DNA Repair最新文献

{"title":"53BP1-the ‘Pandora’s box’ of genome integrity","authors":"Susan Kilgas ,&nbsp;Michelle L. Swift ,&nbsp;Dipanjan Chowdhury","doi":"10.1016/j.dnarep.2024.103779","DOIUrl":"10.1016/j.dnarep.2024.103779","url":null,"abstract":"<div><div>53BP1 has several functions in the maintenance of genome integrity. It functions as a key mediator involved in double-strand break (DSB) repair, which functions to maintain a balance in the repair pathway choices and in preserving genomic stability. While its DSB repair functions are relatively well-characterized, its role in DNA replication and replication fork protection is less understood. In response to replication stress, 53BP1 contributes to fork protection by regulating fork reversal and restart. It helps maintain replication fork stability and speed, with 53BP1 loss leading to defective fork progression and increased sensitivity to replication stress agents. However, 53BP1's precise role in fork protection remains debated, as some studies have not observed protective effects. Therefore, it is critical to determine the role of 53BP1 in replication to better understand when it promotes replication fork protection, and the underlying mechanisms involved. Moreover, 53BP1's function in replication stress extends beyond its activity at active replication forks; it also forms specialized nuclear bodies (NBs) which protect stretches of under-replicated DNA (UR-DNA) transmitted from a previous cell cycle to daughter cells through mitosis. The mechanism of 53BP1 NBs in the coordination of replication and repair events at UR-DNA loci is not fully understood and warrants further investigation. The present review article focuses on elucidating 53BP1’s functions in replication stress (RS), its role in replication fork protection, and the significance of 53BP1 NBs in this context to provide a more comprehensive understanding of its less well-established role in DNA replication.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"144 ","pages":"Article 103779"},"PeriodicalIF":3.0,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome organization and stability in mammalian pre-implantation development","authors":"Shuangyi Xu ,&nbsp;Dieter Egli","doi":"10.1016/j.dnarep.2024.103780","DOIUrl":"10.1016/j.dnarep.2024.103780","url":null,"abstract":"<div><div>A largely stable genome is required for normal development, even as genetic change is an integral aspect of reproduction, genetic adaptation and evolution. Recent studies highlight a critical window of mammalian development with intrinsic DNA replication stress and genome instability in the first cell divisions after fertilization. Patterns of DNA replication and genome stability are established very early in mammals, alongside patterns of nuclear organization, and before the emergence of gene expression patterns, and prior to cell specification and germline formation. The study of DNA replication and genome stability in the mammalian embryo provides a unique cellular system due to the resetting of the epigenome to a totipotent state, and the <em>de novo</em> establishment of the patterns of nuclear organization, gene expression, DNA methylation, histone modifications and DNA replication. Studies on DNA replication and genome stability in the early mammalian embryo is relevant for understanding both normal and disease-causing genetic variation, and to uncover basic principles of genome regulation.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"144 ","pages":"Article 103780"},"PeriodicalIF":3.0,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142587374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Positioning loss of PARP1 activity as the central toxic event in BRCA-deficient cancer","authors":"Nathan MacGilvary,&nbsp;Sharon B. Cantor","doi":"10.1016/j.dnarep.2024.103775","DOIUrl":"10.1016/j.dnarep.2024.103775","url":null,"abstract":"<div><div>The mechanisms by which poly(ADP-ribose) polymerase 1 (PARP1) inhibitors (PARPi)s inflict replication stress and/or DNA damage are potentially numerous. PARPi toxicity could derive from loss of its catalytic activity and/or its physical trapping of PARP1 onto DNA that perturbs not only PARP1 function in DNA repair and DNA replication, but also obstructs compensating pathways. The combined disruption of PARP1 with either of the hereditary breast and ovarian cancer genes, <em>BRCA1</em> or <em>BRCA2</em> (BRCA), results in synthetic lethality. This has driven the development of PARP inhibitors as therapies for BRCA-mutant cancers. In this review, we focus on recent findings that highlight loss of PARP1 catalytic activity, rather than PARPi-induced allosteric trapping, as central to PARPi efficacy in BRCA deficient cells. However, we also review findings that PARP-trapping is an effective strategy in other genetic deficiencies. Together, we conclude that the mechanism-of-action of PARP inhibitors is not unilateral; with loss of activity or enhanced trapping differentially killing depending on the genetic context. Therefore, effectively targeting cancer cells requires an intricate understanding of their key underlying vulnerabilities.