scholarly journals Role of Base Excision Repair Pathway in the Processing of Complex DNA Damage Generated by Oxidative Stress and Anticancer Drugs

2021 ◽  
Vol 8 ◽  
Author(s):  
Yeldar Baiken ◽  
Damira Kanayeva ◽  
Sabira Taipakova ◽  
Regina Groisman ◽  
Alexander A. Ishchenko ◽  
...  
Keyword(s):  
Dna Damage ◽  
Base Excision Repair ◽  
Genome Instability ◽  
Excision Repair ◽  
Chromosomal Rearrangements ◽  
Strand Break ◽  
Dna Lesions ◽  
Complex Nature ◽  
Base Excision

Chemical alterations in DNA induced by genotoxic factors can have a complex nature such as bulky DNA adducts, interstrand DNA cross-links (ICLs), and clustered DNA lesions (including double-strand breaks, DSB). Complex DNA damage (CDD) has a complex character/structure as compared to singular lesions like randomly distributed abasic sites, deaminated, alkylated, and oxidized DNA bases. CDD is thought to be critical since they are more challenging to repair than singular lesions. Although CDD naturally constitutes a relatively minor fraction of the overall DNA damage induced by free radicals, DNA cross-linking agents, and ionizing radiation, if left unrepaired, these lesions cause a number of serious consequences, such as gross chromosomal rearrangements and genome instability. If not tightly controlled, the repair of ICLs and clustered bi-stranded oxidized bases via DNA excision repair will either inhibit initial steps of repair or produce persistent chromosomal breaks and consequently be lethal for the cells. Biochemical and genetic evidences indicate that the removal of CDD requires concurrent involvement of a number of distinct DNA repair pathways including poly(ADP-ribose) polymerase (PARP)-mediated DNA strand break repair, base excision repair (BER), nucleotide incision repair (NIR), global genome and transcription coupled nucleotide excision repair (GG-NER and TC-NER, respectively), mismatch repair (MMR), homologous recombination (HR), non-homologous end joining (NHEJ), and translesion DNA synthesis (TLS) pathways. In this review, we describe the role of DNA glycosylase-mediated BER pathway in the removal of complex DNA lesions.

scholarly journals DNA polymerase X from Deinococcus radiodurans implicated in bacterial tolerance to DNA damage is characterized as a short patch base excision repair polymerase

Microbiology ◽  
2009 ◽  
Vol 155 (9) ◽  
pp. 3005-3014 ◽  
Author(s):  
Nivedita P. Khairnar ◽  
Hari S. Misra
Keyword(s):  
Dna Damage ◽  
Dna Polymerase ◽  
Base Excision Repair ◽  
Deinococcus Radiodurans ◽  
Excision Repair ◽  
Strand Break ◽  
Klenow Fragment ◽  
E Coli ◽  
Base Excision

The Deinococcus radiodurans R1 genome encodes an X-family DNA repair polymerase homologous to eukaryotic DNA polymerase β. The recombinant deinococcal polymerase X (PolX) purified from transgenic Escherichia coli showed deoxynucleotidyltransferase activity. Unlike the Klenow fragment of E. coli, this enzyme showed short patch DNA synthesis activity on heteropolymeric DNA substrate. The recombinant enzyme showed 5′-deoxyribose phosphate (5′-dRP) lyase activity and base excision repair function in vitro, with the help of externally supplied glycosylase and AP endonuclease functions. A polX disruption mutant of D. radiodurans expressing 5′-dRP lyase and a truncated polymerase domain was comparatively less sensitive to γ-radiation than a polX deletion mutant. Both mutants showed higher sensitivity to hydrogen peroxide. Excision repair mutants of E. coli expressing this polymerase showed functional complementation of UV sensitivity. These results suggest the involvement of deinococcal polymerase X in DNA-damage tolerance of D. radiodurans, possibly by contributing to DNA double-strand break repair and base excision repair.

scholarly journals The Influence of (5′R)- and (5′S)-5′,8-Cyclo-2′-Deoxyadenosine on UDG and hAPE1 Activity. Tandem Lesions are the Base Excision Repair System’s Nightmare

Cells ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1303 ◽  
Author(s):  
Karwowski
Keyword(s):  
Dna Damage ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Repair Process ◽  
Dna Lesions ◽  
Repair System ◽  
Base Excision ◽  
Base Excision Repair System ◽  
Tandem Lesions ◽  
Ap Site

