirms endogenous DPC accumulation in actively transcribed regions. Collectively, our data provide evidence that transcription-coupled DPC repair (TC-DPCR) as well as aldehyde clearance are crucial for protecting against metabolic genotoxin, thus explaining the molecular pathogenesis of AMeDS and other disorders associated with defects in TCR, such as Cockayne syndrome.
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Affiliation(s)
- Yasuyoshi Oka
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mayuko Shimada
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan.
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
- Division of Animal Medical Science, Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya, Japan.
- Division of Molecular Physiology and Dynamics, Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan.
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17
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Carnie CJ, Acampora AC, Bader AS, Erdenebat C, Zhao S, Bitensky E, van den Heuvel D, Parnas A, Gupta V, D'Alessandro G, Sczaniecka-Clift M, Weickert P, Aygenli F, Götz MJ, Cordes J, Esain-Garcia I, Melidis L, Wondergem AP, Lam S, Robles MS, Balasubramanian S, Adar S, Luijsterburg MS, Jackson SP, Stingele J. Transcription-coupled repair of DNA-protein cross-links depends on CSA and CSB. Nat Cell Biol 2024; 26:797-810. [PMID: 38600235 PMCID: PMC11098753 DOI: 10.1038/s41556-024-01391-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 02/29/2024] [Indexed: 04/12/2024]
Abstract
Covalent DNA-protein cross-links (DPCs) are toxic DNA lesions that block replication and require repair by multiple pathways. Whether transcription blockage contributes to the toxicity of DPCs and how cells respond when RNA polymerases stall at DPCs is unknown. Here we find that DPC formation arrests transcription and induces ubiquitylation and degradation of RNA polymerase II. Using genetic screens and a method for the genome-wide mapping of DNA-protein adducts, DPC sequencing, we discover that Cockayne syndrome (CS) proteins CSB and CSA provide resistance to DPC-inducing agents by promoting DPC repair in actively transcribed genes. Consequently, CSB- or CSA-deficient cells fail to efficiently restart transcription after induction of DPCs. In contrast, nucleotide excision repair factors that act downstream of CSB and CSA at ultraviolet light-induced DNA lesions are dispensable. Our study describes a transcription-coupled DPC repair pathway and suggests that defects in this pathway may contribute to the unique neurological features of CS.
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Affiliation(s)
- Christopher J Carnie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Aleida C Acampora
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Aldo S Bader
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chimeg Erdenebat
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shubo Zhao
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Elnatan Bitensky
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Avital Parnas
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Giuseppina D'Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Pedro Weickert
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fatih Aygenli
- Institute of Medical Psychology and Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maximilian J Götz
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jacqueline Cordes
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Isabel Esain-Garcia
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Larry Melidis
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Annelotte P Wondergem
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Maria S Robles
- Institute of Medical Psychology and Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Stephen P Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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18
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Hisama FM, Pillai RK, Sidorova J, Patterson K, Gokingco C, Yacobi-Bach M, Oshima J. Caspase 5 depletion is linked to hyper-inflammatory response and progeroid syndrome. GeroScience 2024; 46:2771-2775. [PMID: 37603195 PMCID: PMC10828386 DOI: 10.1007/s11357-023-00907-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/06/2023] [Indexed: 08/22/2023] Open
Abstract
A progeroid family was found to harbor a pathogenic variant in the CASP5 gene that encodes inflammatory caspase 5. Caspase 5-depleted fibroblasts exhibited hyper-activation of inflammatory cytokines in response to pro-inflammatory stimuli. Long-term intermittent hyper-inflammatory response is likely the cause of the accelerated aging phenotype comprised of earlier onset of common aging diseases, supporting inflammaging as a potential common disease mechanism of progeroid syndromes and possibly normative aging.
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Affiliation(s)
- Fuki M Hisama
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, USA
| | - Renuka Kandhaya Pillai
- Department of Laboratory Medicine and Pathology, University of Washington, Box35747, Seattle, 98195, USA
| | - Julia Sidorova
- Department of Laboratory Medicine and Pathology, University of Washington, Box35747, Seattle, 98195, USA
| | - Karynne Patterson
- Department of Genome Science, University of Washington, Seattle, USA
| | - Carolina Gokingco
- Department of Laboratory Medicine and Pathology, University of Washington, Box35747, Seattle, 98195, USA
| | - Michal Yacobi-Bach
- Endocrine and Genetics Institutes, Sourasky Medical Center, Tel Aviv, Israel
| | - Junko Oshima
- Department of Laboratory Medicine and Pathology, University of Washington, Box35747, Seattle, 98195, USA.
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19
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Batel A, Polović M, Glumac M, Šuman O, Jadrijević S, Lozić B, Petrović M, Samardžija B, Bradshaw NJ, Skube K, Palada V, Acman M, Marinović Terzić I. SPRTN is involved in hepatocellular carcinoma development through the ER stress response. Cancer Gene Ther 2024; 31:376-386. [PMID: 38086993 DOI: 10.1038/s41417-023-00708-w] [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: 07/31/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 03/16/2024]
Abstract
Endoplasmic reticulum (ER) stress, prompted by the accumulation of misfolded or unfolded proteins, triggers the activation of the unfolded protein response (UPR) pathway to restore ER homeostasis. This stress response is implicated in the development of hepatocellular carcinoma (HCC). A biallelic mutation in SPRTN is currently the only known single-gene mutation implicated in the early onset of HCC. However, the exact mechanism linking SPRTN mutations to HCC remains unclear. In our study, we analyzed SPRTN and UPR in 21 human HCC tissue samples using RT-qPCR, immunoblot, and immunohistochemistry. We found alterations in the expression levels of SPRTN and UPR-related genes and proteins in HCC samples. The impact of SPRTN on the ER stress response was assessed in SPRTN-depleted HepG2 cells through RNA sequencing, pull-down assay, comet assay, and mitotic index calculation. We demonstrated that SPRTN interacts with the UPR sensor GRP78. Furthermore, we observed a decrease in SPRTN levels during ER stress, and increased sensitivity to ER stress in SPRTN-depleted cells. These findings suggest an essential role for SPRTN in the ER stress response and provide new insights into HCC pathogenesis. This newly discovered function of SPRTN could significantly enhance our understanding and treatment of HCC.
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Affiliation(s)
- Anja Batel
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
| | - Mirjana Polović
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
| | - Mateo Glumac
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
| | - Oliver Šuman
- Department of Abdominal Surgery, Merkur Clinical Hospital, Zajčeva 19, 10000, Zagreb, Croatia
| | - Stipislav Jadrijević
- Department of Abdominal Surgery, Merkur Clinical Hospital, Zajčeva 19, 10000, Zagreb, Croatia
| | - Bernarda Lozić
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
- Laboratory for Human Genetics, University Hospital Split, Spinčićeva 1, 21000, Split, Croatia
| | - Marija Petrović
- Laboratory for Human Genetics, University Hospital Split, Spinčićeva 1, 21000, Split, Croatia
| | - Bobana Samardžija
- Faculty of Biotechnology & Drug Development, University of Rijeka, Radmile Matejčić 2, 51000, Rijeka, Croatia
| | - Nicholas J Bradshaw
- Faculty of Biotechnology & Drug Development, University of Rijeka, Radmile Matejčić 2, 51000, Rijeka, Croatia
| | - Karlo Skube
- Selvita, Prilaz baruna Filipovića 29, 10000, Zagreb, Croatia
| | - Vinko Palada
- Department of Physiology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
| | - Mislav Acman
- Omics solutions, trg 101. Brigade HV 1, 10000, Zagreb, Croatia
| | - Ivana Marinović Terzić
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia.
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20
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Torrecilla I, Ruggiano A, Kiianitsa K, Aljarbou F, Lascaux P, Hoslett G, Song W, Maizels N, Ramadan K. Isolation and detection of DNA-protein crosslinks in mammalian cells. Nucleic Acids Res 2024; 52:525-547. [PMID: 38084926 PMCID: PMC10810220 DOI: 10.1093/nar/gkad1178] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 01/26/2024] Open
Abstract
DNA-protein crosslinks (DPCs) are toxic DNA lesions wherein a protein is covalently attached to DNA. If not rapidly repaired, DPCs create obstacles that disturb DNA replication, transcription and DNA damage repair, ultimately leading to genome instability. The persistence of DPCs is associated with premature ageing, cancer and neurodegeneration. In mammalian cells, the repair of DPCs mainly relies on the proteolytic activities of SPRTN and the 26S proteasome, complemented by other enzymes including TDP1/2 and the MRN complex, and many of the activities involved are essential, restricting genetic approaches. For many years, the study of DPC repair in mammalian cells was hindered by the lack of standardised assays, most notably assays that reliably quantified the proteins or proteolytic fragments covalently bound to DNA. Recent interest in the field has spurred the development of several biochemical methods for DPC analysis. Here, we critically analyse the latest techniques for DPC isolation and the benefits and drawbacks of each. We aim to assist researchers in selecting the most suitable isolation method for their experimental requirements and questions, and to facilitate the comparison of results across different laboratories using different approaches.
