DNA Repair最新文献

{"title":"Irc20 modulates LOH frequency and distribution in S. cerevisiae","authors":"Sameer Joshi ,&nbsp;Suman Dash ,&nbsp;Nikilesh Vijayan ,&nbsp;Koodali T. Nishant","doi":"10.1016/j.dnarep.2024.103727","DOIUrl":"10.1016/j.dnarep.2024.103727","url":null,"abstract":"<div><p>Loss of Heterozygosity (LOH) due to mitotic recombination is frequently associated with the development of various cancers (e.g. retinoblastoma). LOH is also an important source of genetic diversity, especially in organisms where meiosis is infrequent. Irc20 is a putative helicase, and E3 ubiquitin ligase involved in DNA double-strand break repair pathway. We analyzed genome-wide LOH events, gross chromosomal changes, small insertion-deletions and single nucleotide mutations in eleven <em>S. cerevisiae</em> mutation accumulation lines of <em>irc20∆</em>, which underwent 50 mitotic bottlenecks. LOH enhancement in <em>irc20∆</em> was small (1.6 fold), but statistically significant as compared to the wild type. Short (≤ 1 kb) and long (&gt; 10 kb) LOH tracts were significantly enhanced in <em>irc20∆</em>. Both interstitial and terminal LOH events were also significantly enhanced in <em>irc20∆</em> compared to the wild type. LOH events in <em>irc20∆</em> were more telomere proximal and away from centromeres compared to the wild type. Gross chromosomal changes, single nucleotide mutations and in-dels were comparable between <em>irc20∆</em> and wild type. Locus based and genome-wide analysis of meiotic recombination showed that meiotic crossover frequencies are not altered in <em>irc20∆</em>. These results suggest Irc20 primarily regulates mitotic recombination and does not affect meiotic crossovers. Our results suggest that the <em>IRC20</em> gene is important for regulating LOH frequency and distribution.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"141 ","pages":"Article 103727"},"PeriodicalIF":3.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141840555","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":"Inhibition of human DNA alkylation damage repair enzyme ALKBH2 by HIV protease inhibitor ritonavir","authors":"Unnikrishnan P. Shaji ,&nbsp;Nikhil Tuti ,&nbsp;S.K. Alim ,&nbsp;Monisha Mohan ,&nbsp;Susmita Das ,&nbsp;Gargi Meur ,&nbsp;Musti J. Swamy ,&nbsp;Roy Anindya","doi":"10.1016/j.dnarep.2024.103732","DOIUrl":"10.1016/j.dnarep.2024.103732","url":null,"abstract":"<div><p>The human DNA repair enzyme AlkB homologue-2 (ALKBH2) repairs methyl adducts from genomic DNA and is overexpressed in several cancers. However, there are no known inhibitors available for this crucial DNA repair enzyme. The aim of this study was to examine whether the first-generation HIV protease inhibitors having strong anti-cancer activity can be repurposed as inhibitors of ALKBH2. We selected four such inhibitors and performed <em>in vitro</em> binding analysis against ALKBH2 based on alterations of its intrinsic tryptophan fluorescence and differential scanning fluorimetry. The effect of these HIV protease inhibitors on the DNA repair activity of ALKBH2 was also evaluated. Interestingly, we observed that one of the inhibitors, ritonavir, could inhibit ALKBH2-mediated DNA repair significantly via competitive inhibition and sensitized cancer cells to alkylating agent methylmethane sulfonate (MMS). This work may provide new insights into the possibilities of utilizing HIV protease inhibitor ritonavir as a DNA repair antagonist.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"141 ","pages":"Article 103732"},"PeriodicalIF":3.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141841512","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 Eyes Absent family: At the intersection of DNA repair, mitosis, and replication","authors":"Christopher B. Nelson,&nbsp;Jadon K. Wells,&nbsp;Hilda A. Pickett","doi":"10.1016/j.dnarep.2024.103729","DOIUrl":"10.1016/j.dnarep.2024.103729","url":null,"abstract":"<div><p>The Eyes Absent family (EYA1–4) are a group of dual function proteins that act as both tyrosine phosphatases and transcriptional co-activators. EYA proteins play a vital role in development, but are also aberrantly overexpressed in cancers, where they often confer an oncogenic effect. Precisely how the EYAs impact cell biology is of growing interest, fuelled by the therapeutic potential of an expanding repertoire of EYA inhibitors. Recent functional studies suggest that the EYAs are important players in the regulation of genome maintenance pathways including DNA repair, mitosis, and DNA replication. While the characterized molecular mechanisms have predominantly been ascribed to EYA phosphatase activities, EYA co-transcriptional activity has also been found to impact the expression of genes that support these pathways. This indicates functional convergence of EYA phosphatase and co-transcriptional activities, highlighting the emerging importance of the EYA protein family at the intersection of genome maintenance mechanisms. In this review, we discuss recent progress in defining EYA protein substrates and transcriptional effects, specifically in the context of genome maintenance. We then outline future directions relevant to the field and discuss the clinical utility of EYA inhibitors.