DNA Repair最新文献_第2页

Weaponizing CRISPR/Cas9 for selective elimination of cells with an aberrant genome 武器化CRISPR/Cas9选择性消除具有异常基因组的细胞

IF 3 3区生物学

DNA Repair Pub Date : 2025-05-01 DOI: 10.1016/j.dnarep.2025.103840

Sara Tavella , Alessia di Lillo , Anastasia Conti , Fabio Iannelli , Alexandra Mancheno-Ferris , Valentina Matti , Raffaella Di Micco , Fabrizio d’Adda di Fagagna

{"title":"Weaponizing CRISPR/Cas9 for selective elimination of cells with an aberrant genome","authors":"Sara Tavella , Alessia di Lillo , Anastasia Conti , Fabio Iannelli , Alexandra Mancheno-Ferris , Valentina Matti , Raffaella Di Micco , Fabrizio d’Adda di Fagagna","doi":"10.1016/j.dnarep.2025.103840","DOIUrl":"10.1016/j.dnarep.2025.103840","url":null,"abstract":"<div><div>The CRISPR/Cas9 technology is a powerful and versatile tool to disrupt genes’ functions by introducing sequence-specific DNA double-strand breaks (DSBs). Here, we repurpose this technology to eradicate aberrant cells by specifically targeting silent and non-functional genomic sequences present only in target cells to be eliminated. Indeed, an intrinsic challenge of most current therapies against cancer and viral infections is the non-specific toxicity that they can induce in normal tissues because of their impact on important cellular mechanisms shared, to different extents, between unhealthy and healthy cells. The CRISPR/Cas9 technology has potential to overcome this limitation; however, so far effectiveness of these approaches was made dependent on the targeting and inactivation of a functional gene product. Here, we generate proof-of-principle evidence by engineering HeLa and RKO cells with a promoterless Green Fluorescent Protein (GFP) construct. The integration of this construct simulates either a genomic alteration, as in cancer cells, or a silent proviral genome. Cas9-mediated DSBs in the GFP sequence activate the DNA damage response (DDR), reduce cell viability and increase mortality. This is associated with increased cell size, multinucleation, cGAS-positive micronuclei accumulation and the activation of an inflammatory response. Pharmacological inhibition of the DNA repair factor DNA-PK enhances cell death. These results demonstrate the therapeutic potential of the CRISPR/Cas9 system in eliminating cells with an aberrant genome, regardless of the expression or the function of the target DNA sequence.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"149 ","pages":"Article 103840"},"PeriodicalIF":3.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902250","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}

引用次数: 0

Targeting DNA damage sensors for cancer therapy 靶向DNA损伤传感器用于癌症治疗

IF 3 3区生物学

DNA Repair Pub Date : 2025-05-01 DOI: 10.1016/j.dnarep.2025.103841

Matthew R. Jordan , Pamela L. Mendoza-Munoz , Katherine S. Pawelczak , John J. Turchi

引用次数: 0

Reversible association of ubiquitin with PCNA is important for template switching in S. cerevisiae 泛素与PCNA的可逆结合对于酿酒葡萄球菌的模板转换是重要的

IF 3 3区生物学

DNA Repair Pub Date : 2025-05-01 DOI: 10.1016/j.dnarep.2025.103842

Cindy Meister, Ronald P. Wong, Zhi-Hoon Park, Helle D. Ulrich

{"title":"Reversible association of ubiquitin with PCNA is important for template switching in S. cerevisiae","authors":"Cindy Meister, Ronald P. Wong, Zhi-Hoon Park, Helle D. Ulrich","doi":"10.1016/j.dnarep.2025.103842","DOIUrl":"10.1016/j.dnarep.2025.103842","url":null,"abstract":"<div><div>Polyubiquitylation of the replication factor PCNA activates the replicative bypass of DNA lesions via an error-free pathway involving template switching. However, the mechanism by which the K63-linked polyubiquitin chains facilitate damage bypass is poorly understood. Intriguingly, stable fusions of linear ubiquitin oligomers to PCNA, designed as mimics of the native K63-linked chains, are not functional, while enzymatic modification of PCNA with linear chains supports template switching in budding yeast. To investigate the cause of this discrepancy, we have taken an alternative approach to identify the features of polyubiquitylated PCNA essential for activating damage bypass. We designed linear, non-cleavable ubiquitin constructs that can be recruited non-covalently to PCNA via a PIP motif. We found that these partially suppress the damage sensitivity and elevated spontaneous mutation rates of yeast strains defective in PCNA ubiquitylation. Genetic analysis confirms that this rescue is due to an activation of the template switching pathway. Surprisingly, even the recruitment of monoubiquitin units promotes activity in this setting. These observations suggest that the reversibility of ubiquitin’s association with PCNA is more important than the actual linkage of the polyubiquitin chain. Thus, our study highlights the dynamic nature of ubiquitin signaling in the context of DNA damage bypass.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"149 ","pages":"Article 103842"},"PeriodicalIF":3.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902249","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}