DNA lesions are formed continuously in each living cell as a result of environmental factors, ionisation radiation, metabolic processes, etc. Most lesions are removed from the genome by the base excision repair system (BER). The activation of the BER protein cascade starts with DNA damage recognition by glycosylases. Uracil-DNA glycosylase (UDG) is one of the most evolutionary preserved glycosylases which remove the frequently occurring 2′-deoxyuridine from single (ss) and double-stranded (ds) oligonucleotides. Conversely, the unique tandem lesions (5′R)- and (5′S)-5′,8-cyclo-2′-deoxyadenosine (cdA) are not suitable substrates for BER machinery and are released from the genome by the nucleotide excision repair (NER) system. However, the cyclopurines appearing in a clustered DNA damage structure can influence the BER process of other lesions like dU. In this article, UDG inhibition by 5′S- and 5′R-cdA is shown and discussed in an experimental and theoretical manner. This phenomenon was observed when a tandem lesion appears in single or double-stranded oligonucleotides next to dU, on its 3′-end side. The cdA shift to the 5′-end side of dU in ss-DNA stops this effect in both cdA diastereomers. Surprisingly, in the case of ds-DNA, 5′S-cdA completely blocks uracil excision by UDG. Conversely, 5′R-cdA allows glycosylase for uracil removal, but the subsequently formed apurinic/apyrimidinic (AP) site is not suitable for human AP-site endonuclease 1 (hAPE1) activity. In conclusion, the appearance of the discussed tandem lesion in the structure of single or double-stranded DNA can stop the entire base repair process at its beginning, which due to UDG and hAPE1 inhibition can lead to mutagenesis. On the other hand, the presented results can cast some light on the UDG or hAPE1 inhibitors being used as a potential treatment.

Role Of Base Excision Repair Associated AP Nuclease Activity In The Induction Of Homologous Recombination Repair Pathway and Survival Of MM Cells Following DNA Damage

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1248-1248
Author(s):  
Subodh Kumar ◽  
Jagannath Pal ◽  
Jialan Shi ◽  
Puru Nanjappa ◽  
Maria Gkotzamanidou ◽  
...  
Keyword(s):  
Dna Damage ◽  
Homologous Recombination ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Critical Role ◽  
Nuclease Activity ◽  
Repair Pathway ◽  
Control Shrna ◽  
Base Excision

Abstract We have previously shown that endonuclease activity is deregulated in myeloma and suppression of base excision repair (BER) associated apurinic/apyrimidinic endonuclease (APE) activity, mediated chemically or transgenically, reduces homologous recombination (HR) and genomic instability in multiple myeloma (MM). The purpose of this study was to investigate the role of BER-specific AP nucleases APE1 and APE2, separately or together, in the activation of HR pathway following exposure of MM cells to different DNA damaging agents and unravel possible mechanism/s and translational significance of this cross talk between two repair pathways in MM. We transduced MM cells with lentivirus-based shRNAs, either control (CS) or those targeting APE1, APE2, or both (APE1/2; double knockdown) and selected the transduced cells in puromycin. Knockdowns were confirmed by Western blotting and Q-PCR. Using evaluation by Q-PCR we observed that whereas APE2 was suppressed by 80% in APE2- as well as double-knockdown cells, it was upregulated by 70% in APE1 knock down cells. These data indicate that certain level of AP nuclease activity is probably required by MM cell to function and is consistent with a 25-30% reduced proliferation rate of double-knockdown cells under spontaneous condition. To study the impact of these modulations on ability of cells to activate HR-mediated repair pathway in response to DNA damage, the cells were exposed to either UV (20 J/m2) and incubated for 2 and 48 hrs or melphalan (2.5 µM) treatment for 24 hrs, and then incubation for further 1 and 24 hrs and evaluated for RAD51 and γ-H2AX foci. Following UV treatment, RAD51 foci were detected in 91%, 48%, 49%, and 28% of cells transduced with control, APE1, APE2, or both shRNAs, respectively. Similary melphalan treatment induced RAD51 foci in 76% of control shRNA transduced cells whereas only in 46%, 47%, and 27% of APE1, APE2, and APE1/2-knockdown cells. These data show that AP nuclease activity is involved in DNA damaging agent-induced activation of HR repair pathway. Impact of the suppression of AP nucleases was also assessed on cell proliferation at 48 hrs after treatment with melphalan. Viability of cells lacking APE1, APE2, and APE1/2 relative to control shRNA-transduced cells was reduced by 28%, 26%, and 43% (P<0.00005), respectively, within 48 hrs of treatment. In summary, we show that: 1) AP nuclease activity plays a critical role in the activation of HR-mediated DNA repair and survival of MM cells following DNA damage; 2) Although suppression of APE1 or APE2 alone does not significantly affect spontaneous proliferation rates, simultaneous suppression of both reduces proliferation by ∼25-30%; 3) Suppression of APE1 leads to induction of APE2, indicating that certain level of AP nuclease activity (from either APE1 or APE2) is required by MM cell to function and is consistent with the reduced proliferation rate of double-knockdown cells; 4) Simultaneous suppression of both AP nucleases impairs the activation of HR repair following DNA damage. These data combined with our previous observations conclude that AP nucleases (APE1 and APE2) play critical role in HR-mediated repair and survival of MM cells following DNA damage and are important targets to reduce genomic instability as well as to sensitize MM cells to radio/chemotherapy. Disclosures: No relevant conflicts of interest to declare.