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Affiliation(s)
- Ignacio Torrecilla
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Annamaria Ruggiano
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Kostantin Kiianitsa
- Department of Immunology, University of Washington, Seattle, WA 98195-7350, USA
| | - Ftoon Aljarbou
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Pauline Lascaux
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Gwendoline Hoslett
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Wei Song
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Nancy Maizels
- Department of Immunology, University of Washington, Seattle, WA 98195-7350, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7350, USA
| | - Kristijan Ramadan
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
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21
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Mórocz M, Qorri E, Pekker E, Tick G, Haracska L. Exploring RAD18-dependent replication of damaged DNA and discontinuities: A collection of advanced tools. J Biotechnol 2024; 380:1-19. [PMID: 38072328 DOI: 10.1016/j.jbiotec.2023.12.001] [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: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/21/2023]
Abstract
DNA damage tolerance (DDT) pathways mitigate the effects of DNA damage during replication by rescuing the replication fork stalled at a DNA lesion or other barriers and also repair discontinuities left in the newly replicated DNA. From yeast to mammalian cells, RAD18-regulated translesion synthesis (TLS) and template switching (TS) represent the dominant pathways of DDT. Monoubiquitylation of the polymerase sliding clamp PCNA by HRAD6A-B/RAD18, an E2/E3 protein pair, enables the recruitment of specialized TLS polymerases that can insert nucleotides opposite damaged template bases. Alternatively, the subsequent polyubiquitylation of monoubiquitin-PCNA by Ubc13-Mms2 (E2) and HLTF or SHPRH (E3) can lead to the switching of the synthesis from the damaged template to the undamaged newly synthesized sister strand to facilitate synthesis past the lesion. When immediate TLS or TS cannot occur, gaps may remain in the newly synthesized strand, partly due to the repriming activity of the PRIMPOL primase, which can be filled during the later phases of the cell cycle. The first part of this review will summarize the current knowledge about RAD18-dependent DDT pathways, while the second part will offer a molecular toolkit for the identification and characterization of the cellular functions of a DDT protein. In particular, we will focus on advanced techniques that can reveal single-stranded and double-stranded DNA gaps and their repair at the single-cell level as well as monitor the progression of single replication forks, such as the specific versions of the DNA fiber and comet assays. This collection of methods may serve as a powerful molecular toolkit to monitor the metabolism of gaps, detect the contribution of relevant pathways and molecular players, as well as characterize the effectiveness of potential inhibitors.
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Affiliation(s)
- Mónika Mórocz
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Erda Qorri
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Faculty of Science and Informatics, Doctoral School of Biology, University of Szeged, Szeged H-6720, Hungary.
| | - Emese Pekker
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Doctoral School of Interdisciplinary Medicine, University of Szeged, Korányi fasor 10, 6720 Szeged, Hungary.
| | - Gabriella Tick
- Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Lajos Haracska
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; National Laboratory for Drug Research and Development, Magyar tudósok krt. 2. H-1117 Budapest, Hungary.
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22
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Quaglia A, Roberts EA, Torbenson M. Developmental and Inherited Liver Disease. MACSWEEN'S PATHOLOGY OF THE LIVER 2024:122-294. [DOI: 10.1016/b978-0-7020-8228-3.00003-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2025]
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23
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Zhao S, Cordes J, Caban KM, Götz MJ, Mackens-Kiani T, Veltri AJ, Sinha NK, Weickert P, Kaya S, Hewitt G, Nedialkova DD, Fröhlich T, Beckmann R, Buskirk AR, Green R, Stingele J. RNF14-dependent atypical ubiquitylation promotes translation-coupled resolution of RNA-protein crosslinks. Mol Cell 2023; 83:4290-4303.e9. [PMID: 37951216 PMCID: PMC10783637 DOI: 10.1016/j.molcel.2023.10.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/17/2023] [Accepted: 10/13/2023] [Indexed: 11/13/2023]
Abstract
Reactive aldehydes are abundant endogenous metabolites that challenge homeostasis by crosslinking cellular macromolecules. Aldehyde-induced DNA damage requires repair to prevent cancer and premature aging, but it is unknown whether cells also possess mechanisms that resolve aldehyde-induced RNA lesions. Here, we establish photoactivatable ribonucleoside-enhanced crosslinking (PAR-CL) as a model system to study RNA crosslinking damage in the absence of confounding DNA damage in human cells. We find that such RNA damage causes translation stress by stalling elongating ribosomes, which leads to collisions with trailing ribosomes and activation of multiple stress response pathways. Moreover, we discovered a translation-coupled quality control mechanism that resolves covalent RNA-protein crosslinks. Collisions between translating ribosomes and crosslinked mRNA-binding proteins trigger their modification with atypical K6- and K48-linked ubiquitin chains. Ubiquitylation requires the E3 ligase RNF14 and leads to proteasomal degradation of the protein adduct. Our findings identify RNA lesion-induced translational stress as a central component of crosslinking damage.
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Affiliation(s)
- Shubo Zhao
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jacqueline Cordes
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Karolina M Caban
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maximilian J Götz
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Timur Mackens-Kiani
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anthony J Veltri
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Niladri K Sinha
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Pedro Weickert
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Selay Kaya
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Graeme Hewitt
- King's College London School of Cancer & Pharmaceutical Sciences, London, UK
| | - Danny D Nedialkova
- Max Planck Institute of Biochemistry, Martinsried, Germany; Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany
| | - Thomas Fröhlich
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Roland Beckmann
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Julian Stingele
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.
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24
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Suryo Rahmanto A, Blum CJ, Scalera C, Heidelberger JB, Mesitov M, Horn-Ghetko D, Gräf JF, Mikicic I, Hobrecht R, Orekhova A, Ostermaier M, Ebersberger S, Möckel MM, Krapoth N, Da Silva Fernandes N, Mizi A, Zhu Y, Chen JX, Choudhary C, Papantonis A, Ulrich HD, Schulman BA, König J, Beli P. K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution. Mol Cell 2023; 83:4272-4289.e10. [PMID: 37951215 DOI: 10.1016/j.molcel.2023.10.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/17/2023] [Accepted: 10/13/2023] [Indexed: 11/13/2023]
Abstract
Reactive aldehydes are produced by normal cellular metabolism or after alcohol consumption, and they accumulate in human tissues if aldehyde clearance mechanisms are impaired. Their toxicity has been attributed to the damage they cause to genomic DNA and the subsequent inhibition of transcription and replication. However, whether interference with other cellular processes contributes to aldehyde toxicity has not been investigated. We demonstrate that formaldehyde induces RNA-protein crosslinks (RPCs) that stall the ribosome and inhibit translation in human cells. RPCs in the messenger RNA (mRNA) are recognized by the translating ribosomes, marked by atypical K6-linked ubiquitylation catalyzed by the RING-in-between-RING (RBR) E3 ligase RNF14, and subsequently resolved by the ubiquitin- and ATP-dependent unfoldase VCP. Our findings uncover an evolutionary conserved formaldehyde-induced stress response pathway that protects cells against RPC accumulation in the cytoplasm, and they suggest that RPCs contribute to the cellular and tissue toxicity of reactive aldehydes.
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Affiliation(s)
- Aldwin Suryo Rahmanto
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | | | | | | | | | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Justus F Gräf
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Ivan Mikicic
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Anna Orekhova
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | | | | | - Nils Krapoth
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Yajie Zhu
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jia-Xuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany.
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25
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Mima K, Hamada T, Inamura K, Baba H, Ugai T, Ogino S. The microbiome and rise of early-onset cancers: knowledge gaps and research opportunities. Gut Microbes 2023; 15:2269623. [PMID: 37902043 PMCID: PMC10730181 DOI: 10.1080/19490976.2023.2269623] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/06/2023] [Indexed: 10/31/2023] Open
Abstract
Accumulating evidence indicates an alarming increase in the incidence of early-onset cancers, which are diagnosed among adults under 50 years of age, in the colorectum, esophagus, extrahepatic bile duct, gallbladder, liver, stomach, pancreas, as well as the bone marrow (multiple myeloma), breast, head and neck, kidney, prostate, thyroid, and uterine corpus (endometrium). While the early-onset cancer studies have encompassed research on the wide variety of organs, this article focuses on research on digestive system cancers. While a minority of early-onset cancers in the digestive system are associated with cancer-predisposing high penetrance germline genetic variants, the majority of those cancers are sporadic and multifactorial. Although potential etiological roles of diets, lifestyle, environment, and the microbiome from early life to adulthood (i.e. in one's life course) have been hypothesized, exact contribution of each of these factors remains uncertain. Diets, lifestyle patterns, and environmental exposures have been shown to alter the oral and intestinal microbiome. To address the rising trend of early-onset cancers, transdisciplinary research approaches including lifecourse epidemiology and molecular pathological epidemiology frameworks, nutritional and environmental sciences, multi-omics technologies, etc. are needed. We review current evidence and discuss emerging research opportunities, which can improve our understanding of their etiologies and help us design better strategies for prevention and treatment to reduce the cancer burden in populations.
