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Author: Grafiati

Published: 31 May 2022

Last updated: 7 July 2024

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1

Shinmura, Kazuya, Hisami Kato, Yuichi Kawanishi, Hisaki Igarashi, Masanori Goto, Hong Tao, Yusuke Inoue, et al. "Abnormal Expressions of DNA Glycosylase Genes NEIL1, NEIL2, and NEIL3 Are Associated with Somatic Mutation Loads in Human Cancer." Oxidative Medicine and Cellular Longevity 2016 (2016): 1–10. http://dx.doi.org/10.1155/2016/1546392.

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The effects of abnormalities in the DNA glycosylases NEIL1, NEIL2, and NEIL3 on human cancer have not been fully elucidated. In this paper, we found that the median somatic total mutation loads and the median somatic single nucleotide mutation loads exhibited significant inverse correlations with the median NEIL1 and NEIL2 expression levels and a significant positive correlation with the median NEIL3 expression level using data for 13 cancer types from the Cancer Genome Atlas (TCGA) database. A subset of the cancer types exhibited reduced NEIL1 and NEIL2 expressions and elevated NEIL3 expression, and such abnormal expressions of NEIL1, NEIL2, and NEIL3 were also significantly associated with the mutation loads in cancer. As a mechanism underlying the reduced expression of NEIL1 in cancer, the epigenetic silencing ofNEIL1through promoter hypermethylation was found. Finally, we investigated the reason why an elevated NEIL3 expression level was associated with an increased number of somatic mutations in cancer and found that NEIL3 expression was positively correlated with the expression of APOBEC3B, a potent inducer of mutations, in diverse cancers. These results suggested that the abnormal expressions of NEIL1, NEIL2, and NEIL3 are involved in cancer through their association with the somatic mutation load.

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2

Albelazi, Martin, Mohammed, Mutti, and Elder. "The Biochemical Role of the Human NEIL1 and NEIL3 DNA Glycosylases on Model DNA Replication Forks." Genes 10, no. 4 (April 23, 2019): 315. http://dx.doi.org/10.3390/genes10040315.

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Endonuclease VIII-like (NEIL) 1 and 3 proteins eliminate oxidative DNA base damage and psoralen DNA interstrand crosslinks through initiation of base excision repair. Current evidence points to a DNA replication associated repair function of NEIL1 and NEIL3, correlating with induced expression of the proteins in S/G2 phases of the cell cycle. However previous attempts to express and purify recombinant human NEIL3 in an active form have been challenging. In this study, both human NEIL1 and NEIL3 have been expressed and purified from E. coli, and the DNA glycosylase activity of these two proteins confirmed using single- and double-stranded DNA oligonucleotide substrates containing the oxidative bases, 5-hydroxyuracil, 8-oxoguanine and thymine glycol. To determine the biochemical role that NEIL1 and NEIL3 play during DNA replication, model replication fork substrates were designed containing the oxidized bases at one of three specific sites relative to the fork. Results indicate that whilst specificity for 5- hydroxyuracil and thymine glycol was observed, NEIL1 acts preferentially on double-stranded DNA, including the damage upstream to the replication fork, whereas NEIL3 preferentially excises oxidized bases from single stranded DNA and within open fork structures. Thus, NEIL1 and NEIL3 act in concert to remove oxidized bases from the replication fork.

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3

Hanna, Bishoy M. F., Maurice Michel, Thomas Helleday, and Oliver Mortusewicz. "NEIL1 and NEIL2 Are Recruited as Potential Backup for OGG1 upon OGG1 Depletion or Inhibition by TH5487." International Journal of Molecular Sciences 22, no. 9 (April 27, 2021): 4542. http://dx.doi.org/10.3390/ijms22094542.

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DNA damage caused by reactive oxygen species may result in genetic mutations or cell death. Base excision repair (BER) is the major pathway that repairs DNA oxidative damage in order to maintain genomic integrity. In mammals, eleven DNA glycosylases have been reported to initiate BER, where each recognizes a few related DNA substrate lesions with some degree of overlapping specificity. 7,8-dihydro-8-oxoguanine (8-oxoG), one of the most abundant DNA oxidative lesions, is recognized and excised mainly by 8-oxoguanine DNA glycosylase 1 (OGG1). Further oxidation of 8-oxoG generates hydantoin lesions, which are recognized by NEIL glycosylases. Here, we demonstrate that NEIL1, and to a lesser extent NEIL2, can potentially function as backup BER enzymes for OGG1 upon pharmacological inhibition or depletion of OGG1. NEIL1 recruitment kinetics and chromatin binding after DNA damage induction increase in cells treated with OGG1 inhibitor TH5487 in a dose-dependent manner, whereas NEIL2 accumulation at DNA damage sites is prolonged following OGG1 inhibition. Furthermore, depletion of OGG1 results in increased retention of NEIL1 and NEIL2 at damaged chromatin. Importantly, oxidatively stressed NEIL1- or NEIL2-depleted cells show excessive genomic 8-oxoG lesions accumulation upon OGG1 inhibition, suggesting a prospective compensatory role for NEIL1 and NEIL2. Our study thus exemplifies possible backup mechanisms within the base excision repair pathway.

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4

Makasheva, Kristina A., Anton V. Endutkin, and Dmitry O. Zharkov. "Requirements for DNA bubble structure for efficient cleavage by helix–two-turn–helix DNA glycosylases." Mutagenesis 35, no. 1 (November 30, 2019): 119–28. http://dx.doi.org/10.1093/mutage/gez047.

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Abstract Oxidative DNA lesions, constantly generated by both endogenous and environmentally induced reactive oxygen species, are removed via the base excision repair pathway. In bacteria, Fpg and Nei DNA glycosylases, belonging to the helix–two-turn–helix (H2TH) structural superfamily, remove oxidised purines and pyrimidines, respectively. Interestingly, the human H2TH family glycosylases, NEIL1, NEIL2 and NEIL3, have been reported to prefer oxidative lesions in DNA bubbles or single-stranded DNA. It had been hypothesised that NEIL2 might be involved in the repair of lesions in transcription bubbles; however, bubble-like structures may appear in other cellular contexts such as displacement loops (D-loops) associated with transcription, recombination or telomere maintenance. The activities of bacterial Fpg and Nei on bubble substrates were not addressed. Also, it is not known whether H2TH enzymes process bubbles containing the third DNA or RNA strand, and how the bubble length and position of the lesion within a bubble affect the excision. We have investigated the removal of 8-oxoguanine (8-oxoG) and 5,6-dihydrouracil (DHU) by Escherichia coli Fpg and Nei and human NEIL1 and NEIL2 from single-strand oligonucleotides, perfect duplexes, bubbles with different numbers of unpaired bases (6–30), bubbles containing the lesion in different positions and D-loops with the third strand made of DNA or RNA. Fpg, NEIL1 and NEIL2 efficiently excised lesions located within bubbles, with NEIL1 and NEIL2 being specific for DHU, and Fpg removing both 8-oxoG and DHU. Nei, in contrast, was significantly active only on DHU located in double-stranded DNA. Fpg and NEIL1 also tolerated the presence of the third strand of either DNA or RNA in D-loops if the lesion was in the single-stranded part, and Fpg, Nei and NEIL1 excised lesions from the double-stranded DNA part of D-loops. The presence of an additional unpaired 5′-tail of DNA or RNA did not affect the activity. No significant position preference for lesions in a 12-mer bubble was found. Overall, the activities of Fpg, NEIL1 and NEIL2 on these non-canonical substrates are consistent with the possibility that these enzymes may participate in the repair in structures arising during transcription or homologous recombination.

