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Ecotoxicology and Human Environmental Health
Molecular Toxicity of Metal Oxide Nanoparticles in Danio rerio Jing Hou, Haiqiang liu, Luyao Wang, Linshuai Duan, Shiguo Li, and Xiangke Wang Environ. Sci. Technol., Just Accepted Manuscript • DOI: 10.1021/acs.est.8b01464 • Publication Date (Web): 26 Jun 2018 Downloaded from http://pubs.acs.org on July 1, 2018
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Molecular Toxicity of Metal Oxide Nanoparticles in Danio rerio
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Jing Hou a, Haiqiang Liu a, Luyao Wang a, Linshuai Duan a, Shiguo Li b*, Xiangke Wang a*
3
a
4
Beijing 102206, China
5
b
6
China
College of Environmental Science and Engineering, North China Electric Power University,
Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing 100085,
7 8
ABSTRACT
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Metal oxide nanoparticles can exert adverse effects on humans and aquatic organisms, however,
10
their toxic mechanisms are still unclear. We investigated the toxic effects and mechanisms of
11
copper oxide, zinc oxide, and nickel oxide nanoparticles in Danio rerio using microarray analysis
12
and the comet assay. Copper oxide nanoparticles were more lethal than the other metal oxide
13
nanoparticles. Gene ontology analysis of genes that were differentially expressed following
14
exposure to all three metal oxide nanoparticles showed that the nanoparticles mainly affected
15
nucleic acid metabolism in the nucleus via alterations in nucleic acid binding. KEGG analysis
16
classified the differentially expressed genes to the genotoxicity-related pathways “cell cycle”,
17
“Fanconi anemia”, “DNA replication”, and “homologous recombination”. The toxicity of metal
18
oxide nanoparticles may be related to impairments in DNA synthesis and repair, as well as to
19
increased production of reactive oxygen species.
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INTRODUCTION
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With the rapid development of nanotechnology, a wide range of metal oxide nanoparticles
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(MO-NPs) have been incorporated into various commercial products such as food, sunscreen, and
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electronic and medical devices because of their superior magnetism, conductivity, reactivity, and
25
optical properties
26
through sewage
27
tissues and cells of aquatic organisms
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beings as the ultimate reservoir
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biological systems, causing cytotoxicity, inflammation, and cell membrane leakage
30
thorough understanding of the toxicity of MO-NPs, from molecular mechanisms to physiology
31
and morphology, is required to mitigate their adverse effects. However, the study on the molecular
32
mechanisms of MO-NPs is not clear, which is not conducive to the scientific assessment and
33
prediction of the ecological risk of NPs.
[1, 2]
. Inevitably, MO-NPs are released into the aquatic environment, especially
[3, 4]
. The small MO-NPs (27-nm TiO2 and 24-nm CeO2) can easily enter the [5]
, and thereby accumulate up the food chain, with human
[6]
. Multiple studies have demonstrated that MO-NPs can impair [7-9]
. A
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Many of the published studies have been devoted to assessing the environmental risk of NPs by
35
observing responses at the whole-organism level, including growth inhibition [10], reproduction [11],
36
and mortality
37
require higher exposure doses, when low doses not causing large-scale damage may in fact induce
38
effects sufficient to disrupt normal function
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powerful experimental tool for assessing cellular alterations at the transcriptional level
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expression analysis can provide information on low-level toxic effects at lower concentrations and
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elucidate the underlying molecular mechanisms [15, 16]. Moreover, the complex constituents of
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contaminants discharged into the aqueous environment render research with traditional endpoints
43
unsuited. As a sensitive high-throughput genomic technology
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microarrays can screen multiple contaminants rapidly [18]. The responses of fish to environmental
45
toxicants have been studied in the fathead minnow Pimephales promelas
46
caeruleum
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latipes [23].
48
[12]
. These traditional toxicological endpoints are time-consuming and generally
[20]
, Cyprinus carpio
[18]
[13]
. In this context, microarray technology is a
, Gasterosteus aculeatus
[14]
. Gene
[17]
, expression profiling with
[19]
, Etheostoma
[21]
, Salmo trutta [22], and Oryzias
Understanding the toxic effects and mechanisms of MO-NPs requires the use of representative [24]
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research species. Fish are a preferred model in the study of NP toxicity to aquatic organisms
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Danio rerio has long been used as a model organism of vertebrate molecular developmental
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biology [25]. As a model organism recommended by the Organization for Economic Co-operation
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and Development (OECD)
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[27, 28]
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genome is 70% homologous to the human genome, permitting some extrapolations to humans [31].