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Affiliation(s)
- Kosuke Mima
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tsuyoshi Hamada
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Hepato-Biliary-Pancreatic Medicine, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kentaro Inamura
- Division of Pathology, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tomotaka Ugai
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Cancer Epidemiology Program, Dana-Farber Harvard Cancer Center, Boston, MA, USA
| | - Shuji Ogino
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Cancer Epidemiology Program, Dana-Farber Harvard Cancer Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cancer Immunology Program, Dana-Farber Harvard Cancer Center, Boston, MA, USA
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26
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Kirchner K, Seidel C, Paulsen FO, Sievers B, Bokemeyer C, Lessel D. Further Association of Germline CHEK2 Loss-of-Function Variants with Testicular Germ Cell Tumors. J Clin Med 2023; 12:7065. [PMID: 38002677 PMCID: PMC10672725 DOI: 10.3390/jcm12227065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/17/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
Testicular germ cell tumors (TGCTs) represent the most frequent malignancy in young adult men and have one the highest heritability rates among all cancers. A recent multicenter case-control study identified CHEK2 as the first moderate-penetrance TGCT predisposition gene. Here, we analyzed CHEK2 in 129 TGCT cases unselected for age of onset, histology, clinical outcome, and family history of any cancer, and the frequency of identified variants was compared to findings in 27,173 ancestry-matched cancer-free men. We identified four TGCT cases harboring a P/LP variant in CHEK2 (4/129, 3.10%), which reached statistical significance (p = 0.0191; odds ratio (OR), 4.06; 95% CI, 1.59-10.54) as compared to the control group. Cases with P/LP variants in CHEK2 developed TGCT almost 6 years earlier than individuals with CHEK2 wild-type alleles (5.67 years; 29.5 vs. 35.17). No association was found between CHEK2 status and further clinical and histopathological characteristics, including histological subtypes, the occurrence of aggressive TGCT, family history of TGCT, and family history of any cancer. In addition, we found significant enrichment for the low-penetrance CHEK2 variant p.Ile157Thr (p = 0.0259; odds ratio (OR), 3.69; 95% CI, 1.45-9.55). Thus, we provide further independent evidence of CHEK2 being a moderate-penetrance TGCT predisposition gene.
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Affiliation(s)
- Kira Kirchner
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (K.K.); (B.S.)
| | - Christoph Seidel
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (C.S.); (F.-O.P.); (C.B.)
| | - Finn-Ole Paulsen
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (C.S.); (F.-O.P.); (C.B.)
| | - Bianca Sievers
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (K.K.); (B.S.)
| | - Carsten Bokemeyer
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (C.S.); (F.-O.P.); (C.B.)
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (K.K.); (B.S.)
- Institute of Human Genetics, University Hospital Salzburg, Paracelsus Medical University, 5020 Salzburg, Austria
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Xia D, Zhu X, Wang Y, Gong P, Su HS, Xu X. Implications of ubiquitination and the maintenance of replication fork stability in cancer therapy. Biosci Rep 2023; 43:BSR20222591. [PMID: 37728310 PMCID: PMC10550789 DOI: 10.1042/bsr20222591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/21/2023] [Accepted: 09/19/2023] [Indexed: 09/21/2023] Open
Abstract
DNA replication forks are subject to intricate surveillance and strict regulation by sophisticated cellular machinery. Such close regulation is necessary to ensure the accurate duplication of genetic information and to tackle the diverse endogenous and exogenous stresses that impede this process. Stalled replication forks are vulnerable to collapse, which is a major cause of genomic instability and carcinogenesis. Replication stress responses, which are organized via a series of coordinated molecular events, stabilize stalled replication forks and carry out fork reversal and restoration. DNA damage tolerance and repair pathways such as homologous recombination and Fanconi anemia also contribute to replication fork stabilization. The signaling network that mediates the transduction and interplay of these pathways is regulated by a series of post-translational modifications, including ubiquitination, which affects the activity, stability, and interactome of substrates. In particular, the ubiquitination of replication protein A and proliferating cell nuclear antigen at stalled replication forks promotes the recruitment of downstream regulators. In this review, we describe the ubiquitination-mediated signaling cascades that regulate replication fork progression and stabilization. In addition, we discuss the targeting of replication fork stability and ubiquitination system components as a potential therapeutic approach for the treatment of cancer.
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Affiliation(s)
- Donghui Xia
- Shenzhen University General Hospital-Dehua Hospital Joint Research Center on Precision Medicine (sgh-dhhCPM), Dehua Hospital, Dehua, Quanzhou 362500, China
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong 518060, China
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xuefei Zhu
- Department of General Surgery, Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors and Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Ying Wang
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Peng Gong
- Department of General Surgery, Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors and Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Hong-Shu Su
- Shenzhen University General Hospital-Dehua Hospital Joint Research Center on Precision Medicine (sgh-dhhCPM), Dehua Hospital, Dehua, Quanzhou 362500, China
| | - Xingzhi Xu
- Shenzhen University General Hospital-Dehua Hospital Joint Research Center on Precision Medicine (sgh-dhhCPM), Dehua Hospital, Dehua, Quanzhou 362500, China
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong 518060, China
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28
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Anticevic I, Otten C, Vinkovic L, Jukic L, Popovic M. Tyrosyl-DNA phosphodiesterase 1 (TDP1) and SPRTN protease repair histone 3 and topoisomerase 1 DNA-protein crosslinks in vivo. Open Biol 2023; 13:230113. [PMID: 37788708 PMCID: PMC10547559 DOI: 10.1098/rsob.230113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/14/2023] [Indexed: 10/05/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are frequent and damaging DNA lesions that affect all DNA transactions, which in turn can lead to the formation of double-strand breaks, genomic instability and cell death. At the organismal level, impaired DPC repair (DPCR) is associated with cancer, ageing and neurodegeneration. Despite the severe consequences of DPCs, little is known about the processes underlying repair pathways at the organism level. SPRTN is a protease that removes most cellular DPCs during replication, whereas tyrosyl-DNA phosphodiesterase 1 repairs one of the most abundant enzymatic DPCs, topoisomerase 1-DPC (TOP1-DPC). How these two enzymes repair DPCs at the organism level is currently unknown. We perform phylogenetic, syntenic, structural and expression analysis to compare tyrosyl-DNA phosphodiesterase 1 (TDP1) orthologues between human, mouse and zebrafish. Using the zebrafish animal model and human cells, we demonstrate that TDP1 and SPRTN repair endogenous, camptothecin- and formaldehyde-induced DPCs, including histone H3- and TOP1-DPCs. We show that resolution of H3-DNA crosslinks depends on upstream proteolysis by SPRTN and subsequent peptide removal by TDP1 in RPE1 cells and zebrafish embryos, whereas SPRTN and TDP1 function in different pathways in the repair of endogenous TOP1-DPCs and total DPCs. Furthermore, we have found increased TDP2 expression in TDP1-deficient cells and embryos. Understanding the role of TDP1 in DPCR at the cellular and organismal levels could provide an impetus for the development of new drugs and combination therapies with TOP1-DPC inducing drugs.
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Affiliation(s)
- Ivan Anticevic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Cecile Otten
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Luka Vinkovic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Luka Jukic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Marta Popovic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
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29
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Donsbach M, Dürauer S, Grünert F, Nguyen KT, Nigam R, Yaneva D, Weickert P, Bezalel‐Buch R, Semlow DR, Stingele J. A non-proteolytic release mechanism for HMCES-DNA-protein crosslinks. EMBO J 2023; 42:e113360. [PMID: 37519246 PMCID: PMC10505908 DOI: 10.15252/embj.2022113360] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023] Open
Abstract
The conserved protein HMCES crosslinks to abasic (AP) sites in ssDNA to prevent strand scission and the formation of toxic dsDNA breaks during replication. Here, we report a non-proteolytic release mechanism for HMCES-DNA-protein crosslinks (DPCs), which is regulated by DNA context. In ssDNA and at ssDNA-dsDNA junctions, HMCES-DPCs are stable, which efficiently protects AP sites against spontaneous incisions or cleavage by APE1 endonuclease. In contrast, HMCES-DPCs are released in dsDNA, allowing APE1 to initiate downstream repair. Mechanistically, we show that release is governed by two components. First, a conserved glutamate residue, within HMCES' active site, catalyses reversal of the crosslink. Second, affinity to the underlying DNA structure determines whether HMCES re-crosslinks or dissociates. Our study reveals that the protective role of HMCES-DPCs involves their controlled release upon bypass by replication forks, which restricts DPC formation to a necessary minimum.
