Abasic and oxidized ribonucleotides embedded in DNA are processed by human APE1 and not by RNase H2

Malfatti, Matilde Clarissa; Balachander, Sathya; Antoniali, Giulia; Koh, Kyung Duk; Saint-Pierre, Christine; Gasparutto, Didier; Chon, Hyongi; Crouch, Robert J.; Storici, Francesca; Tell, Gianluca

doi:10.1093/nar/gkx723

Cited by 49 publications

(61 citation statements)

References 91 publications

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“…Conversely, the oxidation of a ribonucleotide, i.e., 8-oxo-rG, on the template DNA strongly inhibited DNA synthesis by Pols and contributed to miscoding events. Because 8-oxo-rG also could not be repaired by either RER or BER 21,22 , we hypothesized that such modification of the ribonucleotide enhances the mutagenic potential in cells. Contrary to the initial hypothesis, it seems that 8-oxo-rG did not display greater mutagenic potential than rG in WT cells (Figure 3b and c).…”

Section: Discussionmentioning

confidence: 99%

“…Thus, the modified ribonucleotides could exist in DNA via the oxidation of the embedded ribonucleotide and/or the insertion of damaged rNTPs during DNA replication. Base oxidation in embedded ribonucleotide inhibits RNase H2-mediated excision repair 21,22 .…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, the base excision repair (BER) pathway, involved in the repair of 7,8-dihydro-8-oxo-deoxyguanosine (8-oxo-dG), cannot excise the oxidized ribonucleotide 7,8-dihydro-8-oxo-riboguanosine (8-oxo-rG) in the DNA 21,22 . Therefore, a modified ribonucleotide would exhibit greater mutagenic potential compared with unmodified ribonucleotide in cells.…”

Section: Introductionmentioning

confidence: 99%

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Processing of a single ribonucleotide embedded into DNA by human nucleotide excision repair and DNA polymerase η

Sassa¹,

Tada²,

Takeishi³

et al. 2019

Preprint

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DNA polymerases often incorporate non-canonical nucleotide, i.e., ribonucleoside triphosphates into the genomic DNA. Aberrant accumulation of ribonucleotides in the genome causes various cellular abnormalities. Here, we show the possible role of human nucleotide excision repair (NER) and DNA polymerase η (Pol η ) in processing of a single ribonucleotide embedded into DNA. We found that the reconstituted NER system can excise the oxidized ribonucleotide on the plasmid DNA. Taken together with the evidence that Pol η accurately bypasses a ribonucleotide, i.e., riboguanosine (rG) or its oxidized derivative (8-oxo-rG) in vitro, we further assessed the mutagenic potential of the embedded ribonucleotide in human cells lacking NER or Pol η . A single rG on the supF reporter gene predominantly induced large deletion mutations.An embedded 8-oxo-rG caused base substitution mutations at the 3'-neighboring base rather than large deletions in wild-type cells. The disruption of XPA, an essential factor for NER, orPol η leads to the increased mutant frequency of 8-oxo-rG. Furthermore, the frequency of 8-oxo-rG-mediated large deletions was increased by the loss of Pol η , but not XPA. Collectively, our results suggest that base oxidation of the embedded ribonucleotide enables processing of the ribonucleotide via alternative DNA repair and damage tolerance pathways.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Processing of a single ribonucleotide embedded into DNA by human nucleotide excision repair and DNA polymerase η

Sassa¹,

Tada²,

Takeishi³

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…In fact, APE1 also plays an important role as redox effector on many transcriptional factors, such as NF-κB, HIF-1α, STAT-3, PAX8, AP-1 and p53 [23][24][25][26][27], regulating important genes involved in tumor progression. Moreover, new interesting molecular functions involved in RNA metabolism were recently discovered in our laboratory [23], including processing of damaged RNA [28], miRNAs [29] and abasic and oxidized ribonucleotides embedded in DNA [30]. The different functions of APE1 are finely modulated by expression, localization, posttranslational modifications (PTMs) [31][32][33][34][35][36] and by its protein-protein interactome, as well.…”

Section: Introductionmentioning

confidence: 99%

APE1 and NPM1 protect cancer cells from platinum compounds cytotoxicity and their expression pattern has a prognostic value in TNBC