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5

Zhou, Jia, Minmin Liu, Aaron M. Fleming, Cynthia J. Burrows, and Susan S. Wallace. "Neil3 and NEIL1 DNA Glycosylases Remove Oxidative Damages from Quadruplex DNA and Exhibit Preferences for Lesions in the Telomeric Sequence Context." Journal of Biological Chemistry 288, no. 38 (August 7, 2013): 27263–72. http://dx.doi.org/10.1074/jbc.m113.479055.

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The telomeric DNA of vertebrates consists of d(TTAGGG)n tandem repeats, which can form quadruplex DNA structures in vitro and likely in vivo. Despite the fact that the G-rich telomeric DNA is susceptible to oxidation, few biochemical studies of base excision repair in telomeric DNA and quadruplex structures have been done. Here, we show that telomeric DNA containing thymine glycol (Tg), 8-oxo-7,8-dihydroguanine (8-oxoG), guanidinohydantoin (Gh), or spiroiminodihydantoin (Sp) can form quadruplex DNA structures in vitro. We have tested the base excision activities of five mammalian DNA glycosylases (NEIL1, NEIL2, mNeil3, NTH1, and OGG1) on these lesion-containing quadruplex substrates and found that only mNeil3 had excision activity on Tg in quadruplex DNA and that the glycosylase exhibited a strong preference for Tg in the telomeric sequence context. Although Sp and Gh in quadruplex DNA were good substrates for mNeil3 and NEIL1, none of the glycosylases had activity on quadruplex DNA containing 8-oxoG. In addition, NEIL1 but not mNeil3 showed enhanced glycosylase activity on Gh in the telomeric sequence context. These data suggest that one role for Neil3 and NEIL1 is to repair DNA base damages in telomeres in vivo and that Neil3 and Neil1 may function in quadruplex-mediated cellular events, such as gene regulation via removal of damaged bases from quadruplex DNA.

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6

Cherbuin, Nicolas, Hardip Patel, Erin I. Walsh, Ananthan Ambikairajah, Richard Burns, Anne Brüstle, and Lene Juel Rasmussen. "Cognitive Function Is Associated with the Genetically Determined Efficiency of DNA Repair Mechanisms." Genes 15, no. 2 (January 24, 2024): 153. http://dx.doi.org/10.3390/genes15020153.

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Several modifiable risk factors for neurodegeneration and dementia have been identified, although individuals vary in their vulnerability despite a similar risk of exposure. This difference in vulnerability could be explained at least in part by the variability in DNA repair mechanisms’ efficiency between individuals. Therefore, the aim of this study was to test associations between documented, prevalent genetic variation (single nucleotide polymorphism, SNP) in DNA repair genes, cognitive function, and brain structure. Community-living participants (n = 488,159; 56.54 years (8.09); 54.2% female) taking part in the UK Biobank study and for whom cognitive and genetic measures were available were included. SNPs in base excision repair (BER) genes of the bifunctional DNA glycosylases OGG1 (rs1052133, rs104893751), NEIL1 (rs7402844, rs5745906), NEIL2 (rs6601606), NEIL3 (rs10013040, rs13112390, rs13112358, rs1395479), MUTYH (rs34612342, rs200165598), NTHL1 (rs150766139, rs2516739) were considered. Cognitive measures included fluid intelligence, the symbol–digit matching task, visual matching, and trail-making. Hierarchical regression and latent class analyses were used to test the associations between SNPs and cognitive measures. Associations between SNPs and brain measures were also tested in a subset of 39,060 participants. Statistically significant associations with cognition were detected for 12 out of the 13 SNPs analyzed. The strongest effects amounted to a 1–6% difference in cognitive function detected for NEIL1 (rs7402844), NEIL2 (rs6601606), and NTHL1 (rs2516739). Associations varied by age and sex, with stronger effects detected in middle-aged women. Weaker associations with brain measures were also detected. Variability in some BER genes is associated with cognitive function and brain structure and may explain variability in the risk for neurodegeneration and dementia.

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7

Konis, Sifaddin M. R., Jonathan R. Hughes, and Jason L. Parsons. "TRIM26 Maintains Cell Survival in Response to Oxidative Stress through Regulating DNA Glycosylase Stability." International Journal of Molecular Sciences 23, no. 19 (October 1, 2022): 11613. http://dx.doi.org/10.3390/ijms231911613.

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Oxidative DNA base lesions in DNA are repaired through the base excision repair (BER) pathway, which consequently plays a vital role in the maintenance of genome integrity and in suppressing mutagenesis. 8-oxoguanine DNA glycosylase (OGG1), endonuclease III-like protein 1 (NTH1), and the endonuclease VIII-like proteins 1–3 (NEIL1–3) are the key enzymes that initiate repair through the excision of the oxidized base. We have previously identified that the E3 ubiquitin ligase tripartite motif 26 (TRIM26) controls the cellular response to oxidative stress through regulating both NEIL1 and NTH1, although its potential, broader role in BER is unclear. We now show that TRIM26 is a central player in determining the response to different forms of oxidative stress. Using siRNA-mediated knockdowns, we demonstrate that the resistance of cells to X-ray radiation and hydrogen peroxide generated as a consequence of trim26 depletion can be reversed through suppression of selective DNA glycosylases. In particular, a knockdown of neil1 or ogg1 can enhance sensitivity and DNA repair rates in response to X-rays, whereas a knockdown of neil1 or neil3 can produce the same effect in response to hydrogen peroxide. Our study, therefore, highlights the importance of TRIM26 in balancing cellular DNA glycosylase levels required for an efficient BER response.

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8

Kabziński, Jacek, Anna Walczak, Michał Mik, and Ireneusz Majsterek. "Sirt3 regulates the level of mitochondrial DNA repair activity through deacetylation of NEIL1, NEIL2, OGG1, MUTYH, APE1 and LIG3 in colorectal cancer." Polish Journal of Surgery 92, no. 1 (November 4, 2019): 1–5. http://dx.doi.org/10.5604/01.3001.0013.5539.