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"141 ","pages":"Article 103729"},"PeriodicalIF":3.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141849419","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 role of SLFN11 in DNA replication stress response and its implications for the Fanconi anemia pathway","authors":"Anfeng Mu ,&nbsp;Yusuke Okamoto ,&nbsp;Yoko Katsuki ,&nbsp;Minoru Takata","doi":"10.1016/j.dnarep.2024.103733","DOIUrl":"10.1016/j.dnarep.2024.103733","url":null,"abstract":"<div><p>Fanconi anemia (FA) is a hereditary disorder characterized by a deficiency in the repair of DNA interstrand crosslinks and the response to replication stress. Endogenous DNA damage, most likely caused by aldehydes, severely affects hematopoietic stem cells in FA, resulting in progressive bone marrow failure and the development of leukemia. Recent studies revealed that expression levels of <em>SLFN11</em> affect the replication stress response and are a strong determinant in cell killing by DNA-damaging cancer chemotherapy. Because <em>SLFN11</em> is highly expressed in the hematopoietic system, we speculated that <em>SLFN11</em> may have a significant role in FA pathophysiology. Indeed, we found that DNA damage sensitivity in FA cells is significantly mitigated by the loss of <em>SLFN11</em> expression. Mechanistically, we demonstrated that <em>SLFN11</em> destabilizes the nascent DNA strands upon replication fork stalling. In this review, we summarize our work regarding an interplay between <em>SLFN11</em> and the FA pathway, and the role of <em>SLFN11</em> in the response to replication stress.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"141 ","pages":"Article 103733"},"PeriodicalIF":3.0,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141839693","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":"Mechanisms and regulation of replication fork reversal","authors":"Madison B. Adolph,&nbsp;David Cortez","doi":"10.1016/j.dnarep.2024.103731","DOIUrl":"10.1016/j.dnarep.2024.103731","url":null,"abstract":"<div><p>DNA replication is remarkably accurate with estimates of only a handful of mutations per human genome per cell division cycle. Replication stress caused by DNA lesions, transcription-replication conflicts, and other obstacles to the replication machinery must be efficiently overcome in ways that minimize errors and maximize completion of DNA synthesis. Replication fork reversal is one mechanism that helps cells tolerate replication stress. This process involves reannealing of parental template DNA strands and generation of a nascent-nascent DNA duplex. While fork reversal may be beneficial by facilitating DNA repair or template switching, it must be confined to the appropriate contexts to preserve genome stability. Many enzymes have been implicated in this process including ATP-dependent DNA translocases like SMARCAL1, ZRANB3, HLTF, and the helicase FBH1. In addition, the RAD51 recombinase is required. Many additional factors and regulatory activities also act to ensure reversal is beneficial instead of yielding undesirable outcomes. Finally, reversed forks must also be stabilized and often need to be restarted to complete DNA synthesis. Disruption or deregulation of fork reversal causes a variety of human diseases. In this review we will describe the latest models for reversal and key mechanisms of regulation.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"141 ","pages":"Article 103731"},"PeriodicalIF":3.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1568786424001071/pdfft?md5=bb6f6902e0f7dc930ab44cf546520bf3&pid=1-s2.0-S1568786424001071-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141780444","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":"Regulation, functional impact, and therapeutic targeting of APOBEC3A in cancer","authors":"Ajinkya S. Kawale ,&nbsp;Lee Zou","doi":"10.1016/j.dnarep.2024.103734","DOIUrl":"10.1016/j.dnarep.2024.103734","url":null,"abstract":"<div><p>Enzymes of the apolipoprotein B mRNA editing catalytic polypeptide like (APOBEC) family are cytosine deaminases that convert cytosine to uracil in DNA and RNA. Among these proteins, APOBEC3 sub-family members, APOBEC3A (A3A) and APOBEC3B (A3B), are prominent sources of mutagenesis in cancer cells. The aberrant expression of A3A and A3B in cancer cells leads to accumulation of mutations with specific single-base substitution (SBS) signatures, characterized by C→T and C→G changes, in a number of tumor