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D. rerio adults are highly fecund, and embryos are transparent and easy to handle [32], allowing the
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study of embryonic toxicity and malformation [13].
[26]
, D. rerio is gaining recognition in the fields of aquatic toxicology
drug discovery, and disease research
[29]
because of its characteristics [30]. The D. rerio
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The aim of this study was to investigate the transcriptional toxicity of MO-NPs on D. rerio and
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to explore its toxicity mechanisms of various MO-NPs in the same valence state. We used
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microarrays to identify differentially expressed genes (DEGs) common to copper oxide (CuO),
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zinc oxide (ZnO), and nickel oxide (NiO) NP exposure. Next, we used bioinformatics approaches
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to suggest the molecular mechanism of toxicity. These findings contribute to our understanding of
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the toxicity of MO-NPs to aquatic organisms, and are of significance in evaluating the ecological
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risk of MO-NPs.
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MATERIALS AND METHODS
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D. rerio maintenance. All experimental D. rerio were kindly provided by the Chinese Research
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Academy of Environmental Sciences. D. rerio were 5 months old and had an average length of 2.8
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cm and an average weight of 12.5 g. Fish were healthy and free of any signs of disease. During the
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acclimation period (not less than 14 days), D. rerio were housed in 60-L tanks (40 cm height × 30
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cm width × 50 cm length) at a maximum density of seven D. rerio per liter. The tanks were filled
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with water previously treated by aeration and kept under filtration at a temperature of 24 ± 2°C
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and pH of 7.0-8.0. Fish were fed commercially available dry flakes twice a day. Dead fish were
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removed in a timely manner and the cumulative mortality did not exceed 2%.
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Preparation of NPs. CuO NPs (< 50 nm), ZnO NPs, (< 50 nm), and NiO (< 50 nm) were
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purchased from Sigma-Aldrich (St. Louis, MO, USA). Stock solutions were prepared by
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dispersing nanopowders in distilled water and sonicating at 600 W and 40 kHz for 30 min to
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decompose aggregates prior to dilution to exposure concentrations. The hydrodynamic size
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distribution and zeta potential of freshly prepared and 96-h aged NP solutions were determined
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using a Malvern Zetasizer Nano-ZS instrument (Malvern, UK).
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Experimental design. After two weeks of acclimation, D. rerio were exposed to eight
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concentrations of each NP solution (ZnO: 1.0, 2.0, 4.0, 8.0, 16.0, 32.0, 64.0, and 128.0 mg/L; CuO:
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0.0625, 0.125, 0.25, 0.5, 1.0, 2.0, 4.0, and 8.0 mg/L; NiO: 2.0, 4.0, 8.0, 16.0, 32.0, 64.0, 128.0,
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and 256.0 mg/L) with a day/night cycle of 16/8 h. Three biological replicates were used in each
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treatment and each replicate consisted of 10 individuals. D. rerio were exposed for 96 h without
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feeding. Survival rates were recorded each day and the median lethal concentration (LC50) was
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calculated using the probit method. All subsequent exposures for the microarray, real-time
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quantitative PCR (RT-qPCR), and comet assays were performed using one-tenth of the LC50 for
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each NP solution (0.2 mg/L CuO, 4.8 mg/L ZnO, and 17.5 mg/L NiO). These concentrations have
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been shown to fall below the level causing specific gene expression responses
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were sacrificed for each treatment, and the gills were pooled as a sample. Three biological
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replicates were used for each treatment.
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Microarray Analysis. Agilent zebrafish (V3) gene expression microarray (4x44K) were used in
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our study. Total RNA was isolated from the gills of D. rerio exposed to the NPs and the controls
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using Trizol reagent (Invitrogen, Carlsbad, CA, USA). To remove contaminated DNA, the
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isolated RNA sample was digested with DNase I at 37°C for 15 min. To avoid dye-based bias, the
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RNA sample was then labeled with cyanine 5 and cyanine 3 using the Low Input QuickAmp
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Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) with a dye swap design. RNeasy
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Plant Mini Kit (Qiagen, Hilden, Germany) was used to purify the labeled cRNA, which was then
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fragmented and hybridized on a D. rerio microarray. Fifteen micrograms of the fragmented cRNA
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were hybridized to each microarray at 45°C for 15 h in an Affymetrix GeneChip Hybridization
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Oven 640 (Affymetrix, Santa Clara, CA, USA). The microarray was washed after hybridization.