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Colorectal cancer (CRC) is one of the most common malignant tumors. One of the factors increasing the risk of its occurrence may be the reduced efficiency of repairing DNA damage, both nuclear and mitochondrial. The main mechanism for repairing oxidative damage is the BER system (in mitochondria mtBER), whose key proteins NEIL1, NEIL2, OGG1, MUTYH, APE1 and LIG3 obtain full efficiency only at the appropriate level of acetylation. Sirtuin 3 is a key protein for mitochondrial homeostasis, regulating a number of metabolic processes related mainly to the control of the level of reactive oxygen species. Because Sirt3 possesses acetylase activity, it can modulate the level of activity of mtBER proteins by their deacetylation. The conducted study showed that the tested proteins NEIL1, NEIL2, OGG1, MUTYH, APE1 and LIG3 are the substrate for the enzymatic deacetylation activity of Sirt3, which may lead to modulation of the risk of CRC, and in cancer cells may be a potential therapeutic target enhancing the action of cytostatic drugs.

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9

Kabzinski, J., A. Walczak, and I. Majsterek. "Sirt3 Regulates Response to Oxidative Stress by Interacting with BER Proteins in Colorectal Cancer." Genetics Research 2022 (April 7, 2022): 1–10. http://dx.doi.org/10.1155/2022/7299555.

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The oxidative damages are well-recognized factors in the pathogenesis of colorectal cancer (CRC). Increased levels of reactive oxygen species (ROS) can lead to oxidative DNA damage, which, if unrepaired, can be an underlying cause of cancerogenic transformation. To defend against these threats, cells have developed a range of defense mechanisms. One of the most important protection mechanisms is DNA repair systems, both nuclear and mitochondrial. Sirt3 is a mitochondrial protein involved in regulating NEIL1, NEIL2, MUTYH, APE1, and LIG3 proteins, which are involved in DNA repair, including mitochondrial repair through mtBER (mitochondrial Base Excision Repair). In this work, we show that NEIL1, NEIL2, MUTYH, APE1, and LIG3 are regulated by Sirt3 through deacetylation, and moreover, Sirt3 is directly involved in physical interaction with MUTYH, NEIL1, and APE1, which indicates the controlling role of Sirt3 over the mtBER mechanism. Also, if the cells deprived of Sirt3 are exposed to oxidative stress, altered levels of those proteins can be observed, which supports the theory of the regulatory role of Sirt3. Finally, to fully confirm the role of Sirt3 in DNA repair, we examined its role in apoptosis and found the impact of this protein on cell survival rate. Using the knowledge obtained in the course of conducted experiments, we postulate consideration of Sirt3 as a target in the rising vulnerability of cancer cells during therapy and therefore increasing the effectiveness of cancer treatment.

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10

Xue, Wanjuan, Yongcheng Liu, Ningning Xin, Jiyu Miao, Juan Du, Yu Wang, Haiyan Shi, et al. "Nei Endonuclease VIII-Like1 (NEIL1) Inhibits Apoptosis of Human Colorectal Cancer Cells." BioMed Research International 2020 (June 27, 2020): 1–11. http://dx.doi.org/10.1155/2020/5053975.

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The study is aimed at investigating the role of Nei endonuclease VIII-like1 (NEIL1) in the pathogenesis of colorectal cancer (CRC). The human CRC (HCT116 and SW480) cells were subjected to the siRNA silencing and recombinant plasmid overexpression of NEIL1. Transfection of siNEIL1 significantly inhibited the cell growth. It also increased the Bax expression levels, while it decreased the Bcl-2 expression levels in human CRC cells, leading the Bax/Bcl-2 balance toward apoptosis. Moreover, the apoptosis was promoted through the caspase-9 signaling pathway. One the other hand, high expression of NEIL1 promoted the cell viability and reduced the apoptosis, inducing the balance of Bax/Bcl-2 in the human colon cancer cells to be antiapoptotic. In addition, the caspase-9 signaling pathway inhibited apoptosis, contrary to the results obtained by downregulating NEIL1 expression. Furthermore, NEIL1 was negatively regulated by miR-7-5p, indicating that miR-7-5p inhibited the NEIL1 expression after transcription. Overexpression of miR-7-5p reversed the effects of NEIL1 on these CRC cells. In conclusion, NEIL1 promotes the proliferation of CRC cells, which is regulated negatively by miR-7-5p. These findings suggest that NEIL1 is a potential therapeutic target for CRC.

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Sampath, Harini, Ayesha K. Batra, Vladimir Vartanian, J. Russ Carmical, Deborah Prusak, Irena B. King, Brian Lowell, et al. "Variable penetrance of metabolic phenotypes and development of high-fat diet-induced adiposity in NEIL1-deficient mice." American Journal of Physiology-Endocrinology and Metabolism 300, no. 4 (April 2011): E724—E734. http://dx.doi.org/10.1152/ajpendo.00387.2010.

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Exposure to chronic and acute oxidative stress is correlated with many human diseases, including, but not limited to, cancer, heart disease, diabetes, and obesity. In addition to cellular lipids and proteins, cellular oxidative stress can result in damage to DNA bases, especially in mitochondrial DNA. We previously described the development of spontaneous late-onset obesity, hepatic steatosis, hyperinsulinemia, and hyperleptinemia in mice that are deficient in the DNA glycosylase nei-like 1 (NEIL1), which initiates base excision repair of several oxidatively damaged bases. In the current study, we report that exposure to a chronic oxidative stress in the form of a high-fat diet greatly accelerates the development of obesity in neil1−/− mice. Following a 5-wk high-fat diet challenge, neil1−/− mice gained significantly more body weight than neil1+/+ littermates and had increased body fat accumulation and moderate to severe hepatic steatosis. Analysis of oxygen consumption by indirect calorimetry indicated a modest reduction in total oxygen consumption in neil1−/− mice that was abolished upon correction for lean body mass. Additionally, hepatic expression of several inflammatory genes was significantly upregulated in neil1−/− mice following high-fat diet challenge compared with chow-fed or neil1+/+ counterparts. A long-term high-fat diet also induced glucose intolerance as well as a significant reduction in mitochondrial DNA and protein content in neil1−/− mice. Collectively, these data indicate that NEIL1 deficiency results in an increased susceptibility to obesity and related complications potentially by lowering the threshold for tolerance of cellular oxidative stress in neil1−/− mice.

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Diatlova, Evgeniia A., Grigory V. Mechetin, and Dmitry O. Zharkov. "Distinct Mechanisms of Target Search by Endonuclease VIII-like DNA Glycosylases." Cells 11, no. 20 (October 11, 2022): 3192. http://dx.doi.org/10.3390/cells11203192.

