Mismatch repair dependence of replication stress-associated DSB recognition and repair

Fujimori, Haruka; Hyodo, Mai; Matsuno, Yusuke; Shimizu, Atsuhiro; Minakawa, Yusuke; Atsumi, Yuko; Nakatsu, Yoshimichi; Tsuzuki, Teruhisa; Murakami, Yasufumi; Yoshioka, Ken

doi:10.1016/j.heliyon.2019.e03057

Cited by 10 publications

(15 citation statements)

References 32 publications

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“…The MMR pathway is known to have some interaction with MMEJ ( 32 , 33 ). We therefore tested whether the loss of proteins within MMR would alter eccDNA abundance.…”

Section: Resultsmentioning

confidence: 99%

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MicroDNA levels are dependent on MMEJ, repressed by c-NHEJ pathway, and stimulated by DNA damage

Paulsen

Malapati

Shibata

et al. 2021

Nucleic Acids Research

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Extrachromosomal circular DNA (eccDNA) are present within all eukaryotic organisms and actively contribute to gene expression changes. MicroDNA (200-1000bp) are the most abundant type of eccDNA and can amplify tRNA, microRNA, and novel si-like RNA sequences. Due to the heterogeneity of microDNA and the limited technology to directly quantify circular DNA molecules, the specific DNA repair pathways that contribute to microDNA formation have not been fully elucidated. Using a sensitive and quantitative assay that quantifies eight known abundant microDNA, we report that microDNA levels are dependent on resection after double-strand DNA break (DSB) and repair by Microhomology Mediated End Joining (MMEJ). Further, repair of DSB without resection by canonical Non-Homologous End Joining (c-NHEJ) diminishes microDNA formation. MicroDNA levels are induced locally even by a single site-directed DSB, suggesting that excision of genomic DNA by two closely spaced DSB is not necessary for microDNA formation. Consistent with all this, microDNA levels accumulate as cells undergo replication in S-phase, when DNA breaks and repair are elevated, and microDNA levels are decreased if DNA synthesis is prevented. Thus, formation of microDNA occurs during the repair of endogenous or induced DNA breaks by resection-based DNA repair pathways.

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“…The MMR pathway is known to have some interaction with MMEJ ( 32 , 33 ). We therefore tested whether the loss of proteins within MMR would alter eccDNA abundance.…”

Section: Resultsmentioning

confidence: 99%

“…We speculate that MMR may be involved in microDNA formation because the MMR genes have a role in recognizing and repairing mismatches and looping structures that occur during annealing of short homologous sequences ( 32 , 48 ).…”

Section: Discussionmentioning

confidence: 99%

MicroDNA levels are dependent on MMEJ, repressed by c-NHEJ pathway, and stimulated by DNA damage

Paulsen

Malapati

Shibata

et al. 2021

Nucleic Acids Research

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“…75 We speculate that MMR may be involved in eccDNA formation because they have an undiscovered role in recognizing and repairing mismatches and looping structures that may occur during annealing of homologous sequences. 25,43 The increase of eccDNA in hydroxyurea-blocked cells (when the cells have replication stress), and during S phase, suggests that endogenous eccDNA formation is connected to repair pathways associated with fork stalling. The decrease of eccDNA as cells pass through mitosis into G1 suggests that the eccDNA experiences some degradation in dividing cells.…”

Section: Discussionmentioning

confidence: 99%

“…The MMR pathway is known to have some interaction with MMEJ. 25,26 We therefore tested whether the loss of proteins within MMR would alter eccDNA abundance. Knock-out of MSH2 or MLH1 in U2OS cells, as well as knock-out of MSH3 in DT40 cells, led to a substantial decrease of eccDNA ( Figure 2J, 2K).…”

Section: Eccdna Formation Is Facilitated By Alt-nhej Repairmentioning

confidence: 99%

EccDNA formation is dependent on MMEJ, repressed by c-NHEJ pathway, and stimulated by DNA double-strand break