scholarly journals A Multi-Endpoint Approach to Base Excision Repair Incision Activity Augmented by PARylation and DNA Damage Levels in Mice: Impact of Sex and Age

2020 ◽  
Vol 21 (18) ◽  
pp. 6600
Author(s):  
Nicola Winkelbeiner ◽  
Viktoria K. Wandt ◽  
Franziska Ebert ◽  
Kristina Lossow ◽  
Ezgi E. Bankoglu ◽  
...  
Keyword(s):  
Dna Damage ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Decisive Role ◽  
Dna Lesions ◽  
Dna Integrity ◽  
Repair Mechanisms ◽  
Murine Liver ◽  
Base Excision ◽  
Cellular Dna

Investigation of processes that contribute to the maintenance of genomic stability is one crucial factor in the attempt to understand mechanisms that facilitate ageing. The DNA damage response (DDR) and DNA repair mechanisms are crucial to safeguard the integrity of DNA and to prevent accumulation of persistent DNA damage. Among them, base excision repair (BER) plays a decisive role. BER is the major repair pathway for small oxidative base modifications and apurinic/apyrimidinic (AP) sites. We established a highly sensitive non-radioactive assay to measure BER incision activity in murine liver samples. Incision activity can be assessed towards the three DNA lesions 8-oxo-2’-deoxyguanosine (8-oxodG), 5-hydroxy-2’-deoxyuracil (5-OHdU), and an AP site analogue. We applied the established assay to murine livers of adult and old mice of both sexes. Furthermore, poly(ADP-ribosyl)ation (PARylation) was assessed, which is an important determinant in DDR and BER. Additionally, DNA damage levels were measured to examine the overall damage levels. No impact of ageing on the investigated endpoints in liver tissue were found. However, animal sex seems to be a significant impact factor, as evident by sex-dependent alterations in all endpoints investigated. Moreover, our results revealed interrelationships between the investigated endpoints indicative for the synergetic mode of action of the cellular DNA integrity maintaining machinery.

scholarly journals Oxidative Damage in Sporadic Colorectal Cancer: Molecular Mapping of Base Excision Repair Glycosylases in Colorectal Cancer Patients

2020 ◽  
Vol 21 (7) ◽  
pp. 2473 ◽  
Author(s):  
Pavel Vodicka ◽  
Marketa Urbanova ◽  
Pavol Makovicky ◽  
Kristyna Tomasova ◽  
Michal Kroupa ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Dna Damage ◽  
Dna Repair ◽  
Base Excision Repair ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Sporadic Colorectal Cancer ◽  
Base Excision ◽  
Colorectal Cancer Patients

Oxidative stress with subsequent premutagenic oxidative DNA damage has been implicated in colorectal carcinogenesis. The repair of oxidative DNA damage is initiated by lesion-specific DNA glycosylases (hOGG1, NTH1, MUTYH). The direct evidence of the role of oxidative DNA damage and its repair is proven by hereditary syndromes (MUTYH-associated polyposis, NTHL1-associated tumor syndrome), where germline mutations cause loss-of-function in glycosylases of base excision repair, thus enabling the accumulation of oxidative DNA damage and leading to the adenoma-colorectal cancer transition. Unrepaired oxidative DNA damage often results in G:C>T:A mutations in tumor suppressor genes and proto-oncogenes and widespread occurrence of chromosomal copy-neutral loss of heterozygosity. However, the situation is more complicated in complex and heterogeneous disease, such as sporadic colorectal cancer. Here we summarized our current knowledge of the role of oxidative DNA damage and its repair on the onset, prognosis and treatment of sporadic colorectal cancer. Molecular and histological tumor heterogeneity was considered. Our study has also suggested an additional important source of oxidative DNA damage due to intestinal dysbiosis. The roles of base excision repair glycosylases (hOGG1, MUTYH) in tumor and adjacent mucosa tissues of colorectal cancer patients, particularly in the interplay with other factors (especially microenvironment), deserve further attention. Base excision repair characteristics determined in colorectal cancer tissues reflect, rather, a disease prognosis. Finally, we discuss the role of DNA repair in the treatment of colon cancer, since acquired or inherited defects in DNA repair pathways can be effectively used in therapy.