types. In addition to fueling mutagenesis, A3A and A3B, particularly A3A, induce DNA replication stress, DNA damage, and chromosomal instability through their catalytic activities, triggering a range of cellular responses. Thus, A3A/B have emerged as key drivers of genome evolution during cancer development, contributing to tumorigenesis, tumor heterogeneity, and therapeutic resistance. Yet, the expression of A3A/B in cancer cells presents a cancer vulnerability that can be exploited therapeutically. In this review, we discuss the recent studies that shed light on the mechanisms regulating A3A expression and the impact of A3A in cancer. We also review recent advances in the development of A3A inhibitors and provide perspectives on the future directions of A3A research.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"141 ","pages":"Article 103734"},"PeriodicalIF":3.0,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141763439","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":"Human translesion DNA polymerases ι and κ mediate tolerance to temozolomide in MGMT-deficient glioblastoma cells.","authors":"Marcela Teatin Latancia ,&nbsp;Giovana da Silva Leandro ,&nbsp;André Uchimura Bastos ,&nbsp;Natália Cestari Moreno ,&nbsp;Abu-Bakr Adetayo Ariwoola ,&nbsp;Davi Jardim Martins ,&nbsp;Nicholas William Ashton ,&nbsp;Victória Chaves Ribeiro ,&nbsp;Nicolas Carlos Hoch ,&nbsp;Clarissa Ribeiro Reily Rocha ,&nbsp;Roger Woodgate ,&nbsp;Carlos Frederico Martins Menck","doi":"10.1016/j.dnarep.2024.103715","DOIUrl":"10.1016/j.dnarep.2024.103715","url":null,"abstract":"<div><p>Glioblastoma (GBM) is a highly aggressive brain tumor associated with poor patient survival. The current standard treatment involves invasive surgery, radiotherapy, and chemotherapy employing temozolomide (TMZ). Resistance to TMZ is, however, a major challenge. Previous work from our group has identified candidate genes linked to TMZ resistance, including genes encoding translesion synthesis (TLS) DNA polymerases iota (Polɩ) and kappa (Polκ). These specialized enzymes are known for bypassing lesions and tolerating DNA damage. Here, we investigated the roles of Polɩ and Polκ in TMZ resistance, employing MGMT-deficient U251-MG glioblastoma cells, with knockout of either <em>POLI</em> or <em>POLK</em> genes encoding Polɩ and Polκ, respectively, and assess their viability and genotoxic stress responses upon subsequent TMZ treatment. Cells lacking either of these polymerases exhibited a significant decrease in viability following TMZ treatment compared to parental counterparts. The restoration of the missing polymerase led to a recovery of cell viability. Furthermore, knockout cells displayed increased cell cycle arrest, mainly in late S-phase, and lower levels of genotoxic stress after TMZ treatment, as assessed by a reduction of γH2AX foci and flow cytometry data. This implies that TMZ treatment does not trigger a significant H2AX phosphorylation response in the absence of these proteins. Interestingly, combining TMZ with Mirin (double-strand break repair pathway inhibitor) further reduced the cell viability and increased DNA damage and γH2AX positive cells in TLS KO cells, but not in parental cells. These findings underscore the crucial roles of Polɩ and Polκ in conferring TMZ resistance and the potential backup role of homologous recombination in the absence of these TLS polymerases. Targeting these TLS enzymes, along with double-strand break DNA repair inhibition, could, therefore, provide a promising strategy to enhance TMZ's effectiveness in treating GBM.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"141 ","pages":"Article 103715"},"PeriodicalIF":3.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1568786424000910/pdfft?md5=5c94860c649134a2ff80bcadd7bc1372&pid=1-s2.0-S1568786424000910-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141637256","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":"DSB-induced oxidative stress: Uncovering crosstalk between DNA damage response and cellular metabolism","authors":"Xinyu Li ,&nbsp;Caini Yang ,&nbsp;Hengyu Wu ,&nbsp;Hongran Chen ,&nbsp;Xing Gao ,&nbsp;Sa Zhou ,&nbsp;Tong-Cun Zhang ,&nbsp;Wenjian Ma","doi":"10.1016/j.dnarep.2024.103730","DOIUrl":"10.1016/j.dnarep.2024.103730","url":null,"abstract":"<div><p>While that ROS causes DNA damage is well documented, there has been limited investigation into whether DNA damages and their repair processes can conversely induce oxidative stress. By generating a site-specific DNA double strand break (DSB) via I-SceI endonuclease expression in S. cerevisiae without damaging other cellular components, this study demonstrated that DNA repair does trigger oxidative stress. Deleting genes participating in the initiation of the resection step of homologous recombination (HR), like the MRX complex, resulted in stimulation of ROS. In