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Proteins that recognize specific DNA sequences or structural elements often find their cognate DNA lesions in a processive mode, in which an enzyme binds DNA non-specifically and then slides along the DNA contour by one-dimensional diffusion. Opposite to the processive mechanism is distributive search, when an enzyme binds, samples and releases DNA without significant lateral movement. Many DNA glycosylases, the repair enzymes that excise damaged bases from DNA, use processive search to find their cognate lesions. Here, using a method based on correlated cleavage of multiply damaged oligonucleotide substrates we investigate the mechanism of lesion search by three structurally related DNA glycosylases—bacterial endonuclease VIII (Nei) and its mammalian homologs NEIL1 and NEIL2. Similarly to another homologous enzyme, bacterial formamidopyrimidine–DNA glycosylase, NEIL1 seems to use a processive mode to locate its targets. However, the processivity of Nei was notably lower, and NEIL2 exhibited almost fully distributive action on all types of substrates. Although one-dimensional diffusion is often regarded as a universal search mechanism, our results indicate that even proteins sharing a common fold may be quite different in the ways they locate their targets in DNA.

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Hegde, Pavana M., Arijit Dutta, Shiladitya Sengupta, Joy Mitra, Sanjay Adhikari, Alan E. Tomkinson, Guo-Min Li, et al. "The C-terminal Domain (CTD) of Human DNA Glycosylase NEIL1 Is Required for Forming BERosome Repair Complex with DNA Replication Proteins at the Replicating Genome." Journal of Biological Chemistry 290, no. 34 (July 1, 2015): 20919–33. http://dx.doi.org/10.1074/jbc.m115.642918.

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The human DNA glycosylase NEIL1 was recently demonstrated to initiate prereplicative base excision repair (BER) of oxidized bases in the replicating genome, thus preventing mutagenic replication. A significant fraction of NEIL1 in cells is present in large cellular complexes containing DNA replication and other repair proteins, as shown by gel filtration. However, how the interaction of NEIL1 affects its recruitment to the replication site for prereplicative repair was not investigated. Here, we show that NEIL1 binarily interacts with the proliferating cell nuclear antigen clamp loader replication factor C, DNA polymerase δ, and DNA ligase I in the absence of DNA via its non-conserved C-terminal domain (CTD); replication factor C interaction results in ∼8-fold stimulation of NEIL1 activity. Disruption of NEIL1 interactions within the BERosome complex, as observed for a NEIL1 deletion mutant (N311) lacking the CTD, not only inhibits complete BER in vitro but also prevents its chromatin association and reduced recruitment at replication foci in S phase cells. This suggests that the interaction of NEIL1 with replication and other BER proteins is required for efficient repair of the replicating genome. Consistently, the CTD polypeptide acts as a dominant negative inhibitor during in vitro repair, and its ectopic expression sensitizes human cells to reactive oxygen species. We conclude that multiple interactions among BER proteins lead to large complexes, which are critical for efficient BER in mammalian cells, and the CTD interaction could be targeted for enhancing drug/radiation sensitivity of tumor cells.

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Ha, Anh, Yunfeng Lin, and Shan Yan. "A non-canonical role for the DNA glycosylase NEIL3 in suppressing APE1 endonuclease-mediated ssDNA damage." Journal of Biological Chemistry 295, no. 41 (August 14, 2020): 14222–35. http://dx.doi.org/10.1074/jbc.ra120.014228.

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The DNA glycosylase NEIL3 has been implicated in DNA repair pathways including the base excision repair and the interstrand cross-link repair pathways via its DNA glycosylase and/or AP lyase activity, which are considered canonical roles of NEIL3 in genome integrity. Compared with the other DNA glycosylases NEIL1 and NEIL2, Xenopus laevis NEIL3 C terminus has two highly conserved zinc finger motifs containing GRXF residues (designated as Zf-GRF). It has been demonstrated that the minor AP endonuclease APE2 contains only one Zf-GRF motif mediating interaction with single-strand DNA (ssDNA), whereas the major AP endonuclease APE1 does not. It appears that the two NEIL3 Zf-GRF motifs (designated as Zf-GRF repeat) are dispensable for its DNA glycosylase and AP lyase activity; however, the potential function of the NEIL3 Zf-GRF repeat in genome integrity remains unknown. Here, we demonstrate evidence that the NEIL3 Zf-GRF repeat was associated with a higher affinity for shorter ssDNA than one single Zf-GRF motif. Notably, our protein–protein interaction assays show that the NEIL3 Zf-GRF repeat but not one Zf-GRF motif interacted with APE1 but not APE2. We further reveal that APE1 endonuclease activity on ssDNA but not on dsDNA is compromised by a NEIL3 Zf-GRF repeat, whereas one Zf-GRF motif within NEIL3 is not sufficient to prevent such activity of APE1. In addition, COMET assays show that excess NEIL3 Zf-GRF repeat reduces DNA damage in oxidative stress in Xenopus egg extracts. Together, our results suggest a noncanonical role of NEIL3 in genome integrity via its distinct Zf-GRF repeat in suppressing APE1 endonuclease-mediated ssDNA breakage.

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15

Vartanian, Vladimir, Irina G. Minko, Supawadee Chawanthayatham, Patricia A. Egner, Ying-Chih Lin, Lauriel F. Earley, Rosemary Makar, et al. "NEIL1 protects against aflatoxin-induced hepatocellular carcinoma in mice." Proceedings of the National Academy of Sciences 114, no. 16 (April 3, 2017): 4207–12. http://dx.doi.org/10.1073/pnas.1620932114.

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Global distribution of hepatocellular carcinomas (HCCs) is dominated by its incidence in developing countries, accounting for >700,000 estimated deaths per year, with dietary exposures to aflatoxin (AFB1) and subsequent DNA adduct formation being a significant driver. Genetic variants that increase individual susceptibility to AFB1-induced HCCs are poorly understood. Herein, it is shown that the DNA base excision repair (BER) enzyme, DNA glycosylase NEIL1, efficiently recognizes and excises the highly mutagenic imidazole ring-opened AFB1-deoxyguanosine adduct (AFB1-Fapy-dG). Consistent with this in vitro result, newborn mice injected with AFB1 show significant increases in the levels of AFB1-Fapy-dG in Neil1−/− vs. wild-type liver DNA. Further, Neil1−/− mice are highly susceptible to AFB1-induced HCCs relative to WT controls, with both the frequency and average size of hepatocellular carcinomas being elevated in Neil1−/−. The magnitude of this effect in Neil1−/− mice is greater than that previously measured in Xeroderma pigmentosum complementation group A (XPA) mice that are deficient in nucleotide excision repair (NER). Given that several human polymorphic variants of NEIL1 are catalytically inactive for their DNA glycosylase activity, these deficiencies may increase susceptibility to AFB1-associated HCCs.