Paulsen

Malapati

Eki

et al. 2020

Preprint

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Extrachromosomal circular DNAs (eccDNA) are widespread in normal and cancer cells and are known to amplify oncogenic genes. However, the mechanisms that form eccDNA have never been fully elucidated due to the complex interactions of DNA repair pathways and lack of a method to quantify eccDNA abundance. Through the development of a sensitive and quantitative assay for eccDNA we show that the formation of eccDNA is through resection dependent repair of double-strand DNA breaks, especially micro-homology mediated end joining, and through mismatch repair. The most significant decreases in eccDNA levels occurred in cells lacking PARP1, POLQ, NBS1, RAD54, and FAN1. Further, a significant increase in eccDNA occurred in cells lacking c-NHEJ proteins DNA-PKcs, XRCC4, XLF, LIG4 and 53BP1. This suggests that when alt-NHEJ pathways are utilized to repair DNA breaks by necessity, the formation of eccDNA is increased. Induced and site-directed double-strand DNA breaks increase eccDNA formation, even from a single break. Additionally, we find that eccDNA levels accumulate as cells undergo replication in S-phase and that levels of eccDNA are decreased if DNA synthesis is prevented. Together, these results show that the bulk of eccDNA form by resection based alt-NHEJ pathways, especially during DNA replication and the repair of double-strand breaks.

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“…The choice of DNA repair pathway determines which type of genomic instability arises from replication stress-associated DNA double-strand breaks [86]. MSI induction in vitro was triggered by replication stress-associated DSBs via DNA repair dependent on both Polθ and PARP1, which is likely mediated by MMEJ in MMR-deficient background [87].…”

Section: Mmr-deficient Phenotypes In Colorectal Cancersmentioning

confidence: 99%

Analyzing the Opportunities to Target DNA Double-Strand Breaks Repair and Replicative Stress Responses to Improve Therapeutic Index of Colorectal Cancer

Tomasini

Guecheva²,

Leguisamo³

et al. 2021

Cancers

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Despite the ample improvements of CRC molecular landscape, the therapeutic options still rely on conventional chemotherapy-based regimens for early disease, and few targeted agents are recommended for clinical use in the metastatic setting. Moreover, the impact of cytotoxic, targeted agents, and immunotherapy combinations in the metastatic scenario is not fully satisfactory, especially the outcomes for patients who develop resistance to these treatments need to be improved. Here, we examine the opportunity to consider therapeutic agents targeting DNA repair and DNA replication stress response as strategies to exploit genetic or functional defects in the DNA damage response (DDR) pathways through synthetic lethal mechanisms, still not explored in CRC. These include the multiple actors involved in the repair of DNA double-strand breaks (DSBs) through homologous recombination (HR), classical non-homologous end joining (NHEJ), and microhomology-mediated end-joining (MMEJ), inhibitors of the base excision repair (BER) protein poly (ADP-ribose) polymerase (PARP), as well as inhibitors of the DNA damage kinases ataxia-telangiectasia and Rad3 related (ATR), CHK1, WEE1, and ataxia-telangiectasia mutated (ATM). We also review the biomarkers that guide the use of these agents, and current clinical trials with targeted DDR therapies.

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Mismatch repair dependence of replication stress-associated DSB recognition and repair

Cited by 10 publications

References 32 publications

MicroDNA levels are dependent on MMEJ, repressed by c-NHEJ pathway, and stimulated by DNA damage

MicroDNA levels are dependent on MMEJ, repressed by c-NHEJ pathway, and stimulated by DNA damage

EccDNA formation is dependent on MMEJ, repressed by c-NHEJ pathway, and stimulated by DNA double-strand break

Analyzing the Opportunities to Target DNA Double-Strand Breaks Repair and Replicative Stress Responses to Improve Therapeutic Index of Colorectal Cancer

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