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Streptavidin phycoerythrinonan was used to stain the microarray on an Affymetrix Fluidics
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Station 450 (Affymetrix), and a GeneChip Scanner 3000 7G (Affymetrix) was used to scan the
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microarray. Three replicate experiments were conducted using cRNA prepared independently
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from individual D. rerio. Microarray data were further analyzed with Microarray Suite version 5.0
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at the default settings, and global scaling was used as the normalization method. Genes with a
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false discovery rate-adjusted fold-change ≥ 2 and p-value < 0.05 were considered differentially
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expressed.
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Bioinformatics Analysis. Gene ontology (GO) enrichment of the obtained DEGs was analyzed
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using R and corrected for gene-length bias. The DEGs were then checked against the Kyoto
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Encyclopedia of Genes and Genomes (KEGG) database (http://www.genome.jp/kegg/) to identify
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significantly enriched KEGG pathways (p-value < 0.01). Principal component analysis (PCA) was
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used to plot numeric data from experimental observations.
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RT-qPCR. We performed RT-qPCR to validate the reliability of the microarray data. Total RNA
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was isolated from D. rerio samples and purified according to the methods described above.
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First-strand cDNA was synthesized using a Superscript III First-Strand Synthesis kit (Invitrogen).
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RT-qPCR was performed using a reaction system of 2 × SYBR Premix Ex TaqII (Takara, Shiga,
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Japan) with 0.2 µM of each primer, 100 ng cDNA, and PCR-grade water on a 7500 Fast
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Real-Time PCR system (Applied Biosystems, Foster City, CA, USA). The reaction conditions
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were as follows: One cycle of 55°C for 3 min and 95°C for 3 min for initial denaturation, and 40
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cycles of 95°C for 15 s and 60°C for 30 s. Each sample was analyzed three times. Dr-ACTIN was
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used as a housekeeping reference gene. Primers used in RT-qPCR were all designed using the
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Primer3 online program (http://primer3.ut.ee/). The 2-∆∆CT method was used to calculate the
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fold-changes of the selected genes in D. rerio exposed to the MO-NPs. Fold-change data
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are presented as the mean ± standard error from three biological replicates.
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Comet assay. The assay was performed following the method of Collins
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modification. Briefly, after treatment according to the protocol above, 1% trypsin was added to
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cells, and the supernatant was removed after centrifugation for 4 min at 500 × g. Cells were
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washed and re-suspended in 85 µL phosphate-buffered saline. More than 2.5 × 104 cells were
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obtained in 200 µL of 0.5% low-melting agarose gel. Before solidification, classic slides were
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treated and covered with a thin layer of normal-melting-point agarose. After preheating to 37°C in
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a water bath, a total of 85 µL of sample were dripped onto slides, coverslipped, and refrigerated at
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4°C for 5 min to solidify. The gels were then incubated in a freshly prepared lysis solution (pH
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10.0; 2.5 M NaCl, 10% dimethyl sulfoxide, 1% Na lauroylsarcosinate, 100 mM Na2 EDTA, 10
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mM Tris-HCl, and 1% Triton X-100) at 4°C overnight. After lysis, running buffer (300 mM
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NaOH, 1 mM EDTA, pH > 13) was added onto the slides. The slides were incubated for 20 min
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and then subjected to horizontal electrophoresis at 10°C and 200 mA for 25 min. Finally, the
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slides were neutralized in a solution of 0.4 mol/L Tris-HCl (pH 7.5), washed, and dried at 37°C.
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DNA damage in individual cells was identified by an epifluorescence microscope (Olympus BX50,
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Tokyo, Japan) under 400× magnification. The tail moment was used to indicate the degree of
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DNA damage. Each sample was randomly measured for 30 tail lengths, and the data were
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averaged.
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RESULTS
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Lethality. D. rerio were exposed to eight concentrations of CuO, ZnO, and NiO NPs for 96 h. The
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survival rate following exposure to low concentrations was comparable to that of the control
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(Figure 1). Survival decreased sharply in a concentration-dependent manner. The 96-h LC50 values
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for CuO, ZnO, and NiO NPs were 2.25, 48.2, and 175 mg/L, respectively, demonstrating that CuO
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NPs were the most toxic.