Associations between DNA Damage, DNA Base Excision Repair Gene Variability and Alzheimer's Disease Risk

2016 ◽  
Vol 41 (3-4) ◽  
pp. 152-171 ◽  
Author(s):  
Dominik Kwiatkowski ◽  
Piotr Czarny ◽  
Monika Toma ◽  
Natalia Jurkowska ◽  
Agnieszka Sliwinska ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Dna Damage ◽  
Dna Repair ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Dna Lesions ◽  
Polymorphic Variants ◽  
Base Excision

Background: Increased oxidative damage to DNA is one of the pathways involved in Alzheimer's disease (AD). Insufficient base excision repair (BER) is in part responsible for increased oxidative DNA damage. The aim of the present study was to assess the effect of polymorphic variants of BER-involved genes and the peripheral markers of DNA damage and repair in patients with AD. Material and Methods: Comet assays and TaqMan probes were used to assess DNA damage, BER efficiency and polymorphic variants of 12 BER genes in blood samples from 105 AD patients and 130 controls. The DNA repair efficacy (DRE) was calculated according to a specific equation. Results: The levels of endogenous and oxidative DNA damages were higher in AD patients than controls. The polymorphic variants of XRCC1 c.580C>T XRCC1 c.1196A>G and OGG1 c.977C>G are associated with increased DNA damage in AD. Conclusion: Our results show that oxidative stress and disturbances in DRE are particularly responsible for the elevated DNA lesions in AD. The results suggest that oxidative stress and disruption in DNA repair may contribute to increased DNA damage in AD patients and risk of this disease. In addition, disturbances in DRE may be associated with polymorphisms of OGG1 and XRCC1.

scholarly journals Yeast RAD26, a Homolog of the Human CSB Gene, Functions Independently of Nucleotide Excision Repair and Base Excision Repair in Promoting Transcription through Damaged Bases

2002 ◽  
Vol 22 (12) ◽  
pp. 4383-4389 ◽  
Author(s):  
Sung-Keun Lee ◽  
Sung-Lim Yu ◽  
Louise Prakash ◽  
Satya Prakash
Keyword(s):  
Rna Polymerase Ii ◽  
Nucleotide Excision Repair ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Dna Lesions ◽  
Nucleotide Excision ◽  
Severe Reduction ◽  
Base Excision ◽  
Group B

ABSTRACT RAD26 in the yeast Saccharomyces cerevisiae is the counterpart of the human Cockayne syndrome group B (CSB) gene. Both RAD26 and CSB act in the preferential repair of UV lesions on the transcribed strand, and in this process, they function together with the components of nucleotide excision repair (NER). Here, we examine the role of RAD26 in the repair of DNA lesions induced upon treatment with the alkylating agent methyl methanesulfonate (MMS). MMS-induced DNA lesions include base damages such as 3-methyl adenine and 7-methyl guanine, and these lesions are removed in yeast by the alternate competing pathways of base excision repair (BER), which is initiated by the action of MAG1-encoded N-methyl purine DNA glycosylase, and NER. Interestingly, a synergistic increase in MMS sensitivity was observed in the rad26Δ strain upon inactivation of NER or BER, indicating that RAD26 promotes the survival of MMS-treated cells by a mechanism that acts independently of either of these repair pathways. The galactose-inducible transcription of the GAL2, GAL7, and GAL10 genes is reduced in MMS-treated rad26Δ cells and also in mag1Δ rad14Δ cells, whereas a very severe reduction in transcription occurs in MMS-treated mag1Δ rad14Δ rad26Δ cells. From these observations, we infer that RAD26 plays a role in promoting transcription by RNA polymerase II through damaged bases. The implications of these observations are discussed in this paper.

scholarly journals Role of Oligoadenylate Synthetases in Myeloid Neoplasia

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 29-30
Author(s):  
Metis Hasipek ◽  
Yihong Guan ◽  
Dale Grabowski ◽  
Xiaorong Gu ◽  
Yogenthiran Saunthararajah ◽  
...  
Keyword(s):  
Dna Damage ◽  
Cell Death ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Over Expression ◽  
Myeloid Leukemias ◽  
Base Excision ◽  
Acute Myeloid ◽  
Novel Therapeutic