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Affiliation(s)
- Maximilian Donsbach
- Department of BiochemistryLudwig‐Maximilians‐University MunichMunichGermany
- Gene Center, Ludwig‐Maximilians‐University MunichMunichGermany
| | - Sophie Dürauer
- Department of BiochemistryLudwig‐Maximilians‐University MunichMunichGermany
- Gene Center, Ludwig‐Maximilians‐University MunichMunichGermany
| | - Florian Grünert
- Department of BiochemistryLudwig‐Maximilians‐University MunichMunichGermany
- Gene Center, Ludwig‐Maximilians‐University MunichMunichGermany
| | - Kha T Nguyen
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Richa Nigam
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Denitsa Yaneva
- Department of BiochemistryLudwig‐Maximilians‐University MunichMunichGermany
- Gene Center, Ludwig‐Maximilians‐University MunichMunichGermany
| | - Pedro Weickert
- Department of BiochemistryLudwig‐Maximilians‐University MunichMunichGermany
- Gene Center, Ludwig‐Maximilians‐University MunichMunichGermany
| | - Rachel Bezalel‐Buch
- Department of Biological Chemistry and Molecular BiophysicsWashington University School of MedicalSaint LouisMOUSA
| | - Daniel R Semlow
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Julian Stingele
- Department of BiochemistryLudwig‐Maximilians‐University MunichMunichGermany
- Gene Center, Ludwig‐Maximilians‐University MunichMunichGermany
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30
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Saha LK, Saha S, Yang X, Huang SYN, Sun Y, Jo U, Pommier Y. Replication-associated formation and repair of human topoisomerase IIIα cleavage complexes. Nat Commun 2023; 14:1925. [PMID: 37024461 PMCID: PMC10079683 DOI: 10.1038/s41467-023-37498-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023] Open
Abstract
Topoisomerase IIIα (TOP3A) belongs to the conserved Type IA family of DNA topoisomerases. Here we report that human TOP3A is associated with DNA replication forks and that a "self-trapping" TOP3A mutant (TOP3A-R364W) generates cellular TOP3A DNA cleavage complexes (TOP3Accs). We show that trapped TOP3Accs that interfere with replication, induce DNA damage and genome instability. To elucidate how TOP3Accs are repaired, we explored the role of Spartan (SPRTN), the metalloprotease associated with DNA replication, which digests proteins forming DNA-protein crosslinks (DPCs). We find that SPRTN-deficient cells show elevated TOP3Accs, whereas overexpression of SPRTN lowers cellular TOP3Accs. SPRTN is deubiquitinated and epistatic with TDP2 in response to TOP3Accs. In addition, we found that MRE11 can excise TOP3Accs, and that cell cycle determines the preference for the SPRTN-TDP2 vs. the ATM-MRE11 pathways, in S vs. G2, respectively. Our study highlights the prevalence of TOP3Accs repair mechanisms to ensure normal DNA replication.
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Affiliation(s)
- Liton Kumar Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Xi Yang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yilun Sun
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Ukhyun Jo
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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31
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Wang H, Cai Y, Jin M, Huang CQ, Ning C, Niu S, Fan L, Li B, Zhang M, Lu Z, Dong X, Luo Z, Zhong R, Li H, Zhu Y, Miao X, Yang X, Chang J, Li N, Tian J. Identification of specific susceptibility loci for the early-onset colorectal cancer. Genome Med 2023; 15:13. [PMID: 36869385 PMCID: PMC9983269 DOI: 10.1186/s13073-023-01163-w] [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: 06/30/2022] [Accepted: 02/15/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND The incidence of early-onset colorectal cancer (EOCRC; patients < 50 years old) has been rising rapidly, whereas the EOCRC genetic susceptibility remains incompletely investigated. Here, we aimed to systematically identify specific susceptible genetic variants for EOCRC. METHODS Two parallel GWASs were conducted in 17,789 CRC cases (including 1490 EOCRC cases) and 19,951 healthy controls. A polygenic risk score (PRS) model was built based on identified EOCRC-specific susceptibility variants by using the UK Biobank cohort. We also interpreted the potential biological mechanisms of the prioritized risk variant. RESULTS We identified 49 independent susceptibility loci that were significantly associated with the susceptibility to EOCRC and the diagnosed age of CRC (both P < 5.0×10-4), replicating 3 previous CRC GWAS loci. There are 88 assigned susceptibility genes involved in chromatin assembly and DNA replication pathways, mainly associating with precancerous polyps. Additionally, we assessed the genetic effect of the identified variants by developing a PRS model. Compared to the individuals in the low genetic risk group, the individuals in the high genetic risk group have increased EOCRC risk, and these results were replicated in the UKB cohort with a 1.63-fold risk (95% CI: 1.32-2.02, P = 7.67×10-6). The addition of the identified EOCRC risk loci significantly increased the prediction accuracy of the PRS model, compared to the PRS model derived from the previous GWAS-identified loci. Mechanistically, we also elucidated that rs12794623 may contribute to the early stage of CRC carcinogenesis via allele-specific regulating the expression of POLA2. CONCLUSIONS These findings will broaden the understanding of the etiology of EOCRC and may facilitate the early screening and individualized prevention.
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Affiliation(s)
- Haoxue Wang
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan, 430071, China
| | - Yimin Cai
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan, 430071, China
| | - Meng Jin
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Chao Qun Huang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China
| | - Caibo Ning
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Siyuan Niu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Linyun Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zequn Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuesi Dong
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Chinese Academy of Medical Sciences Key Laboratory for National Cancer Big Data Analysis and Implement, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zilin Luo
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Chinese Academy of Medical Sciences Key Laboratory for National Cancer Big Data Analysis and Implement, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Li
- Department of Urology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan, 430071, China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan, 430071, China.,Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Xiaojun Yang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China.
| | - Jiang Chang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Ni Li
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. .,Chinese Academy of Medical Sciences Key Laboratory for National Cancer Big Data Analysis and Implement, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan, 430071, China.
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32
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Weickert P, Li HY, Götz MJ, Dürauer S, Yaneva D, Zhao S, Cordes J, Acampora AC, Forne I, Imhof A, Stingele J. SPRTN patient variants cause global-genome DNA-protein crosslink repair defects. Nat Commun 2023; 14:352. [PMID: 36681662 PMCID: PMC9867749 DOI: 10.1038/s41467-023-35988-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 01/10/2023] [Indexed: 01/22/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are pervasive DNA lesions that are induced by reactive metabolites and various chemotherapeutic agents. Here, we develop a technique for the Purification of x-linked Proteins (PxP), which allows identification and tracking of diverse DPCs in mammalian cells. Using PxP, we investigate DPC repair in cells genetically-engineered to express variants of the SPRTN protease that cause premature ageing and early-onset liver cancer in Ruijs-Aalfs syndrome patients. We find an unexpected role for SPRTN in global-genome DPC repair, that does not rely on replication-coupled detection of the lesion. Mechanistically, we demonstrate that replication-independent DPC cleavage by SPRTN requires SUMO-targeted ubiquitylation of the protein adduct and occurs in addition to proteasomal DPC degradation. Defective ubiquitin binding of SPRTN patient variants compromises global-genome DPC repair and causes synthetic lethality in combination with a reduction in proteasomal DPC repair capacity.
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Affiliation(s)
- Pedro Weickert
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Hao-Yi Li
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Maximilian J Götz
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Sophie Dürauer
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Denitsa Yaneva
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Shubo Zhao
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Jacqueline Cordes
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Aleida C Acampora
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Ignasi Forne
- Protein Analysis Unit (ZfP), BioMedical Center (BMC), Ludwig-Maximilians-University, 82152, Martinsried, Germany
| | - Axel Imhof
- Protein Analysis Unit (ZfP), BioMedical Center (BMC), Ludwig-Maximilians-University, 82152, Martinsried, Germany
| | - Julian Stingele
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany.
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany.