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NP characteristics. Table 1 shows that the 96-h hydrodynamic diameter of the NPs was greater
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than the diameter at baseline. The absolute value of the 96-h zeta potential also increased from
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baseline measurements. These results indicate that the MO-NPs aggregate and tend to stabilize
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after 96 h of exposure. In addition, the 96-h zeta potential measurements suggest that the CuO NPs
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were more stable than the other NPs and could resist aggregation, resulting in smaller particles.
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Differential expression. We used volcano plots to illustrate the distribution of DEGs by statistical
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significance and fold-change between treated and control D. rerio. A total of 10,671, 8,680, and
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8,382 DEGs were identified for CuO, ZnO, and NiO NPs, respectively (fold-change > 2.0 and
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p-value < 0.5) (Figure 2A–C, File S1). The number of down-regulated genes was greater than the
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number of up-regulated genes for all NP treatments. We also identified 4,792 DEGs that
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overlapped in all three treatments (Figure 2D), accounting for 33.5% of the total DEGs detected
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(File S2). Moreover, we identified 2,976 (20.8%), 1,434 (10.0%), and 1,237 (8.7%) DEGs that
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were specific for only CuO, ZnO, and NiO NP exposures, respectively.
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GO enrichment analysis. To assess the putative mechanisms of MO-NP toxicity, the 4,792 genes
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differentially expressed in all three treatments were subjected to GO enrichment analysis, which is
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used to predict the functions of DEGs. The results of the GO enrichment analysis were classified
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into three categories: 3,793 GO terms for biological processes, 615 terms for cellular components,
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and 1,370 terms for molecular function (File S3). The top terms in each category, sorted by
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p-value, demonstrated that nucleic acid metabolism (GO: 0090304) (p = 1.4 × 10−14) was the most
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enriched biological process term, the nucleus (GO: 0005634) (p = 5.8 × 10−14) was the most
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enriched cellular component term, and nucleic acid binding (GO: 0003676) (p = 8.3 × 10−15) was
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the most enriched molecular function term (Figure 3).
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KEGG Pathway Analysis of DEGs. Further insight into the biological function of the 4792
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co-expressed DEGs was gained by examining the distribution of DEGs across KEGG pathway
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analysis. A total of 147 KEGG pathways were obtained (File S4). Taking p-value < 0.01 as a
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threshold, four significantly enriched pathways cell cycle pathway (Figure S1, p=5.3×10-5),
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fanconi anemia pathway (Figure S2, p=0.1×10-2), DNA replication pathway (Figure S3, p=0.1×
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10-2) and homologous recombination pathway (Figure S4, p=0.2×10-2) were identified.
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PCA. We used PCA to compare the similarities and differences of treatment effects, and determine
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which treatments were most responsible for the variations observed. Figure 4 illustrates a
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three-dimensional PCA plot of the 12 replicates. The control group was significantly different
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from the treatment groups, and the results from the three NP exposures are located in a relatively
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concentrated region, suggesting that the toxic effects of CuO, ZnO, and NiO NPs on D. rerio were
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similar at the molecular level. The contributions of the first three principal components were
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35.21%, 25.62%, and 9.83%. The higher loads of samples from CuO and ZnO NP exposures
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treatment on the first component reflect the contribution of CuO and ZnO NPs to D. rerio toxicity.
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Microarray validation. Fifteen DEGs were selected at random from each treatment for a total of
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45 DEGs for RT-qPCR analysis to verify the reliability of microarray results. Table S1 gives
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detailed information on these genes and their fold-changes. Trends in all tested DEGs were
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consistent with their trends in microarray analysis (Figure 5). The results from the two methods
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correlated well, with correlation coefficients of 0.958, 0.935, and 0.929 for CuO, ZnO, and NiO
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NP exposures, respectively, confirming the accuracy and reliability of the microarray data.
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Comet Assay. All D. rerio treated with MO-NPs showed a tailing phenomenon, while the control
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group did not (Figure 6). The DNA tail moment caused by CuO NPs was 1.92 times greater than
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that of ZnO NPs and 2.09 times greater than that of NiO NPs. These results indicate that MO-NPs
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can damage the DNA structure of D. rerio cells, and are consistent with the results obtained from
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GO and KEGG analysis.