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"144 ","pages":"Article 103775"},"PeriodicalIF":3.0,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142515219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global screening of base excision repair in nucleosome core particles","authors":"Treshaun B. Sutton ,&nbsp;Danielle L. Sawyer ,&nbsp;Tasmin Naila ,&nbsp;Joann B. Sweasy ,&nbsp;Alan E. Tomkinson ,&nbsp;Sarah Delaney","doi":"10.1016/j.dnarep.2024.103777","DOIUrl":"10.1016/j.dnarep.2024.103777","url":null,"abstract":"<div><div>DNA damage is a fundamental molecular cause of genomic instability. Base excision repair (BER) is one line of defense to minimize the potential mutagenicity and/or toxicity derived from damaged nucleobase lesions. However, BER in the context of chromatin, in which eukaryotic genomic DNA is compacted through a hierarchy of DNA-histone protein interactions, is not fully understood. Here, we investigate the activity of BER enzymes at 27 unique geometric locations in a nucleosome core particle (NCP), which is the minimal unit of packaging in chromatin. The BER enzymes include uracil DNA glycosylase (UDG), AP endonuclease 1 (APE1), DNA polymerase β (Pol β), and DNA ligase IIIα complexed with X-ray repair cross complementing group 1 (LigIIIα/XRCC1). This global analysis of BER reveals that initiation of the repair event by UDG is dictated by the rotational position of the lesion. APE1 has robust activity at locations where repair is initiated whereas the repair event stalls at the Pol β nucleotide incorporation step within the central ∼45 bp of nucleosomal DNA. The final step of the repair, catalyzed by LigIIIα/XRCC1, is achieved only in the entry/exit regions of the NCP when nick sites are transiently exposed by unwrapping from the histones. Kinetic assays further elucidate that the location of the damaged lesion modulates enzymatic activity. Notably, these data indicate that some of the BER enzymes can act at a significant number of locations even in the absence of chromatin remodelers or other cellular factors. These results inform genome wide maps of DNA damage and mutations and contribute to our understanding of mutational hotspots and signatures.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"144 ","pages":"Article 103777"},"PeriodicalIF":3.0,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combined effects of carbon ion radiation and PARP inhibitor on non-small cell lung carcinoma cells: Insights into DNA repair pathways and cell death mechanisms","authors":"Payel Dey,&nbsp;Rima Das,&nbsp;Sandipan Chatterjee,&nbsp;Roni Paul,&nbsp;Utpal Ghosh","doi":"10.1016/j.dnarep.2024.103778","DOIUrl":"10.1016/j.dnarep.2024.103778","url":null,"abstract":"<div><div>The utilization of high linear energy transfer (LET) carbon ion (¹²C-ion) in radiotherapy has witnessed a notable rise in managing highly metastatic, recurrent, and chemo/radio-resistant human cancers. Non-small cell lung cancer (NSCLC) presents a formidable challenge due to its chemo-resistance and aggressive nature, resulting in poor prognosis and survival rates. In a previous study, we demonstrated that the combination of ¹²C-ion with the poly (ADP-ribose) polymerase (PARP) inhibitor (PARPi) olaparib significantly mitigated metastasis in A549 cells. Here, we delve into the underlying rationale behind the combined action of olaparib with ¹²C-ion, focusing on DNA repair pathways and cell death mechanisms in asynchronous NSCLC A549 cells following single and combined treatments. Evaluation included analysis of colony-forming ability, DNA damage assessed by γH2AX foci, expression profiling of key proteins involved in Homologous Recombination (HR) and Non-Homologous End Joining (NHEJ) repair pathways, caspase-3 activation, apoptotic body formation, and autophagic cell death. Our findings reveal that both PARPi olaparib and rucaparib sensitize A549 cells to ¹²C-ion exposure, with olaparib exhibiting superior sensitization. Moreover, ¹²C-ion exposure alone significantly downregulates both HR and NHEJ repair pathways by reducing the expression of MRE11--RAD51 and Ku70-Ku80 protein complexes at 24 h post-treatment. Notably, the combination of olaparib pre-treatment with ¹²C-ion markedly inhibits both HR and NHEJ pathways, culminating in DNA damage-induced apoptotic and autophagic cell death. Thus we are the first to demonstrate that olaparib sensitizes NSCLC cells to carbon ion by interfering with HR and NHEJ pathway. These insights underscore the promising therapeutic potential of combining PARP inhibition with carbon ion exposure for effective NSCLC management.