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33
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Kilgas S, Ramadan K. Inhibitors of the ATPase p97/VCP: From basic research to clinical applications. Cell Chem Biol 2023; 30:3-21. [PMID: 36640759 DOI: 10.1016/j.chembiol.2022.12.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/13/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023]
Abstract
Protein homeostasis deficiencies underlie various cancers and neurodegenerative diseases. The ubiquitin-proteasome system (UPS) and autophagy are responsible for most of the protein degradation in mammalian cells and, therefore, represent attractive targets for cancer therapy and that of neurodegenerative diseases. The ATPase p97, also known as VCP, is a central component of the UPS that extracts and disassembles its substrates from various cellular locations and also regulates different steps in autophagy. Several UPS- and autophagy-targeting drugs are in clinical trials. In this review, we focus on the development of various p97 inhibitors, including the ATPase inhibitors CB-5083 and CB-5339, which reached clinical trials by demonstrating effective anti-tumor activity across various tumor models, providing an effective alternative to targeting protein degradation for cancer therapy. Here, we provide an overview of how different p97 inhibitors have evolved over time both as basic research tools and effective UPS-targeting cancer therapies in the clinic.
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Affiliation(s)
- Susan Kilgas
- Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK.
| | - Kristijan Ramadan
- Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK.
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34
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Yaneva D, Sparks JL, Donsbach M, Zhao S, Weickert P, Bezalel-Buch R, Stingele J, Walter JC. The FANCJ helicase unfolds DNA-protein crosslinks to promote their repair. Mol Cell 2023; 83:43-56.e10. [PMID: 36608669 PMCID: PMC9881729 DOI: 10.1016/j.molcel.2022.12.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 08/12/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023]
Abstract
Endogenous and exogenous agents generate DNA-protein crosslinks (DPCs), whose replication-dependent degradation by the SPRTN protease suppresses aging and liver cancer. SPRTN is activated after the replicative CMG helicase bypasses a DPC and polymerase extends the nascent strand to the adduct. Here, we identify a role for the 5'-to-3' helicase FANCJ in DPC repair. In addition to supporting CMG bypass, FANCJ is essential for SPRTN activation. FANCJ binds ssDNA downstream of the DPC and uses its ATPase activity to unfold the protein adduct, which exposes the underlying DNA and enables cleavage of the adduct. FANCJ-dependent DPC unfolding is also essential for translesion DNA synthesis past DPCs that cannot be degraded. In summary, our results show that helicase-mediated protein unfolding enables multiple events in DPC repair.
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Affiliation(s)
- Denitsa Yaneva
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany; Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Justin L Sparks
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Maximilian Donsbach
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany; Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Shubo Zhao
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany; Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Pedro Weickert
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany; Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Rachel Bezalel-Buch
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Julian Stingele
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany; Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany.
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute.
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35
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Mailand N. A DNA helicase remodeling proteins: How DNA-protein crosslink repair unfolds via FANCJ. Mol Cell 2023; 83:3-5. [PMID: 36608668 DOI: 10.1016/j.molcel.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/09/2022] [Accepted: 12/09/2022] [Indexed: 01/07/2023]
Abstract
In this issue of Molecular Cell, Yaneva et al.1 demonstrate that the DNA helicase FANCJ promotes DNA replication-coupled DNA-protein crosslink (DPC) repair via an unexpected ability to unfold the protein adduct, thereby enabling its proteolysis by the DPC protease SPRTN.
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Affiliation(s)
- Niels Mailand
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark; Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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36
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Ahn J, Jeong H, Seo BG, Park KS, Hwangbo C, Kim HG, Koh JS, Kim J. Genome-wide association study for vascular aging highlights pathways shared with cardiovascular traits in Koreans. Front Cardiovasc Med 2022; 9:1058308. [PMID: 36620623 PMCID: PMC9813851 DOI: 10.3389/fcvm.2022.1058308] [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: 09/30/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Vascular aging plays a pivotal role in the morbidity and mortality of older people. Reactive hyperemia index (RHI) detected by pulse amplitude tonometry (PAT) is a non-invasive measure of vascular endothelial function and aging-induced pathogenesis of both microvascular and macrovascular diseases. We conducted a genome-wide association study (GWAS) to comprehensively identify germline genetic variants associated with vascular aging in a Korean population, which revealed 60 suggestive genes underlying angiogenesis, inflammatory response in blood vessels, and cardiovascular diseases. Subsequently, we show that putative protective alleles were significantly enriched in an independent population with decelerated vascular aging phenotypes. Finally, we show the differential mRNA expression levels of putative causal genes in aging human primary endothelial cells via quantitative real-time polymerase chain reaction (PCR). These results highlight the potential contribution of genetic variants in the etiology of vascular aging and may suggest the link between vascular aging and cardiovascular traits.
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Affiliation(s)
- JaeKyoung Ahn
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea,Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Hankyeol Jeong
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea,Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Bo-Gyeong Seo
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea,Division of Life Science, College of National Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Ki-Soo Park
- Department of Preventive Medicine, College of Medicine and Institute of Health Science, Gyeongsang National University, Jinju, Republic of Korea,Center for Farmer’s Safety and Health, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Cheol Hwangbo
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea,Division of Life Science, College of National Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Han-Gyul Kim
- Department of Internal Medicine, Gyeongsang National University School of Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Jin-Sin Koh
- Department of Internal Medicine, Gyeongsang National University School of Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea,*Correspondence: Jin-Sin Koh,
| | - Jaemin Kim
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea,Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea,Jaemin Kim,
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37
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Wang TM, He YQ, Xue WQ, Zhang JB, Xia YF, Deng CM, Zhang WL, Xiao RW, Liao Y, Yang DW, Zhou T, Li DH, Luo LT, Tong XT, Wu YX, Chen XY, Li XZ, Zhang PF, Zheng XH, Zhang SD, Hu YZ, Wang F, Wu ZY, Zheng MQ, Huang JW, Jia YJ, Yuan LL, You R, Zhou GQ, Lu LX, Liu YY, Chen MY, Feng L, Dai W, Ren ZF, Mai HQ, Sun Y, Ma J, Zheng W, Lung ML, Jia WH. Whole-Exome Sequencing Study of Familial Nasopharyngeal Carcinoma and Its Implication for Identifying High-Risk Individuals. J Natl Cancer Inst 2022; 114:1689-1697. [PMID: 36066420 DOI: 10.1093/jnci/djac177] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/28/2022] [Accepted: 08/31/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is closely associated with genetic factors and Epstein-Barr virus infection, showing strong familial aggregation. Individuals with a family history suffer elevated NPC risk, requiring effective genetic counseling for risk stratification and individualized prevention. METHODS We performed whole-exome sequencing on 502 familial NPC patients and 404 unaffected relatives and controls. We systematically evaluated the established cancer predisposition genes and investigated novel NPC susceptibility genes, making comparisons with 21 other familial cancers in the UK biobank (N = 5218). RESULTS Rare pathogenic mutations in the established cancer predisposition genes were observed in familial NPC patients, including ERCC2 (1.39%), TP63 (1.00%), MUTYH (0.80%), and BRCA1 (0.80%). Additionally, 6 novel susceptibility genes were identified. RAD54L, involved in the DNA repair pathway together with ERCC2, MUTYH, and BRCA1, showed the highest frequency (4.18%) in familial NPC. Enrichment analysis found mutations in TP63 were enriched in familial NPC, and RAD54L and EML2 were enriched in both NPC and other Epstein-Barr virus-associated cancers. Besides rare variants, common variants reported in the studies of sporadic NPC were also associated with familial NPC risk. Individuals in the top quantile of common variant-derived genetic risk score while carrying rare variants exhibited increased NPC risk (odds ratio = 13.47, 95% confidence interval = 6.33 to 28.68, P = 1.48 × 10-11); men in this risk group showed a cumulative lifetime risk of 24.19%, much higher than those in the bottom common variant-derived genetic risk score quantile and without rare variants (2.04%). CONCLUSIONS This study expands the catalog of NPC susceptibility genes and provides the potential for risk stratification of individuals with an NPC family history.