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Zhu, Chenxu, Lining Lu, Jun Zhang, Zongwei Yue, Jinghui Song, Shuai Zong, Menghao Liu, Olivia Stovicek, Yi Qin Gao, and Chengqi Yi. "Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair." Proceedings of the National Academy of Sciences 113, no. 28 (June 27, 2016): 7792–97. http://dx.doi.org/10.1073/pnas.1604591113.

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NEIL1 (Nei-like 1) is a DNA repair glycosylase guarding the mammalian genome against oxidized DNA bases. As the first enzymes in the base-excision repair pathway, glycosylases must recognize the cognate substrates and catalyze their excision. Here we present crystal structures of human NEIL1 bound to a range of duplex DNA. Together with computational and biochemical analyses, our results suggest that NEIL1 promotes tautomerization of thymine glycol (Tg)—a preferred substrate—for optimal binding in its active site. Moreover, this tautomerization event also facilitates NEIL1-catalyzed Tg excision. To our knowledge, the present example represents the first documented case of enzyme-promoted tautomerization for efficient substrate recognition and catalysis in an enzyme-catalyzed reaction.

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17

Ferino, Annalisa, and Luigi E. Xodo. "Effect of DNA Glycosylases OGG1 and Neil1 on Oxidized G-Rich Motif in the KRAS Promoter." International Journal of Molecular Sciences 22, no. 3 (January 24, 2021): 1137. http://dx.doi.org/10.3390/ijms22031137.

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The promoter of the Kirsten ras (KRAS) proto-oncogene contains, upstream of the transcription start site, a quadruplex-forming motif called 32R with regulatory functions. As guanine under oxidative stress can be oxidized to 8-oxoguanine (8OG), we investigated the capacity of glycosylases 8-oxoguanine glycosylase (OGG1) and endonuclease VIII-like 1 (Neil1) to excise 8OG from 32R, either in duplex or G-quadruplex (G4) conformation. We found that OGG1 efficiently excised 8OG from oxidized 32R in duplex but not in G4 conformation. By contrast, glycosylase Neil1 showed more activity on the G4 than the duplex conformation. We also found that the excising activity of Neil1 on folded 32R depended on G4 topology. Our data suggest that Neil1, besides being involved in base excision repair pathway (BER), could play a role on KRAS transcription.

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Larsen, Knud, and Mads Peter Heide-Jørgensen. "Conservation of A-to-I RNA editing in bowhead whale and pig." PLOS ONE 16, no. 12 (December 9, 2021): e0260081. http://dx.doi.org/10.1371/journal.pone.0260081.

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RNA editing is a post-transcriptional process in which nucleotide changes are introduced into an RNA sequence, many of which can contribute to proteomic sequence variation. The most common type of RNA editing, contributing to nearly 99% of all editing events in RNA, is A-to-I (adenosine-to-inosine) editing mediated by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. A-to-I editing at ‘recoding’ sites results in non-synonymous substitutions in protein-coding sequences. Here, we present studies of the conservation of A-to-I editing in selected mRNAs between pigs, bowhead whales, humans and two shark species. All examined mRNAs–NEIL1, COG3, GRIA2, FLNA, FLNB, IGFBP7, AZIN1, BLCAP, GLI1, SON, HTR2C and ADAR2 –showed conservation of A-to-I editing of recoding sites. In addition, novel editing sites were identified in NEIL1 and GLI1 in bowhead whales. The A-to-I editing site of human NEIL1 in position 242 was conserved in the bowhead and porcine homologues. A novel editing site was discovered in Tyr244. Differential editing was detected at the two adenosines in the NEIL1 242 codon in both pig and bowhead NEIL1 mRNAs in various tissues and organs. No conservation of editing of KCNB1 and EEF1A mRNAs was seen in bowhead whales. In silico analyses revealed conservation of five adenosines in ADAR2, some of which are subject to A-to-I editing in bowheads and pigs, and conservation of a regulatory sequence in GRIA2 mRNA that is responsible for recognition of the ADAR editing enzyme.

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Ma, Huaxian, Jianling Wang, Sherif Z. Abdel-Rahman, Tapas K. Hazra, Paul J. Boor, and M. Firoze Khan. "Induction of NEIL1 and NEIL2 DNA glycosylases in aniline-induced splenic toxicity." Toxicology and Applied Pharmacology 251, no. 1 (February 2011): 1–7. http://dx.doi.org/10.1016/j.taap.2010.12.001.

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Lloyd, R. Stephen. "Complex Roles of NEIL1 and OGG1: Insights Gained from Murine Knockouts and Human Polymorphic Variants." DNA 2, no. 4 (December 1, 2022): 279–301. http://dx.doi.org/10.3390/dna2040020.

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DNA glycosylases promote genomic stability by initiating base excision repair (BER) in both the nuclear and mitochondrial genomes. Several of these enzymes have overlapping substrate recognition, through which a degree of redundancy in lesion recognition is achieved. For example, OGG1 and NEIL1 both recognize and release the imidazole-ring-fragmented guanine, FapyGua as part of a common overall pathway to cleanse the genome of damaged bases. However, these glycosylases have many differences, including their differential breadth of substrate specificity, the contrasting chemistries through which base release occurs, the subsequent steps required to complete the BER pathway, and the identity of specific protein-binding partners. Beyond these differences, the complexities and differences of their in vivo biological roles have been primarily elucidated in studies of murine models harboring a knockout of Neil1 or Ogg1, with the diversity of phenotypic manifestations exceeding what might have been anticipated for a DNA glycosylase deficiency. Pathologies associated with deficiencies in nuclear DNA repair include differential cancer susceptibilities, where Ogg1-deficient mice are generally refractory to carcinogenesis, while deficiencies in Neil1-deficient mice confer cancer susceptibility. In contrast to NEIL1, OGG1 functions as a key transcription factor in regulating inflammation and other complex gene cascades. With regard to phenotypes attributed to mitochondrial repair, knockout of either of these genes results in age- and diet-induced metabolic syndrome. The adverse health consequences associated with metabolic syndrome can be largely overcome by expression of a mitochondrial-targeted human OGG1 in both wild-type and Ogg1-deficient mice. The goal of this review is to compare the roles that NEIL1 and OGG1 play in maintaining genomic integrity, with emphasis on insights gained from not only the diverse phenotypes that are manifested in knockout and transgenic mice, but also human disease susceptibility associated with polymorphic variants.

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Minko, Irina G., Plamen P. Christov, Liang Li, Michael P. Stone, Amanda K. McCullough, and R. Stephen Lloyd. "Processing of N-substituted formamidopyrimidine DNA adducts by DNA glycosylases NEIL1 and NEIL3." DNA Repair 73 (January 2019): 49–54. http://dx.doi.org/10.1016/j.dnarep.2018.11.001.