contrast, deleting genes acting downstream of HR resection suppressed ROS levels. Additionally, blocking non-homologous end joining (NHEJ) also suppressed ROS. Further analysis identified Rad53 as a key player that relays DNA damage signals to alter redox metabolism in an HR-specific manner. These results suggest both HR and NHEJ can drive metabolism changes and oxidative stress, with NHEJ playing a more prominent role in ROS stimulation. Further analysis revealed a correlation between DSB-induced ROS increase and enhanced activity of NADPH oxidase Yno1 and various antioxidant enzymes. Deleting the antioxidant gene SOD1 induced synthetic lethality in HR-deficient mutants like <em>mre11Δ</em> and <em>rad51Δ</em> upon DSB induction. These findings uncover a significant interplay between DNA repair mechanisms and cellular metabolism, providing insights into understanding the side effects of genotoxic therapies and potentially aiding development of more effective cancer treatment strategies.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"141 ","pages":"Article 103730"},"PeriodicalIF":3.0,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141630845","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":"Protein-protein interactions in the core nucleotide excision repair pathway","authors":"Areetha D’Souza ,&nbsp;Mihyun Kim ,&nbsp;Walter J. Chazin ,&nbsp;Orlando D. Schärer","doi":"10.1016/j.dnarep.2024.103728","DOIUrl":"10.1016/j.dnarep.2024.103728","url":null,"abstract":"<div><p>Nucleotide excision repair (NER) clears genomes of DNA adducts formed by UV light, environmental agents, and antitumor drugs. Gene mutations that lead to defects in the core NER reaction cause the skin cancer-prone disease <em>xeroderma pigmentosum</em>. In NER, DNA lesions are excised within an oligonucleotide of 25–30 residues via a complex, multi-step reaction that is regulated by protein-protein interactions. These interactions were first characterized in the 1990s using pull-down, co-IP and yeast two-hybrid assays. More recently, high-resolution structures and detailed functional studies have started to yield detailed pictures of the progression along the NER reaction coordinate. In this review, we highlight how the study of interactions among proteins by structural and/or functional studies have provided insights into the mechanisms by which the NER machinery recognizes and excises DNA lesions. Furthermore, we identify reported, but poorly characterized or unsubstantiated interactions in need of further validation.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"141 ","pages":"Article 103728"},"PeriodicalIF":3.0,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141637257","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":"DNA-PK: A synopsis beyond synapsis","authors":"Noah J. Goff ,&nbsp;Mariia Mikhova ,&nbsp;Jens C. Schmidt ,&nbsp;Katheryn Meek","doi":"10.1016/j.dnarep.2024.103716","DOIUrl":"https://doi.org/10.1016/j.dnarep.2024.103716","url":null,"abstract":"<div><p>Given its central role in life, DNA is remarkably easy to damage. Double strand breaks (DSBs) are the most toxic form of DNA damage, and DSBs pose the greatest danger to genomic integrity. In higher vertebrates, the non-homologous end joining pathway (NHEJ) is the predominate pathway that repairs DSBs. NHEJ has three steps: 1) DNA end recognition by the DNA dependent protein kinase [DNA-PK], 2) DNA end-processing by numerous NHEJ accessory factors, and 3) DNA end ligation by the DNA ligase IV complex (LX4). Although this would appear to be a relatively simple mechanism, it has become increasingly apparent that it is not.</p><p>Recently, much insight has been derived regarding the mechanism of non-homologous end joining through a proliferation of cryo-EM studies, structure-function mutational experiments informed by these new structural data, and novel single-molecule imaging approaches. An emerging consensus in the field is that NHEJ progresses from initial DSB end recognition by DNA-PK to synapsis of the two DNA ends in a long-range synaptic complex where ends are held too far apart (115 Å) for ligation, and then progress to a short-range synaptic complex where ends are positioned close enough for ligation. What was surprising from these structural studies was the observation of two distinct types of DNA-PK dimers that represent NHEJ long-range complexes. In this review, we summarize current knowledge about the function of the distinct NHEJ synaptic complexes and align this new information with emerging cellular single-molecule microscopy studies as well as with previous studies of DNA-PK’s function in repair.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"141 ","pages":"Article 103716"},"PeriodicalIF":3.0,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141593053","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}