Acute myeloid leukemias (AML), the most lethal forms of blood cancer, are genomic instability disorders primarily driven by somatic mutations that greatly impact proliferation and survival of mutant clones1. The multistep mechanism of disease progression can be attributed, in part, to the defects in one or more pathways involving responses to, or repair of, damaged DNA (DD) and base excision repair (BER). The basal levels of DD and BER are higher in myeloid leukemias due to higher levels of reactive oxygen species (ROS)-mediated accumulation of 8-oxyguanine (8-OG)2. Poly(ADP) Ribosylation (PARylation) by PAR polymerases (PARPs) is one of the early key steps in sensing and repairing ROS-induced DNA damage response (DDR) 3. Consistent with recent findings4,5 here we report that 2'-5'oligoadenylate synthases (OASs), a family of latent 2'-5'-adenylyl transferases, otherwise involved in cellular antiviral responses6, are also involved in PAR remodeling of the DDR in MDS and AML cells. The 2'-hydroxyl group of PAR ribose acts as an acceptor for 2'AMP in the OAS enzymatic reaction and terminates chain elongation (Fig. A). OAS1 over expression can increase genomic instability by increasing the flux of PARP-mediated DNA repair, promoting cellular proliferation (Fig. B)5. Expression analysis of OASs in AML patients (n=451, Beat AML) showed that OAS1 is upregulated (2-fold) in AML patients compared to normal bone marrow-derived CD34+ hematopoietic stem and progenitor cells (HSPC)(Fig. C). Knockout of OAS1 and OAS2 using Crispr-Cas9 in MDS-L cells (Fig. D), a cell line derived from an MDS patient, confers sensitivity to H2O2-induced DNA damage-mediated cell death; however, OAS3 has no effect. Conversely, ectopic over expression of OAS1 or OAS2 but not OAS3 in HEK293 cells provides protection against H2O2-induced cell death (Fig. E-F). Proteomic analysis of the OAS1 and OAS2 interactome using LCMS/MS suggests that over expression of OAS1 and OAS2 perturbs the differentiation program of HSPCs that may result in neoplastic evolution. Thus, OASs modify PAR chains, promoting speedy DNA repair and cell survival along with the induction of a differentiation block in HSPCs that leads to clonal expansion. In summary, an overburdened DDR may contribute to AML pathogenesis. Therefore, inhibiting this stimulator of BER/DDR can provide a novel therapeutic avenue in myeloid neoplasms. The current study points to the probable utility of a novel therapeutic approach of targeting OAS in combination with DNA damaging agents to prevent relapse and resistance in the treatment of leukemias. References 1. Abelson S, Collord G, Ng SWK, et al. Prediction of acute myeloid leukaemia risk in healthy individuals. Nature. 2018;559(7714):400-404. doi:10.1038/s41586-018-0317-6 2. Jankowska AM, Gondek LP, Szpurka H, Nearman ZP, Tiu RV, Maciejewski JP. Base excision repair dysfunction in a subgroup of patients with myelodysplastic syndrome. Leukemia. 2008;22(3):551-558. doi:10.1038/sj.leu.2405055 3. Rogge RA, Gibson BA, Kraus WL. Identifying Genomic Sites of ADP-Ribosylation Mediated by Specific Nuclear PARP Enzymes Using Click-ChIP. Methods Mol Biol. 2018;1813:371-387. doi:10.1007/978-1-4939-8588-3_25 4. Khodarev NN, Minn AJ, Efimova EV, et al. Signal transducer and activator of transcription 1 regulates both cytotoxic and prosurvival functions in tumor cells. Cancer Res. 2007;67(19):9214-9220. doi:10.1158/0008-5472.CAN-07-1019 5. Kondratova AA, Cheon H, Dong B, et al. Suppressing PARylation by 2',5'-oligoadenylate synthetase 1 inhibits DNA damage-induced cell death. EMBO J. 2020;39(11):e101573. doi:10.15252/embj.2019101573 6. Chakrabarti A, Jha BK, Silverman RH. New insights into the role of RNase L in innate immunity. J Interferon Cytokine Res. 2011;31(1):49-57. doi:10.1089/jir.2010.0120 Disclosures Saunthararajah: EpiDestiny: Consultancy, Current equity holder in private company, Patents & Royalties: University of Illinois at Chicago.

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