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Affiliation(s)
- Tong-Min Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Jiang-Bo Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yun-Fei Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Chang-Mi Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Wen-Li Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Ruo-Wen Xiao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Ying Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Da-Wei Yang
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Dan-Hua Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Lu-Ting Luo
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Xia-Ting Tong
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Yan-Xia Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Xue-Yin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Pei-Fen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Shao-Dan Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Ye-Zhu Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Fang Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Zi-Yi Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Mei-Qi Zheng
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jing-Wen Huang
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Yi-Jing Jia
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Lei-Lei Yuan
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Rui You
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Guan-Qun Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Li-Xia Lu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yu-Ying Liu
- Department of Cancer Prevention, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Ming-Yuan Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Lin Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Wei Dai
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Ze-Fang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Hai-Qiang Mai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Ying Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Jun Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Maria Li Lung
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
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38
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Araújo-Vilar D, Fernández-Pombo A, Cobelo-Gómez S, Castro AI, Sánchez-Iglesias S. Lipodystrophy-associated progeroid syndromes. Hormones (Athens) 2022; 21:555-571. [PMID: 35835948 DOI: 10.1007/s42000-022-00386-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/29/2022] [Indexed: 01/07/2023]
Abstract
With the exception of HIV-associated lipodystrophy, lipodystrophy syndromes are rare conditions characterized by a lack of adipose tissue, which is not generally recovered. As a consequence, an ectopic deposition of lipids frequently occurs, which usually leads to insulin resistance, atherogenic dyslipidemia, and hepatic steatosis. These disorders include certain accelerated aging syndromes or progeroid syndromes. Even though each of them has unique clinical features, most show common clinical characteristics that affect growth, skin and appendages, adipose tissue, muscle, and bone and, in some of them, life expectancy is reduced. Although the molecular bases of these Mendelian disorders are very diverse and not well known, genomic instability is frequent as a consequence of impairment of nuclear organization, chromatin structure, and DNA repair, as well as epigenetic dysregulation and mitochondrial dysfunction. In this review, the main clinical features of the lipodystrophy-associated progeroid syndromes will be described along with their causes and pathogenic mechanisms, and an attempt will be made to identify which of López-Otín's hallmarks of aging are present.
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Affiliation(s)
- David Araújo-Vilar
- UETeM-Molecular Pathology Group, Department of Psychiatry, Radiology, Public Health, Nursing and Medicine (Medicine Area), Center for Research in Molecular Medicine and Chronic Diseases (CIMUS)-IDIS, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain.
- Division of Endocrinology and Nutrition, University Clinical Hospital of Santiago de Compostela, 15706, Santiago de Compostela, Spain.
| | - Antía Fernández-Pombo
- UETeM-Molecular Pathology Group, Department of Psychiatry, Radiology, Public Health, Nursing and Medicine (Medicine Area), Center for Research in Molecular Medicine and Chronic Diseases (CIMUS)-IDIS, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
- Division of Endocrinology and Nutrition, University Clinical Hospital of Santiago de Compostela, 15706, Santiago de Compostela, Spain
| | - Silvia Cobelo-Gómez
- UETeM-Molecular Pathology Group, Department of Psychiatry, Radiology, Public Health, Nursing and Medicine (Medicine Area), Center for Research in Molecular Medicine and Chronic Diseases (CIMUS)-IDIS, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Ana I Castro
- Division of Endocrinology and Nutrition, University Clinical Hospital of Santiago de Compostela, 15706, Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y la Nutrición (CIBERobn), 28029, Madrid, Spain
| | - Sofía Sánchez-Iglesias
- UETeM-Molecular Pathology Group, Department of Psychiatry, Radiology, Public Health, Nursing and Medicine (Medicine Area), Center for Research in Molecular Medicine and Chronic Diseases (CIMUS)-IDIS, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
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Abstract
PURPOSE OF REVIEW Genetic or acquired lipodystrophies are characterized by selective loss of body fat along with predisposition towards metabolic complications of insulin resistance, such as diabetes mellitus, hypertriglyceridemia, hepatic steatosis, polycystic ovarian syndrome, and acanthosis nigricans. In this review, we discuss the various subtypes and when to suspect and how to diagnose lipodystrophy. RECENT FINDINGS The four major subtypes are autosomal recessive, congenital generalized lipodystrophy (CGL); acquired generalized lipodystrophy (AGL), mostly an autoimmune disorder; autosomal dominant or recessive familial partial lipodystrophy (FPLD); and acquired partial lipodystrophy (APL), an autoimmune disorder. Diagnosis of lipodystrophy is mainly based upon physical examination findings of loss of body fat and can be supported by body composition analysis by skinfold measurements, dual-energy x-ray absorptiometry, and whole-body magnetic resonance imaging. Confirmatory genetic testing is helpful in the proband and at-risk family members with suspected genetic lipodystrophies. The treatment is directed towards the specific comorbidities and metabolic complications, and there is no treatment to reverse body fat loss. Metreleptin should be considered as the first-line therapy for metabolic complications in patients with generalized lipodystrophy and for prevention of comorbidities in children. Metformin and insulin therapy are the best options for treating hyperglycemia and fibrates and/or fish oil for hypertriglyceridemia. Lipodystrophy should be suspected in lean and muscular subjects presenting with diabetes mellitus, hypertriglyceridemia, non-alcoholic fatty liver disease, polycystic ovarian syndrome, or amenorrhea. Diabetologists should be aware of lipodystrophies and consider genetic varieties as an important subtype of monogenic diabetes.
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Affiliation(s)
- Nivedita Patni
- Division of Pediatric Endocrinology, Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Abhimanyu Garg
- Division of Nutrition and Metabolic Diseases, Department of Internal Medicine and the Center for Human Nutrition, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8537, USA.
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40
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Ilenwabor BP, Schigt H, Kompatscher A, Bos C, Zuidscherwoude M, van der Eerden BCJ, Hoenderop JGJ, de Baaij JHF. FAM111A is dispensable for electrolyte homeostasis in mice. Sci Rep 2022; 12:10211. [PMID: 35715480 PMCID: PMC9205974 DOI: 10.1038/s41598-022-14054-8] [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: 03/28/2022] [Accepted: 05/31/2022] [Indexed: 11/24/2022] Open
Abstract
Autosomal dominant mutations in FAM111A are causative for Kenny-Caffey syndrome type 2. Patients with Kenny-Caffey syndrome suffer from severe growth retardation, skeletal dysplasia, hypoparathyroidism, hypocalcaemia, hyperphosphataemia and hypomagnesaemia. While recent studies have reported FAM111A to function in antiviral response and DNA replication, its role in regulating electrolyte homeostasis remains unknown. In this study, we assessed the role of FAM111A in the regulation of serum electrolyte balance using a Fam111a knockout (Fam111a-/-) C57BL/6 N mouse model. Fam111a-/- mice displayed normal weight and serum parathyroid hormone (PTH) concentration and exhibited unaltered magnesium, calcium and phosphate levels in serum and 24-hour urine. Expression of calciotropic (including Cabp28k, Trpv5, Klotho and Cyp24a1), magnesiotropic (including Trpm6, Trpm7, Cnnm2 and Cnnm4) and phosphotropic (Slc20a1, Slc20a2, Slc34a1 and Slc34a3) genes in the kidneys, duodenum and colon were not affected by Fam111a depletion. Only Slc34a2 expression was significantly upregulated in the duodenum, but not in the colon. Analysis of femurs showed unaffected bone morphology and density in Fam111a-/- mice. Kidney and parathyroid histology were also normal in Fam111a-/- mice. In conclusion, our study is the first to characterise the function of FAM111A in vivo and we report that mice lacking FAM111A exhibit normal electrolyte homeostasis on a standard diet.
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Affiliation(s)
- Barnabas P Ilenwabor
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Heidi Schigt
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Andreas Kompatscher
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Caro Bos
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Malou Zuidscherwoude
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Bram C J van der Eerden
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joost G J Hoenderop
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Jeroen H F de Baaij
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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41
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Perry M, Ghosal G. Mechanisms and Regulation of DNA-Protein Crosslink Repair During DNA Replication by SPRTN Protease. Front Mol Biosci 2022; 9:916697. [PMID: 35782873 PMCID: PMC9240642 DOI: 10.3389/fmolb.2022.916697] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
DNA-protein crosslinks (DPCs) are deleterious DNA lesions that occur when proteins are covalently crosslinked to the DNA by the action of variety of agents like reactive oxygen species, aldehydes and metabolites, radiation, and chemotherapeutic drugs. Unrepaired DPCs are blockades to all DNA metabolic processes. Specifically, during DNA replication, replication forks stall at DPCs and are vulnerable to fork collapse, causing DNA breakage leading to genome instability and cancer. Replication-coupled DPC repair involves DPC degradation by proteases such as SPRTN or the proteasome and the subsequent removal of DNA-peptide adducts by nucleases and canonical DNA repair pathways. SPRTN is a DNA-dependent metalloprotease that cleaves DPC substrates in a sequence-independent manner and is also required for translesion DNA synthesis following DPC degradation. Biallelic mutations in SPRTN cause Ruijs-Aalfs (RJALS) syndrome, characterized by hepatocellular carcinoma and segmental progeria, indicating the critical role for SPRTN and DPC repair pathway in genome maintenance. In this review, we will discuss the mechanism of replication-coupled DPC repair, regulation of SPRTN function and its implications in human disease and cancer.