引用次数: 0

Obituary: Francis Fabre (1940–2024) 讣告：弗朗西斯·法布尔（1940-2024）

IF 3 3区生物学

DNA Repair Pub Date : 2025-05-01 DOI: 10.1016/j.dnarep.2025.103838

Eric Coïc

引用次数: 0

Role of HSP40 proteins in genome maintenance, insulin signaling and cancer therapy HSP40 蛋白在基因组维护、胰岛素信号传导和癌症治疗中的作用

IF 3 3区生物学

DNA Repair Pub Date : 2025-04-17 DOI: 10.1016/j.dnarep.2025.103839

Yaping Huang , Guo-Min Li

引用次数: 0

Stained DNA Dot Detection (SD3): An automated tool for quantifying fluorescent features along single stretched DNA molecules 染色DNA点检测（SD3）：一种自动化工具，用于定量沿单个拉伸DNA分子的荧光特征

IF 3 3区生物学

DNA Repair Pub Date : 2025-04-15 DOI: 10.1016/j.dnarep.2025.103836

Obed A. Aning , Albertas Dvirnas , My Nyblom , Jens Krog , Johanna Carlson , Pegah Johansson , Tobias Ambjörnsson , Fredrik Westerlund

{"title":"Stained DNA Dot Detection (SD3): An automated tool for quantifying fluorescent features along single stretched DNA molecules","authors":"Obed A. Aning , Albertas Dvirnas , My Nyblom , Jens Krog , Johanna Carlson , Pegah Johansson , Tobias Ambjörnsson , Fredrik Westerlund","doi":"10.1016/j.dnarep.2025.103836","DOIUrl":"10.1016/j.dnarep.2025.103836","url":null,"abstract":"<div><div>The main information in DNA is its four-letter sequence that builds up the genetic information and that is traditionally read using sequencing methodologies. DNA can, however, also carry other important information, such as epigenetic marks and DNA damage. This information has recently been visualized along single DNA molecules using fluorescent labels. Quantifying fluorescent labels along DNA is done by counting the number of “dots” per length of each DNA molecule on DNA stretched on a glass surface. So far, a major challenge has been the lack of standardized data analysis tools. Focusing on DNA damage, we here present a Matlab-based automated software, Stained DNA Dot Detection (SD<sup>3</sup>), which uses a robust method for finding DNA molecules and estimating the number of dots along each molecule. We have validated SD<sup>3</sup> by comparing the outcome to manual analysis using DNA extracted from cells exposed to H<sub>2</sub>O<sub>2</sub> as a model system. Our results show that SD<sup>3</sup> achieves high accuracy and reduced analysis time relative to manual counting. SD<sup>3</sup> allows the user to define specific parameters regarding the DNA molecule and the location of dots to include during analysis via a user-friendly interface. We foresee that our open-source software can have broad use in the analysis of single DNA molecules and their modifications in research and in diagnostics.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"149 ","pages":"Article 103836"},"PeriodicalIF":3.0,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143882273","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}

引用次数: 0

Identification of a novel pathogenic XPC:c.2420 + 1 G>C variant in a patient with xeroderma pigmentosum 一株新型致病性XPC的鉴定。2420 + 1 色素性干皮病患者的G>C变异