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Cheng, Junrui, Baxter Miller, Emilio Balbuena, and Abdulkerim Eroglu. "Lycopene Protects against Smoking-Induced Lung Cancer by Inducing Base Excision Repair." Antioxidants 9, no. 7 (July 21, 2020): 643. http://dx.doi.org/10.3390/antiox9070643.

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Background: Oxidative stress plays a critical role in lung cancer progression. Carotenoids are efficient antioxidants. The objective of this study was to explore the efficacy of all-trans retinoic acid (ATRA) and carotenoids in cigarette smoke-induced oxidative stress within A549 human lung cancer epithelial cells. Methods: A549 cells were pretreated with 1-nM, 10-nM, 100-nM, 1-μM and 10-μM ATRA, β-carotene (BC) and lycopene for 24 h, followed by exposure to cigarette smoke using a smoking chamber. Results: The OxyBlot analysis showed that smoking significantly increased oxidative stress, which was inhibited by lycopene at 1 nM and 10 nM (p < 0.05). In the cells exposed to smoke, lycopene increased 8-oxoguanine DNA glycosylase (OGG1) expression at 1 nM, 10 nM, 100 nM, and 1 μM (p < 0.05), but not at 10 μM. Lycopene at lower doses also improved Nei like DNA glycosylases (NEIL1, NEIL2, NEIL3), and connexin-43 (Cx43) protein levels (p < 0.05). Interestingly, lycopene at lower concentrations promoted OGG1 expression within the cells exposed to smoke to an even greater extent than the cells not exposed to smoke (p < 0.01). This may be attributed to the increased SR-B1 mRNA levels with cigarette smoke exposure (p < 0.05). Conclusions: Lycopene treatment at a lower dosage could inhibit smoke-induced oxidative stress and promote genome stability. These novel findings will shed light on the molecular mechanism of lycopene action against lung cancer.

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Dou, Hong, Sankar Mitra, and Tapas K. Hazra. "Repair of Oxidized Bases in DNA Bubble Structures by Human DNA Glycosylases NEIL1 and NEIL2." Journal of Biological Chemistry 278, no. 50 (September 30, 2003): 49679–84. http://dx.doi.org/10.1074/jbc.m308658200.

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24

Ahmad, Hafiz Ishfaq, Gulnaz Afzal, Sehrish Sadia, Ghulam Haider, Shakeel Ahmed, Saba Saeed, and Jinping Chen. "Structural and Evolutionary Adaptations of Nei-Like DNA Glycosylases Proteins Involved in Base Excision Repair of Oxidative DNA Damage in Vertebrates." Oxidative Medicine and Cellular Longevity 2022 (April 4, 2022): 1–20. http://dx.doi.org/10.1155/2022/1144387.

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Oxidative stress is a type of stress that damages DNA and can occur from both endogenous and exogenous sources. Damage to DNA caused by oxidative stress can result in base modifications that promote replication errors and the formation of sites of base loss, which pose unique challenges to the preservation of genomic integrity. However, the adaptive evolution of the DNA repair mechanism is poorly understood in vertebrates. This research aimed to explore the evolutionary relationships, physicochemical characteristics, and comparative genomic analysis of the Nei-like glycosylase gene family involved in DNA base repair in the vertebrates. The genomic sequences of NEIL1, NEIL2, and NEIL3 genes were aligned to observe selection constraints in the genes, which were relatively low conserved across vertebrate species. The positive selection signals were identified in these genes across the vertebrate lineages. We identified that only about 2.7% of codons in these genes were subjected to positive selection. We also revealed that positive selection pressure was increased in the Fapy-DNA-glyco and H2TH domain, which are involved in the base excision repair of DNA that has been damaged by oxidative stress. Gene structure, motif, and conserved domain analysis indicated that the Nei-like glycosylase genes in mammals and avians are evolutionarily low conserved compared to other glycosylase genes in other “vertebrates” species. This study revealed that adaptive selection played a critical role in the evolution of Nei-like glycosylase in vertebrate species. Systematic comparative genome analyses will give key insights to elucidate the links between DNA repair and the development of lifespan in various organisms as more diverse vertebrate genome sequences become accessible.

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25

Teoh, Phaik Ju, Omer An, Tae-Hoon Chung, Jing Yuan Chooi, Sabrina H. M. Toh, Shuangyi Fan, Wilson Wang, et al. "Aberrant hyperediting of the myeloma transcriptome by ADAR1 confers oncogenicity and is a marker of poor prognosis." Blood 132, no. 12 (September 20, 2018): 1304–17. http://dx.doi.org/10.1182/blood-2018-02-832576.

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Key Points The integrity of the MM transcriptome is compromised by ADAR1 overexpression, conferring oncogenic events in an editing-dependent manner. NEIL1 is an important ADAR1 editing target, and its recoded protein has a defective functional capacity and gain-of-function properties.

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Roy, Laura M., Pawel Jaruga, Thomas G. Wood, Amanda K. McCullough, Miral Dizdaroglu, and R. Stephen Lloyd. "Human Polymorphic Variants of the NEIL1 DNA Glycosylase." Journal of Biological Chemistry 282, no. 21 (March 26, 2007): 15790–98. http://dx.doi.org/10.1074/jbc.m610626200.

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27

Singh, Preety Kadian, and Kinnari Mistry. "Human NEIL1 DNA glycosylase: Structure, function and polymorphisms." Meta Gene 11 (February 2017): 49–57. http://dx.doi.org/10.1016/j.mgene.2016.11.006.

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28

Carter, A., W. M. Md Saad, A. Dumax-Vorzet, A. C. Povey, and R. H. Elder. "164 Characterisation of the NEIL1 knockout mouse phenotype." European Journal of Cancer Supplements 8, no. 5 (June 2010): 43–44. http://dx.doi.org/10.1016/s1359-6349(10)70972-1.

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29

Yang, Beimeng, David M. Figueroa, Yujun Hou, Mansi Babbar, Stephanie L. Baringer, Deborah L. Croteau, and Vilhelm A. Bohr. "NEIL1 stimulates neurogenesis and suppresses neuroinflammation after stress." Free Radical Biology and Medicine 141 (September 2019): 47–58. http://dx.doi.org/10.1016/j.freeradbiomed.2019.05.037.

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30

Ziółkowska, Sylwia, Marcin Kosmalski, Łukasz Kołodziej, Aleksandra Jabłkowska, Janusz Zbigniew Szemraj, Tadeusz Pietras, Maciej Jabłkowski, and Piotr Lech Czarny. "Single-Nucleotide Polymorphisms in Base-Excision Repair-Related Genes Involved in the Risk of an Occurrence of Non-Alcoholic Fatty Liver Disease." International Journal of Molecular Sciences 24, no. 14 (July 11, 2023): 11307. http://dx.doi.org/10.3390/ijms241411307.