Malfatti

Gerratana

Dalla

et al. 2019

J Exp Clin Cancer Res

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Background Triple negative breast cancer (TNBC) is a breast cancer subgroup characterized by a lack of hormone receptors’ expression and no HER2 overexpression. These molecular features both drastically reduce treatment options and confer poor prognosis. Platinum (Pt)-salts are being investigated as a new therapeutic strategy. The base excision repair (BER) pathway is important for resistance to Pt-based therapies. Overexpression of APE1, a pivotal enzyme of the BER pathway, as well as the expression of NPM1, a functional regulator of APE1, are associated with poor outcome and resistance to Pt-based therapies. Methods We evaluated the role of NPM1, APE1 and altered NPM1/APE1 interaction in the response to Pt-salts treatment in different cell lines: APE1 knockout (KO) cells, NPM1 KO cells, cell line models having an altered APE1/NPM1 interaction and HCC70 and HCC1937 TNBC cell lines, having different levels of APE1/NPM1. We evaluated the TNBC cells response to new chemotherapeutic small molecules targeting the endonuclease activity of APE1 or the APE1/NPM1 interaction, in combination with Pt-salts treatments. Expression levels’ correlation between APE1 and NPM1 and their impact on prognosis was analyzed in a cohort of TNBC patients through immunohistochemistry. Bioinformatics analysis, using TCGA datasets, was performed to predict a molecular signature of cancers based on APE1 and NPM1 expression. Results APE1 and NPM1, and their interaction as well, protect from the cytotoxicity induced by Pt-salts treatment. HCC1937 cells, having higher levels of APE1/NPM1 proteins, are more resistant to Pt-salts treatment compared to the HCC70 cells. A sensitization effect by APE1 inhibitors to Pt-compounds was observed. The association of NPM1/APE1 with cancer gene signatures highlighted alterations concerning cell-cycle dependent proteins. Conclusions APE1 and NPM1 protect cancer cells from Pt-compounds cytotoxicity, suggesting a possible improvement of the activity of Pt-based therapy for TNBC, using the NPM1 and APE1 proteins as secondary therapeutic targets. Based on positive or negative correlation with APE1 and NPM1 gene expression levels, we finally propose several TNBC gene signatures that should deserve further attention for their potential impact on TNBC precision medicine approaches. Electronic supplementary material The online version of this article (10.1186/s13046-019-1294-9) contains supplementary material, which is available to authorized users.

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“…On the other hand, it was clearly demonstrated how topoisomerase I is able to recognize and cleave single rNMPs embedded in DNA, when RNase H2 is missing (15,19). Moreover, different studies were carried out to evaluate whether base excision repair (BER) pathway could also work on rNMPs embedded in DNA (9,12,15,20). Our laboratories have recently demonstrated that although BER does not have any role in repairing rNMPs embedded in DNA, apurinic/ apyrimidinic endonuclease 1, APE1, the only AP-endonuclease of BER, acts in the removal of modified rNMPs embedded in DNA, such as ribose monophosphate abasic (both apurinic or apyrimidinic) site (rAP) and oxidized rNMP (20).…”

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confidence: 99%

Unlike the Escherichia coli counterpart, archaeal RNase HII cannot process ribose monophosphate abasic sites and oxidized ribonucleotides embedded in DNA

Malfatti

Henneke

Balachander

et al. 2019

Journal of Biological Chemistry

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Edited by Patrick Sung The presence of ribonucleoside monophosphates (rNMPs) in nuclear DNA decreases genome stability. To ensure survival despite rNMP insertions, cells have evolved a complex network of DNA repair mechanisms, in which the ribonucleotide excision repair pathway, initiated by type 2 RNase H (RNase HII/2), plays a major role. We recently demonstrated that eukaryotic RNase H2 cannot repair damage, that is, ribose monophosphate abasic (both apurinic or apyrimidinic) site (rAP) or oxidized rNMP embedded in DNA. Currently, it remains unclear why RNase H2 is unable to repair these modified nucleic acids having either only a sugar moiety or an oxidized base. Here, we compared the endoribonuclease specificity of the RNase HII enzymes from the archaeon Pyrococcus abyssi and the bacterium Escherichia coli, examining their ability to process damaged rNMPs embedded in DNA in vitro. We found that E. coli RNase HII cleaves both rAP and oxidized rNMP sites. In contrast, like the eukaryotic RNase H2, P. abyssi RNase HII did not display any rAP or oxidized rNMP incision activities, even though it recognized them. Notably, the archaeal enzyme was also inactive on a mismatched rNMP, whereas the E. coli enzyme displayed a strong preference for the mispaired rNMP over the paired rNMP in DNA. On the basis of our biochemical findings and also structural modeling analyses of RNase HII/2 proteins from organisms belonging to all three domains of life, we propose that RNases HII/2's dual roles in ribonucleotide excision repair and RNA/DNA hydrolysis result in limited acceptance of modified rNMPs embedded in DNA.

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Abasic and oxidized ribonucleotides embedded in DNA are processed by human APE1 and not by RNase H2

Cited by 49 publications

References 91 publications

Processing of a single ribonucleotide embedded into DNA by human nucleotide excision repair and DNA polymerase η

Processing of a single ribonucleotide embedded into DNA by human nucleotide excision repair and DNA polymerase η

APE1 and NPM1 protect cancer cells from platinum compounds cytotoxicity and their expression pattern has a prognostic value in TNBC

Unlike the Escherichia coli counterpart, archaeal RNase HII cannot process ribose monophosphate abasic sites and oxidized ribonucleotides embedded in DNA

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