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"144 ","pages":"Article 103778"},"PeriodicalIF":3.0,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142561484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"APE1 is a master regulator of the ATR-/ATM-mediated DNA damage response","authors":"Haichao Zhao ,&nbsp;Christine Richardson ,&nbsp;Ian Marriott ,&nbsp;In Hong Yang ,&nbsp;Shan Yan","doi":"10.1016/j.dnarep.2024.103776","DOIUrl":"10.1016/j.dnarep.2024.103776","url":null,"abstract":"<div><div>To maintain genomic integrity, cells have evolved several conserved DNA damage response (DDR) pathways in response to DNA damage and stress conditions. Apurinic/apyrimidinic endonuclease 1 (APE1) exhibits AP endonuclease, 3′-5′ exonuclease, 3′-phosphodiesterase, and 3′-exoribonuclease activities and plays critical roles in the DNA repair and redox regulation of transcription. However, it remains unclear whether and how APE1 is involved in DDR pathways. In this perspective, we first updated our knowledge of APE1's functional domains and its nuclease activities and their specific associated substrates. We then summarized the newly discovered roles and mechanisms of action of APE1 in the global and nucleolar ATR-mediated DDR pathway. While the ATM-mediated DDR is well known to be activated by DNA double-strand breaks and oxidative stress, here we provided new perspectives as to how ATM DDR signaling is activated by indirect single-strand breaks (SSBs) resulting from genotoxic stress and defined SSB structures, and discuss how ATM kinase is directly activated and regulated by its activator, APE1. Together, accumulating body of new evidence supports the notion that APE1 is a master regulator protein of the ATR- and ATM-mediated DDR pathways. These new findings of APE1 in DDR signaling provide previously uncharacterized but critical functions and regulations of APE1 in genome integrity.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"144 ","pages":"Article 103776"},"PeriodicalIF":3.0,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142515218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How to write an ending: Telomere replication as a multistep process","authors":"Max E. Douglas","doi":"10.1016/j.dnarep.2024.103774","DOIUrl":"10.1016/j.dnarep.2024.103774","url":null,"abstract":"<div><div>Telomeres are protective nucleoprotein caps found at the natural ends of eukaryotic chromosomes and are crucial for the preservation of stable chromosomal structure. In cycling cells, telomeres are maintained by a multi-step process called telomere replication, which involves the eukaryotic replisome navigating a complex repetitive template tightly bound by specific proteins, before terminating at the chromosome end prior to a 5’ resection step that generates a protective 3’ overhang. In this review, we examine mechanistic aspects of the telomere replication process and consider how individual parts of this multistep event are integrated and coordinated with one-another.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"144 ","pages":"Article 103774"},"PeriodicalIF":3.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142483948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The flap endonuclease-1 mediated maturation of Okazaki fragments is critical for the cellular tolerance to remdesivir","authors":"Md Ratul Rahman,&nbsp;Ryotaro Kawasumi,&nbsp;Kouji Hirota","doi":"10.1016/j.dnarep.2024.103773","DOIUrl":"10.1016/j.dnarep.2024.103773","url":null,"abstract":"<div><div>Remdesivir is a 1’-cyano-modified adenine nucleotide analog used for the treatment of COVID-19. Recently, the anti-carcinogenic effect of remdesivir has been also identified in human cancers. However, the impact of this drug and the mechanisms underlying the cellular tolerance to remdesivir have not been elucidated. Here, we explored DNA repair pathways responsible for the cellular tolerance to remdesivir by monitoring the sensitivity of 24 mutant DT40 cells deficient in various DNA repair pathways. We found that cells deficient in FEN1 displayed the highest sensitivity against remdesivir. Since FEN1 contributes to base excision repair (BER), we measured the cellular sensitivity to remdesivir in mutants deficient in BER and found that other BER mutants such as <em>XRCC1</em>^{<em>−/−</em>} and <em>PARP1</em>^{<em>−/−</em>} cells are tolerant to remdesivir, indicating that FEN1 contributes to cellular tolerance to remdesivir through roles other than BER. We observed augmented DNA damage and acute cell cycle arrest at early S-phase after remdesivir treatment in <em>FEN1</em>^{<em>−/−</em>} cells. Moreover, the replication fork progression was significantly slowed by remdesivir in <em>FEN1</em>^{<em>−/−</em>} cells, indicating a direct involvement of FEN1 in replication fork progression when replication is challenged by remdesivir. Since