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Oxidative stress is one of the pillars crucial in the development of a non-alcoholic fatty liver disease (NAFLD) and may cause DNA damage. Since the main pathway responsible for the repair of oxidative DNA damage is the base-excision repair (BER) pathway, we examined the relationship between the presence of different genetic variants of BER-associated genes and the risk of NAFLD. The study evaluates seven single nucleotide polymorphisms (SNPs) within five genes, hOGG1, APEX1, NEIL1, LIG3, LIG1, in 150 NAFLD patients and 340 healthy controls. The genotyping was performed using TaqMan probes and the results were presented as odds ratio with its corresponding 95% confidence interval. The following SNPs were assessed in the study: hOGG1 (rs1052133), APEX1 (rs176094 and rs1130409), NEIL1 (rs4462560), LIG3 (rs1052536), LIG3 (rs4796030), and LIG1 (rs20579). Four of the investigated SNPs, i.e., rs176094, rs1130409, rs4462560 and rs4796030, were found to be associated with NAFLD risk. Furthermore, the occurrence of insulin resistance in patients with steatosis depended on various LIG3 genetic variants. The findings imply the impact of genes involved in BER on NAFLD and fatty liver-related insulin sensitivity.

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31

Calkins, Marcus J., Vladimir Vartanian, Nichole Owen, Guldal Kirkali, Pawel Jaruga, Miral Dizdaroglu, Amanda K. McCullough, and R. Stephen Lloyd. "Enhanced sensitivity of Neil1−/− mice to chronic UVB exposure." DNA Repair 48 (December 2016): 43–50. http://dx.doi.org/10.1016/j.dnarep.2016.10.010.

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32

Yudkina, Anna V., Anton V. Endutkin, Eugenia A. Diatlova, Nina A. Moor, Ivan P. Vokhtantsev, Inga R. Grin, and Dmitry O. Zharkov. "Displacement of Slow-Turnover DNA Glycosylases by Molecular Traffic on DNA." Genes 11, no. 8 (July 30, 2020): 866. http://dx.doi.org/10.3390/genes11080866.

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In the base excision repair pathway, the initiating enzymes, DNA glycosylases, remove damaged bases and form long-living complexes with the abasic DNA product, but can be displaced by AP endonucleases. However, many nuclear proteins can move along DNA, either actively (such as DNA or RNA polymerases) or by passive one-dimensional diffusion. In most cases, it is not clear whether this movement is disturbed by other bound proteins or how collisions with moving proteins affect the bound proteins, including DNA glycosylases. We have used a two-substrate system to study the displacement of human OGG1 and NEIL1 DNA glycosylases by DNA polymerases in both elongation and diffusion mode and by D4, a passively diffusing subunit of a viral DNA polymerase. The OGG1–DNA product complex was disrupted by DNA polymerase β (POLβ) in both elongation and diffusion mode, Klenow fragment (KF) in the elongation mode and by D4. NEIL1, which has a shorter half-life on DNA, was displaced more efficiently. Hence, both possibly specific interactions with POLβ and nonspecific collisions (KF, D4) can displace DNA glycosylases from DNA. The protein movement along DNA was blocked by very tightly bound Cas9 RNA-targeted nuclease, providing an upper limit on the efficiency of obstacle clearance.

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33

YAMAMOTO, Ryohei, Mizuki YAMAMOTO, Hiroyuki KUSAKA, Hideaki MASATSUGU, Satoshi MATSUYAMA, Tomoko TAJIMA, Hiroshi IDE, and Kihei KUBO. "NEIL1 mRNA Splicing Variants are Expressed in Normal Mouse Organs." Journal of Radiation Research 53, no. 2 (2012): 234–41. http://dx.doi.org/10.1269/jrr.11029.

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34

Canugovi, Chandrika, Magdalena Misiak, Morten Scheibye-Knudsen, Deborah L. Croteau, Mark P. Mattson, and Vilhelm A. Bohr. "Loss of NEIL1 causes defects in olfactory function in mice." Neurobiology of Aging 36, no. 2 (February 2015): 1007–12. http://dx.doi.org/10.1016/j.neurobiolaging.2014.09.026.

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35

Kladova, Olga A., Inga R. Grin, Olga S. Fedorova, Nikita A. Kuznetsov, and Dmitry O. Zharkov. "Conformational Dynamics of Damage Processing by Human DNA Glycosylase NEIL1." Journal of Molecular Biology 431, no. 6 (March 2019): 1098–112. http://dx.doi.org/10.1016/j.jmb.2019.01.030.

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36

Minko, Irina G., Vladimir L. Vartanian, Naoto N. Tozaki, Oskar K. Linde, Pawel Jaruga, Sanem Hosbas Coskun, Erdem Coskun, et al. "Characterization of rare NEIL1 variants found in East Asian populations." DNA Repair 79 (July 2019): 32–39. http://dx.doi.org/10.1016/j.dnarep.2019.05.001.

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37

McNeill, Daniel R., Manikandan Paramasivam, Jakita Baldwin, Jing Huang, Vaddadi N. Vyjayanti, Michael M. Seidman, and David M. Wilson. "NEIL1 Responds and Binds to Psoralen-induced DNA Interstrand Crosslinks." Journal of Biological Chemistry 288, no. 18 (March 18, 2013): 12426–36. http://dx.doi.org/10.1074/jbc.m113.456087.

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38

Hailer, M. Katie, Peter G. Slade, Brooke D. Martin, Thomas A. Rosenquist, and Kent D. Sugden. "Recognition of the oxidized lesions spiroiminodihydantoin and guanidinohydantoin in DNA by the mammalian base excision repair glycosylases NEIL1 and NEIL2." DNA Repair 4, no. 1 (January 2005): 41–50. http://dx.doi.org/10.1016/j.dnarep.2004.07.006.

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39

Hildrestrand, Gunn A., Veslemøy Rolseth, Magnar Bjørås, and Luisa Luna. "Human NEIL1 localizes with the centrosomes and condensed chromosomes during mitosis." DNA Repair 6, no. 10 (October 2007): 1425–33. http://dx.doi.org/10.1016/j.dnarep.2007.04.008.

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40

Vik, Erik Sebastian, Ingrun Alseth, Monika Forsbring, Ina Høydal Helle, Ingrid Morland, Luisa Luna, Magnar Bjørås, and Bjørn Dalhus. "Biochemical mapping of human NEIL1 DNA glycosylase and AP lyase activities." DNA Repair 11, no. 9 (September 2012): 766–73. http://dx.doi.org/10.1016/j.dnarep.2012.07.002.