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Affiliation(s)
- Megan Perry
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States,Fred and Pamela Buffett Cancer Center, Omaha, NE, United States,*Correspondence: Gargi Ghosal,
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42
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Kröning A, van den Boom J, Kracht M, Kueck AF, Meyer H. Ubiquitin-directed AAA+ ATPase p97/VCP unfolds stable proteins crosslinked to DNA for proteolysis by SPRTN. J Biol Chem 2022; 298:101976. [PMID: 35469923 PMCID: PMC9127365 DOI: 10.1016/j.jbc.2022.101976] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 12/02/2022] Open
Abstract
The protease SPRTN degrades DNA-protein crosslinks (DPCs) that threaten genome stability. SPRTN has been connected to the ubiquitin-directed protein unfoldase p97 (also called VCP or Cdc48), but a functional cooperation has not been demonstrated directly. Here, we biochemically reconstituted p97-assisted proteolysis with purified proteins and showed that p97 targets ubiquitin-modified DPCs and unfolds them to prepare them for proteolysis by SPRTN. We demonstrate that purified SPRTN alone was unable to degrade a tightly-folded Eos fluorescent reporter protein even when Eos was crosslinked to DNA (Eos-DPC). However, when present, p97 unfolded poly-ubiquitinated Eos-DPC in a manner requiring its ubiquitin adapter, Ufd1-Npl4. Notably, we show that, in cooperation with p97 and Ufd1-Npl4, SPRTN proteolyzed unfolded Eos-DPC, which relied on recognition of the DNA-crosslink by SPRTN. In a simplified unfolding assay, we further demonstrate that p97, while unfolding a protein substrate, can surmount the obstacle of a DNA crosslink site in the substrate. Thus, our data demonstrate that p97, in conjunction with Ufd1-Npl4, assists SPRTN-mediated proteolysis of tightly-folded proteins crosslinked to DNA, even threading bulky protein-DNA adducts. These findings will be relevant for understanding how cells handle DPCs to ensure genome stability and for designing strategies that target p97 in combination cancer therapy.
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Affiliation(s)
- Alexander Kröning
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Johannes van den Boom
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Matthias Kracht
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Anja F Kueck
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Hemmo Meyer
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
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43
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Rai M, Curley M, Coleman Z, Demontis F. Contribution of proteases to the hallmarks of aging and to age-related neurodegeneration. Aging Cell 2022; 21:e13603. [PMID: 35349763 PMCID: PMC9124314 DOI: 10.1111/acel.13603] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/10/2022] [Accepted: 03/13/2022] [Indexed: 12/20/2022] Open
Abstract
Protein quality control ensures the degradation of damaged and misfolded proteins. Derangement of proteostasis is a primary cause of aging and age-associated diseases. The ubiquitin-proteasome and autophagy-lysosome play key roles in proteostasis but, in addition to these systems, the human genome encodes for ~600 proteases, also known as peptidases. Here, we examine the role of proteases in aging and age-related neurodegeneration. Proteases are present across cell compartments, including the extracellular space, and their substrates encompass cellular constituents, proteins with signaling functions, and misfolded proteins. Proteolytic processing by proteases can lead to changes in the activity and localization of substrates or to their degradation. Proteases cooperate with the autophagy-lysosome and ubiquitin-proteasome systems but also have independent proteolytic roles that impact all hallmarks of cellular aging. Specifically, proteases regulate mitochondrial function, DNA damage repair, cellular senescence, nutrient sensing, stem cell properties and regeneration, protein quality control and stress responses, and intercellular signaling. The capacity of proteases to regulate cellular functions translates into important roles in preserving tissue homeostasis during aging. Consequently, proteases influence the onset and progression of age-related pathologies and are important determinants of health span. Specifically, we examine how certain proteases promote the progression of Alzheimer's, Huntington's, and/or Parkinson's disease whereas other proteases protect from neurodegeneration. Mechanistically, cleavage by proteases can lead to the degradation of a pathogenic protein and hence impede disease pathogenesis. Alternatively, proteases can generate substrate byproducts with increased toxicity, which promote disease progression. Altogether, these studies indicate the importance of proteases in aging and age-related neurodegeneration.
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Affiliation(s)
- Mamta Rai
- Department of Developmental NeurobiologySt. Jude Children’s Research HospitalMemphisTennesseeUSA
| | - Michelle Curley
- Department of Developmental NeurobiologySt. Jude Children’s Research HospitalMemphisTennesseeUSA
| | - Zane Coleman
- Department of Developmental NeurobiologySt. Jude Children’s Research HospitalMemphisTennesseeUSA
| | - Fabio Demontis
- Department of Developmental NeurobiologySt. Jude Children’s Research HospitalMemphisTennesseeUSA
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44
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Barbier M, Bahlo M, Pennisi A, Jacoupy M, Tankard RM, Ewenczyk C, Davies KC, Lino-Coulon P, Colace C, Rafehi H, Auger N, Ansell BRE, van der Stelt I, Howell KB, Coutelier M, Amor DJ, Mundwiller E, Guillot-Noël L, Storey E, Gardner RJM, Wallis MJ, Brusco A, Corti O, Rötig A, Leventer RJ, Brice A, Delatycki MB, Stevanin G, Lockhart PJ, Durr A. Heterozygous PNPT1 variants cause spinocerebellar ataxia type 25. Ann Neurol 2022; 92:122-137. [PMID: 35411967 DOI: 10.1002/ana.26366] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Dominant spinocerebellar ataxias (SCA) are characterized by genetic heterogeneity. Some mapped and named loci remain without a causal gene identified. Here we applied next generation sequencing (NGS) to uncover the genetic etiology of the SCA25 locus. METHODS Whole-exome and whole-genome sequencing were performed in families linked to SCA25, including the French family in which the SCA25 locus was originally mapped. Whole exome sequence data was interrogated in a cohort of 796 ataxia patients of unknown aetiology. RESULTS The SCA25 phenotype spans a slowly evolving sensory and cerebellar ataxia, in most cases attributed to ganglionopathy. A pathogenic variant causing exon skipping was identified in the gene encoding Polyribonucleotide Nucleotidyltransferase PNPase 1 (PNPT1) located in the SCA25 linkage interval. A second splice variant in PNPT1 was detected in a large Australian family with a dominant ataxia also mapping to SCA25. An additional nonsense variant was detected in an unrelated individual with ataxia. Both nonsense and splice heterozygous variants result in premature stop codons, all located in the S1-domain of PNPase. In addition, an elevated type I interferon response was observed in blood from all affected heterozygous carriers tested. PNPase notably prevents the abnormal accumulation of double-stranded mtRNAs in the mitochondria and leakage into the cytoplasm, associated with triggering a type I interferon response. INTERPRETATION This study identifies PNPT1 as a new SCA gene, responsible for SCA25, and highlights biological links between alterations of mtRNA trafficking, interferonopathies and ataxia. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mathieu Barbier
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Alessandra Pennisi
- Necker Hospital, APHP, Reference Center for Mitochondrial Diseases, Genetics Department, Institut Imagine, University of Paris, Paris, France.,Inserm UMR_S1163, Institut Imagine, Paris, France
| | - Maxime Jacoupy
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Rick M Tankard
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Claire Ewenczyk
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Kayli C Davies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Patricia Lino-Coulon
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Claire Colace
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Nicolas Auger
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - Brendan R E Ansell
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Ivo van der Stelt
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Donders Centre for Neuroscience, Faculty of Science, Radboud University, The Netherlands
| | - Katherine B Howell
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, 3052, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Marie Coutelier
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - David J Amor
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Emeline Mundwiller
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Lena Guillot-Noël
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - Elsdon Storey
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, 3004, Australia
| | | | - Mathew J Wallis
- Clinical Genetics Service, Austin Health, Melbourne, Australia; Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia.,School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Olga Corti
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Agnès Rötig
- Necker Hospital, APHP, Reference Center for Mitochondrial Diseases, Genetics Department, Institut Imagine, University of Paris, Paris, France.,Inserm UMR_S1163, Institut Imagine, Paris, France
| | - Richard J Leventer
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, 3052, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Alexis Brice
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Victorian Clinical Genetics Service, Melbourne, 3052, Australia
| | - Giovanni Stevanin
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Alexandra Durr
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
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45
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Wang M, Dingler FA, Patel KJ. Genotoxic aldehydes in the hematopoietic system. Blood 2022; 139:2119-2129. [PMID: 35148375 DOI: 10.1182/blood.2019004316] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/24/2022] [Indexed: 11/20/2022] Open
Abstract
Reactive aldehydes are potent genotoxins that threaten the integrity of hematopoietic stem cells and blood production. To protect against aldehydes, mammals have evolved a family of enzymes to detoxify aldehydes, and the Fanconi anemia DNA repair pathway to process aldehyde-induced DNA damage. Loss of either protection mechanisms in humans results in defective hematopoiesis and predisposition to leukemia. This review will focus on the impact of genotoxic aldehydes on hematopoiesis, the sources of endogenous aldehydes, and potential novel protective pathways.