IF 3 3区生物学

DNA Repair Pub Date : 2025-04-12 DOI: 10.1016/j.dnarep.2025.103837

Estu Ratnangganajati , Mukhlissul Faatih , Zulvikar Syambani Ulhaq

{"title":"Identification of a novel pathogenic XPC:c.2420 + 1 G>C variant in a patient with xeroderma pigmentosum","authors":"Estu Ratnangganajati , Mukhlissul Faatih , Zulvikar Syambani Ulhaq","doi":"10.1016/j.dnarep.2025.103837","DOIUrl":"10.1016/j.dnarep.2025.103837","url":null,"abstract":"<div><div>Xeroderma Pigmentosum group C (XP-C) is a rare, inherited autosomal recessive genetic disorder characterized by extreme sensitivity to ultraviolet (UV) radiation, caused by mutations in the <em>XPC</em> gene. Among the eight XP complementation groups, XP-C is the most prevalent worldwide. Here, we present an 8-year-old girl with multiple discrete hyperpigmented and depigmented macules on her face, neck, upper chest, and arms. Her skin abnormalities first appeared around the age of one as dark patches on the face and neck, progressively worsening with sun exposure. The patient was also diagnosed with bilateral blepharoconjunctivitis and severe dry eye syndrome. Histopathological examination revealed hyperkeratinization of stratified squamous epithelium. Moreover, the proband also exhibited increased expression of PCNA, p53, and cleaved-caspase 3. Genetic analysis identified a novel homozygous pathogenic variant in the <em>XPC</em> gene at c.2420 + 1 G>C. We also demonstrated that the mutant can localize to the site of DNA damage, but it is defective in CPD repair. Among all reported intronic <em>XPC</em> variants, the <em>XPC</em>:c.2420 + 1 G>C mutation seems to have a significant impact as it results in a one-base-pair deletion at the splice donor site of exon 13. This leads to a frameshift, triggering nonsense-mediated decay and causing a premature stop codon in exon 14 of the <em>XPC</em> gene. Thus, the patient is advised to undergo regular examinations to monitor the progression of the disease and the development of precancerous lesions.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"149 ","pages":"Article 103837"},"PeriodicalIF":3.0,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143847653","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}

引用次数: 0

Corrigendum to “Role of NEIL1 in genome maintenance” [DNA Repair 148 (2025) 103820] “NEIL1在基因组维持中的作用”[DNA修复148(2025)103820]的更正

IF 3 3区生物学

DNA Repair Pub Date : 2025-04-09 DOI: 10.1016/j.dnarep.2025.103835

Amanda K. McCullough , Irina G. Minko , Michael M. Luzadder , Jamie T. Zuckerman , Vladimir L. Vartanian , Pawel Jaruga , Miral Dizdaroglu , R. Stephen Lloyd

引用次数: 0

Building an integrated view of R-loops, transcription, and chromatin 构建r环、转录和染色质的综合视图

IF 3 3区生物学

DNA Repair Pub Date : 2025-04-08 DOI: 10.1016/j.dnarep.2025.103832

Yingying Meng, Lee Zou

引用次数: 0

The differential roles of rad9 alternatively spliced forms in double- strand DNA break repair during Drosophila meiosis 果蝇减数分裂过程中rad9选择性剪接形式在双链DNA断裂修复中的不同作用

IF 3 3区生物学

DNA Repair Pub Date : 2025-04-08 DOI: 10.1016/j.dnarep.2025.103833

Bareket Goldstein, Suad Sheikh-Suliman, Anna Bakhrat, Uri Abdu

{"title":"The differential roles of rad9 alternatively spliced forms in double- strand DNA break repair during Drosophila meiosis","authors":"Bareket Goldstein, Suad Sheikh-Suliman, Anna Bakhrat, Uri Abdu","doi":"10.1016/j.dnarep.2025.103833","DOIUrl":"10.1016/j.dnarep.2025.103833","url":null,"abstract":"<div><div>The 9–1–1 complex, comprising the Rad9, Hus1 and Rad1 proteins, is believed to operate as a component of a DNA damage checkpoint pathway. Our initial analysis of the <em>Drosophila hus1</em> gene showed that Hus1 plays a dual role in meiosis, regulating both meiotic DNA damage checkpoint and homologous recombination repair. In this study, we further analyzed the meiotic roles of another protein in the complex, Rad9, which has two alternatively spliced forms, Rad9A and Rad9B. Using CRISPR/Cas9, we generated flies mutant for both <em>rad9</em> isoforms. We found that, similarly to <em>hus1</em>, mutations in <em>rad9</em> lead to female sterility. Also, double-strand DNA breaks (DSBs) that form during meiosis are not processed efficiently, and the DNA within the oocyte nucleus fails to form its characteristic shape in <em>rad9</em> mutants. On the other hand, the <em>hus1</em> mutation completely disrupts checkpoint activation in DSB repair enzyme mutants, whereas the <em>rad9</em> mutation only partially impairs checkpoint activation in this context. Moreover, spatial rescue experiments revealed that Rad9B is efficient in repairing meiotic DSBs, while Rad9A is not. Furthermore, we found that female fertility in <em>rad9</em> mutants depends on early efficient meiotic DSB repair but not on karyosome formation. In summary, our results demonstrate a differential role of Rad9 alternatively spliced forms during <em>Drosophila</em> meiosis in oogenesis, and while former studies showed that Hus1 is sufficient for the effective activation of the meiotic recombination checkpoint, our results revealed that this is not true for Rad9.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"149 ","pages":"Article 103833"},"PeriodicalIF":3.0,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143838009","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}

引用次数: 0