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41

Yeo, J., R. A. Goodman, N. T. Schirle, S. S. David, and P. A. Beal. "RNA editing changes the lesion specificity for the DNA repair enzyme NEIL1." Proceedings of the National Academy of Sciences 107, no. 48 (November 10, 2010): 20715–19. http://dx.doi.org/10.1073/pnas.1009231107.

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42

Vartanian, V., B. Lowell, I. G. Minko, T. G. Wood, J. D. Ceci, S. George, S. W. Ballinger, C. L. Corless, A. K. McCullough, and R. S. Lloyd. "The metabolic syndrome resulting from a knockout of the NEIL1 DNA glycosylase." Proceedings of the National Academy of Sciences 103, no. 6 (January 30, 2006): 1864–69. http://dx.doi.org/10.1073/pnas.0507444103.

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43

Zhou, R., S. Hao, Y. Zeng, D. Ai, H. Zhu, Q. Liu, J. Deng, K. Zhao, and Y. Chen. "NEIL1 rs4462560 Affects Acute Radiation-Induced Lung Injury Via MAPK/JNK Pathway." International Journal of Radiation Oncology*Biology*Physics 108, no. 3 (November 2020): e508-e509. http://dx.doi.org/10.1016/j.ijrobp.2020.07.1602.

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44

Dou, Hong, Corey A. Theriot, Aditi Das, Muralidhar L. Hegde, Yoshihiro Matsumoto, Istvan Boldogh, Tapas K. Hazra, Kishor K. Bhakat, and Sankar Mitra. "Interaction of the Human DNA Glycosylase NEIL1 with Proliferating Cell Nuclear Antigen." Journal of Biological Chemistry 283, no. 6 (November 21, 2007): 3130–40. http://dx.doi.org/10.1074/jbc.m709186200.

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45

Yamamoto, Ryohei, Yukari Ohshiro, Tatsuhiko Shimotani, Mizuki Yamamoto, Satoshi Matsuyama, Hiroshi Ide, and Kihei Kubo. "Hypersensitivity of mouse NEIL1-knockdown cells to hydrogen peroxide during S phase." Journal of Radiation Research 55, no. 4 (April 4, 2014): 707–12. http://dx.doi.org/10.1093/jrr/rru021.

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46

Cao, Jing-Hua, Chen-Hui Cao, Jin-Long Lin, Si-Yu Li, Long-Jun He, Kai Han, Jie-Wei Chen, et al. "NEIL1 drives the initiation of colorectal cancer through transcriptional regulation of COL17A1." Cell Reports 43, no. 1 (January 2024): 113654. http://dx.doi.org/10.1016/j.celrep.2023.113654.

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47

Zhai, Xiaodong, Hui Zhao, Zhensheng Liu, Li-E. Wang, Adel K. El-Naggar, Erich M. Sturgis, and Qingyi Wei. "Functional Variants of the NEIL1 and NEIL2 Genes and Risk and Progression of Squamous Cell Carcinoma of the Oral Cavity and Oropharynx." Clinical Cancer Research 14, no. 13 (July 1, 2008): 4345–52. http://dx.doi.org/10.1158/1078-0432.ccr-07-5282.

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48

Thompson, Marlo K., Nidhi Sharma, Andrea Thorn, and Aishwarya Prakash. "Deciphering the crystal structure of a novel nanobody against the NEIL1 DNA glycosylase." Acta Crystallographica Section D Structural Biology 80, no. 2 (January 30, 2024): 137–46. http://dx.doi.org/10.1107/s205979832400038x.

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Nanobodies (VHHs) are single-domain antibodies with three antigenic CDR regions and are used in diverse scientific applications. Here, an ∼14 kDa nanobody (A5) specific for the endonuclease VIII (Nei)-like 1 or NEIL1 DNA glycosylase involved in the first step of the base-excision repair pathway was crystallized and its structure was determined to 2.1 Å resolution. The crystals posed challenges due to potential twinning and anisotropic diffraction. Despite inconclusive twinning indicators, reprocessing in an orthorhombic setting and molecular replacement in space group P21212 enabled the successful modeling of 96% of residues in the asymmetric unit, with final R work and R free values of 0.199 and 0.229, respectively.

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49

Soumya, Kallyadan, Karickal Raman Haridas, Jesna James, and Sudhakaran Sudheesh. "Isolation of a novel quercetin derivative from Terminalia chebula and RT-PCR-assisted probing to investigate its DNA repair in hepatoma cells." Research in Pharmaceutical Sciences 19, no. 3 (May 2024): 303–18. http://dx.doi.org/10.4103/rps.rps_56_23.

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Background and purpose: DNA damage can lead to carcinogenesis if replication proceeds without proper repair. This study focused on the purification of a novel quercetin derivative present in Terminalia chebula fruit and studied its protective role in hepatoma cells due to H2O2-DNA damage. Experimental approach: The pure compound obtained from the silica gel column was subjected to structural characterization using spectroscopic techniques. MTT assay was employed to select a non-toxic concentration of the isolated compounds on HepG2 and Chang liver cells. The antigenotoxic property of the compound on HepG2 and Chang liver cells was carried out by alkaline comet assay. Analyses of expression levels of mRNA for two DNA repair enzymes, OGG1 and NEIL1, in HepG2 and Chang liver cells, were carried out using the RT-PCR method. Findings/Results: The pure compound obtained from the fraction-5 of diethyl ether extract was identified as a novel quercetin derivative and named 7-(but-2-en-1-yloxy)-2-(4(but-2-en-1-yloxy)-3-hydroxyphenyl)-3- (hexa-2,4-dien-1-yloxy)-6-hydroxy-4H-chromen-4-one. This compound recorded modest toxicity at the highest concentration tested (percentage cell viability at 100 μg/mL was 64.71 ± 0.38 for HepG2 and 45.32 ± 0.07 for Chang liver cells). The compound has demonstrated noteworthy protection against H2O2-induced DNA damage in both cell lines. Analyses of mRNA expression levels for enzymes OGGI and NEIL1 enzymes in HepG2 and Chang liver cells asserted the protective role of the isolated compound against H2O2-induced DNA damage. Conclusion and implication: The protective effect of a novel quercetin derivative isolated from T. chebula in the hepatoma cells is reported here for the first time.

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Galick, Heather A., Carolyn G. Marsden, Scott Kathe, Julie A. Dragon, Lindsay Volk, Antonia A. Nemec, Susan S. Wallace, Aishwarya Prakash, Sylvie Doublié, and Joann B. Sweasy. "The NEIL1 G83D germline DNA glycosylase variant induces genomic instability and cellular transformation." Oncotarget 8, no. 49 (September 8, 2017): 85883–95. http://dx.doi.org/10.18632/oncotarget.20716.

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