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Affiliation(s)
- Meng Wang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
- Department of Haematology and
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom; and
| | - Felix A Dingler
- Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - K J Patel
- Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
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46
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USP1-trapping lesions as a source of DNA replication stress and genomic instability. Nat Commun 2022; 13:1740. [PMID: 35365626 PMCID: PMC8975806 DOI: 10.1038/s41467-022-29369-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/08/2022] [Indexed: 12/16/2022] Open
Abstract
The deubiquitinase USP1 is a critical regulator of genome integrity through the deubiquitylation of Fanconi Anemia proteins and the DNA replication processivity factor, proliferating cell nuclear antigen (PCNA). Uniquely, following UV irradiation, USP1 self-inactivates through autocleavage, which enables its own degradation and in turn, upregulates PCNA monoubiquitylation. However, the functional role for this autocleavage event during physiological conditions remains elusive. Herein, we discover that cells harboring an autocleavage-defective USP1 mutant, while still able to robustly deubiquitylate PCNA, experience more replication fork-stalling and premature fork termination events. Using super-resolution microscopy and live-cell single-molecule tracking, we show that these defects are related to the inability of this USP1 mutant to be properly recycled from sites of active DNA synthesis, resulting in replication-associated lesions. Furthermore, we find that the removal of USP1 molecules from DNA is facilitated by the DNA-dependent metalloprotease Spartan to counteract the cytotoxicity caused by “USP1-trapping”. We propose a utility of USP1 inhibitors in cancer therapy based on their ability to induce USP1-trapping lesions and consequent replication stress and genomic instability in cancer cells, similar to how non-covalent DNA-protein crosslinks cause cytotoxicity by imposing steric hindrances upon proteins involved in DNA transactions. Here the authors provide mechanistic insights into how auto-cleavage of the USP1 deubiquitinase regulates DNA replication and genome stability. Implications for the targeting of USP1 activity via protein-DNA trapping in cancer therapy are discussed.
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47
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Abstract
Covalent DNA-protein crosslinks (DPCs) are pervasive DNA lesions that interfere with essential chromatin processes such as transcription or replication. This review strives to provide an overview of the sources and principles of cellular DPC formation. DPCs are caused by endogenous reactive metabolites and various chemotherapeutic agents. However, in certain conditions DPCs also arise physiologically in cells. We discuss the cellular mechanisms resolving these threats to genomic integrity. Detection and repair of DPCs require not only the action of canonical DNA repair pathways but also the activity of specialized proteolytic enzymes-including proteases of the SPRTN/Wss1 family-to degrade the crosslinked protein. Loss of DPC repair capacity has dramatic consequences, ranging from genome instability in yeast and worms to cancer predisposition and premature aging in mice and humans. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pedro Weickert
- Department of Biochemistry, Ludwig Maximilians University, Munich, Germany; .,Gene Center, Ludwig Maximilians University, Munich, Germany
| | - Julian Stingele
- Department of Biochemistry, Ludwig Maximilians University, Munich, Germany; .,Gene Center, Ludwig Maximilians University, Munich, Germany
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48
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Campos JTADM, Oliveira MSD, Soares LP, Medeiros KAD, Campos LRDS, Lima JG. DNA repair-related genes and adipogenesis: Lessons from congenital lipodystrophies. Genet Mol Biol 2022; 45:e20220086. [DOI: 10.1590/1678-4685-gmb-2022-0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
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49
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Kreienkamp HJ, Wagner M, Weigand H, McConkie-Rossell A, McDonald M, Keren B, Mignot C, Gauthier J, Soucy JF, Michaud JL, Dumas M, Smith R, Löbel U, Hempel M, Kubisch C, Denecke J, Campeau PM, Bain JM, Lessel D. Variant-specific effects define the phenotypic spectrum of HNRNPH2-associated neurodevelopmental disorders in males. Hum Genet 2021; 141:257-272. [PMID: 34907471 PMCID: PMC8807443 DOI: 10.1007/s00439-021-02412-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/07/2021] [Indexed: 01/10/2023]
Abstract
Bain type of X-linked syndromic intellectual developmental disorder, caused by pathogenic missense variants in HRNRPH2, was initially described in six female individuals affected by moderate-to-severe neurodevelopmental delay. Although it was initially postulated that the condition would not be compatible with life in males, several affected male individuals harboring pathogenic variants in HNRNPH2 have since been documented. However, functional in-vitro analyses of identified variants have not been performed and, therefore, possible genotype–phenotype correlations remain elusive. Here, we present eight male individuals, including a pair of monozygotic twins, harboring pathogenic or likely pathogenic HNRNPH2 variants. Notably, we present the first individuals harboring nonsense or frameshift variants who, similarly to an individual harboring a de novo p.(Arg29Cys) variant within the first quasi-RNA-recognition motif (qRRM), displayed mild developmental delay, and developed mostly autistic features and/or psychiatric co-morbidities. Additionally, we present two individuals harboring a recurrent de novo p.(Arg114Trp), within the second qRRM, who had a severe neurodevelopmental delay with seizures. Functional characterization of the three most common HNRNPH2 missense variants revealed dysfunctional nucleocytoplasmic shuttling of proteins harboring the p.(Arg206Gln) and p.(Pro209Leu) variants, located within the nuclear localization signal, whereas proteins with p.(Arg114Trp) showed reduced interaction with members of the large assembly of splicing regulators (LASR). Moreover, RNA-sequencing of primary fibroblasts of the individual harboring the p.(Arg114Trp) revealed substantial alterations in the regulation of alternative splicing along with global transcriptome changes. Thus, we further expand the clinical and variant spectrum in HNRNPH2-associated disease in males and provide novel molecular insights suggesting the disorder to be a spliceopathy on the molecular level.
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Affiliation(s)
- Hans-Jürgen Kreienkamp
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Matias Wagner
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Heike Weigand
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Dr. von Hauner's Children's Hospital, University of Munich, Munich, Germany
| | | | - Marie McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, USA
| | - Boris Keren
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Cyril Mignot
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Julie Gauthier
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, QC, Canada
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, QC, Canada
| | - Jean-François Soucy
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, QC, Canada
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, QC, Canada
| | - Jacques L Michaud
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, QC, Canada
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, QC, Canada
| | - Meghan Dumas
- Division of Genetic, Department of Pediatrics, The Barbara Bush Children's Hospital, Maine Medical Center, Portland, ME, USA
| | - Rosemarie Smith
- Division of Genetic, Department of Pediatrics, The Barbara Bush Children's Hospital, Maine Medical Center, Portland, ME, USA
| | - Ulrike Löbel
- Department of Diagnostic and Interventional Neuroradiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, Hamburg, Germany
| | - Philippe M Campeau
- Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, Canada
| | - Jennifer M Bain
- Division of Child Neurology, Department of Neurology, Columbia University Irving Medical Center, New York, USA
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
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50
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Ruggiano A, Vaz B, Kilgas S, Popović M, Rodriguez-Berriguete G, Singh AN, Higgins GS, Kiltie AE, Ramadan K. The protease SPRTN and SUMOylation coordinate DNA-protein crosslink repair to prevent genome instability. Cell Rep 2021; 37:110080. [PMID: 34879279 PMCID: PMC8674535 DOI: 10.1016/j.celrep.2021.110080] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 09/22/2021] [Accepted: 11/10/2021] [Indexed: 11/24/2022] Open
Abstract
DNA-protein crosslinks (DPCs) are a specific type of DNA lesion in which proteins are covalently attached to DNA. Unrepaired DPCs lead to genomic instability, cancer, neurodegeneration, and accelerated aging. DPC proteolysis was recently identified as a specialized pathway for DPC repair. The DNA-dependent protease SPRTN and the 26S proteasome emerged as two independent proteolytic systems. DPCs are also repaired by homologous recombination (HR), a canonical DNA repair pathway. While studying the cellular response to DPC formation, we identify ubiquitylation and SUMOylation as two major signaling events in DNA replication-coupled DPC repair. DPC ubiquitylation recruits SPRTN to repair sites, promoting DPC removal. DPC SUMOylation prevents DNA double-strand break formation, HR activation, and potentially deleterious genomic rearrangements. In this way, SUMOylation channels DPC repair toward SPRTN proteolysis, which is a safer pathway choice for DPC repair and prevention of genomic instability.
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Affiliation(s)
- Annamaria Ruggiano
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Bruno Vaz
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Susan Kilgas
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Marta Popović
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK; Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Gonzalo Rodriguez-Berriguete
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Abhay N Singh
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Geoff S Higgins
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Anne E Kiltie
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Kristijan Ramadan
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK.
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