FEN1 contributes to Okazaki fragment maturation (OFM), a process ligating Okazaki fragments generated during lagging strand synthesis, we analyzed the kinetics of the repair of single-strand breaks (SSBs) in nascent DNA. Strikingly, <em>FEN1</em>^{<em>−/−</em>} cells exhibited slowed kinetics in OFM, and remdesivir incorporation critically impaired this process in <em>FEN1</em>^{<em>−/−</em>} cells. These results indicate that remdesivir is preferentially incorporated in Okazaki fragments leading to the failure of Okazaki fragment maturation and FEN1 plays a critical role in suppressing remdesivir-mediated DNA damage through Okazaki fragment processing. Collectively, we revealed a previously unappreciated role of FEN1 in the cellular tolerance to remdesivir.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"144 ","pages":"Article 103773"},"PeriodicalIF":3.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142434414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"UVSSA facilitates transcription-coupled repair of DNA interstrand crosslinks","authors":"Rowyn C. Liebau ,&nbsp;Crystal Waters ,&nbsp;Arooba Ahmed ,&nbsp;Rajesh K. Soni ,&nbsp;Jean Gautier","doi":"10.1016/j.dnarep.2024.103771","DOIUrl":"10.1016/j.dnarep.2024.103771","url":null,"abstract":"<div><div>DNA interstrand crosslinks (ICLs) are covalent bonds between bases on opposing strands of the DNA helix which prevent DNA melting and subsequent DNA replication or RNA transcription. Here, we show that Ultraviolet Stimulated Scaffold Protein A (UVSSA) is critical for ICL repair in human cells, at least in part via the transcription coupled ICL repair (TC-ICR) pathway. Inactivation of UVSSA sensitizes human cells to ICL-inducing drugs, and delays ICL repair. UVSSA is required for replication-independent repair of a single ICL in a fluorescence-based reporter assay. UVSSA localizes to chromatin following ICL damage, and interacts with transcribing Pol II, CSA, CSB, and TFIIH. Specifically, UVSSA interaction with TFIIH is required for ICL repair and transcription inhibition blocks localization of transcription coupled repair factors to ICL damaged chromatin. Finally, UVSSA expression positively correlates with ICL-based chemotherapy resistance in human cancer cell lines. Our data strongly suggest that UVSSA is a novel ICL repair factor functioning in TC-ICR. These results provide further evidence that TC-ICR is a <em>bona fide</em> ICL repair mechanism that contributes to crosslinker drug resistance independently of replication-coupled ICL repair.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"143 ","pages":"Article 103771"},"PeriodicalIF":3.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Remdesivir triphosphate is a valid substrate to initiate synthesis of DNA primers by human PrimPol","authors":"Marcos Jiménez-Juliana,&nbsp;María I. Martínez-Jiménez,&nbsp;Luis Blanco","doi":"10.1016/j.dnarep.2024.103772","DOIUrl":"10.1016/j.dnarep.2024.103772","url":null,"abstract":"<div><div>Remdesivir is a broad-spectrum antiviral drug which has been approved to treat COVID-19. Remdesivir is in fact a prodrug, which is metabolized <em>in vivo</em> into the active form remdesivir triphosphate (<em>RTP</em>), an analogue of adenosine triphosphate (<em>ATP</em>) with a cyano group substitution in the carbon 1’ of the ribose (1’-CN). <em>RTP</em> is a substrate for RNA synthesis and can be easily incorporated by viral RNA-dependent RNA polymerases (RdRp). Importantly, once remdesivir is incorporated (now monophosphate), it will act as a delayed chain terminator, thus blocking viral RNA synthesis. It has been reported that mitochondrial Polγ is also blocked <em>in vitro</em> by <em>RTP</em>, but the low impact <em>in vivo</em> on mitochondrial DNA replication stalling is likely due to repriming by the human DNA-directed DNA Primase/Polymerase (<em>Hs</em>PrimPol), which also operates in mitochondria. In this work, we have tested if <em>RTP</em> is a valid substrate for both DNA primase and DNA polymerase activities of <em>Hs</em>PrimPol, and its impact in the production of mature DNA primers. <em>RTP</em> resulted to be an invalid substrate for elongation, but it can be used to initiate primers at the 5´site, competing with <em>ATP</em>. Nevertheless, <em>RTP</em>-initiated primers are abortive, ocassionally reaching a maximal length of 4–5 nucleotides, and do not support elongation mediated by primer/template distortions. However, considering that the concentration of <em>ATP</em>, the natural substrate, is much higher than the intracellular concentration of <em>RTP</em>, it is unlikely that <em>Hs</em>PrimPol would use <em>RTP</em> for primer synthesis during a remdesivir treatment in real patients.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"143 ","pages":"Article 103772"},"PeriodicalIF":3.0,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}