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DISCUSSION
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The present study found that the order of toxicity to D. rerio was CuO NPs > ZnO NPs > NiO NPs.
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Particle size is one of the factors that affect its toxicity. The negative charge on the surface of NPs
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increases as the zeta potential increases, leading to greater electrostatic repulsive force between
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NPs and to reduce aggregation. The 96-h zeta potential of CuO NPs was higher than that of ZnO
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and NiO NPs, indicating that CuO NPs were more stable and could resist aggregation, resulting in
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smaller particles. NiO NPs had the lowest zeta potential, indicating a tendency to coagulate or
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aggregate, resulting in larger particles. Aggregation can reduce the toxicity of NPs
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lowest toxicity was indeed observed for NiO NPs.
[35, 36]
, and the
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The expression of multiple genes involved in nucleic acid metabolism was dysregulated, which
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may lead to impairments in the synthesis and/or degradation of nucleic acids. The nucleotide is the
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basic nucleic acid unit, and nucleotide synthesis generally includes the chemical reaction of
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pentose sugar, phosphate, and nitrogenous base in the nucleus. In contrast, degradation of nucleic
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acid is a catabolic nuclear reaction, whereby partial nucleobases and nucleotides can be recycled
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to create new nucleotides, suggesting a complex relationship between degradation and synthesis.
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The expression of multiple genes involved in nucleic acid binding was also dysregulated by
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exposure to MO-NPs. Studies have demonstrated that DNA or RNA binding to proteins affects
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protein structure and function, leading to dysregulation of transcription, translation, DNA
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replication, DNA repair and chromosomal recombination, and RNA processing and translocation
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[37-39]
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rerio.
. Therefore, the GO enrichment analysis provided insights into the effects of MO-NPs on D.
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KEGG pathway analysis indicated that cell cycle, Fanconi anemia, DNA replication, and
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homologous recombination may be involved in the toxicity induced by MO-NPs. These four
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pathways are closely linked. The cell cycle in D. rerio incorporates several successive events,
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including the S phase (DNA replication), M phase (mitosis), and G1 and G2 phases.
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Cyclin-dependent kinases (CDKs) are important regulators of the cell cycle and typically contain
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two subunits, the activating cyclin subunit and the catalytic CDK subunit. CDKs can control the
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cell cycle phases by regulating the activities of their key substrates. Targets downstream of CDKs
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include multiple proteins such as origin recognition complex (ORC), minichromosome
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maintenance (MCM), cell division control (CDC), transcription factor E2F, and its regulator Rb.
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Cyclins usually form a complex with CDKs prior to involvement in the cell cycle process.
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Therefore, orderly cell division requires regular inactivation and activation of CDKs at specific
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points in the cell cycle process. We found that MO-NPs inhibited the expression of CDK1, CDK2,
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and CDK7 and their downstream target genes ORC, CDC6, CDC4, CDC5, CDC7, and MCM, but
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had no significant effect on the expression of CDK4, CDK6, E2F, or Rb. While MO-NPs are
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selective for the CDK gene family, they can inhibit key regulatory enzymes in the cell cycle,
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affecting DNA synthesis. These enzymes are involved in all phases of the cell cycle, suggesting
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that the effect of MO-NPs on D. rerio would not be isolated to one phase. In particular, the
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CycA-CDK2-Cdc6-ORC process has a more direct inhibitory effect on DNA synthesis.
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DNA replication is mainly accomplished during the S phase, and is termed “semi-conservative
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replication” because it contains both newly synthesized and original DNA. Both strands of the
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original DNA serve as templates for the opposite strands. DNA polymerases are enzyme families
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involved in DNA replication and are the rate-limiting factor in DNA replication. These enzymes
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synthesize DNA molecules from deoxyribonucleotides to create uniform DNA strands. Three
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DNA polymerase complexes have been identified in eukaryotes. The genes encoding DNA
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polymerases were down-regulated following exposure to MO-NPs, indicating that enzyme
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production decreased, reducing the efficiency of DNA replication and leading to a blocked S
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phase.
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Numerous studies have reported that NPs penetrating the nucleus through a nuclear pore may
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interact directly with chromosomal DNA. During interphase, NPs can bind or interact with DNA
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molecules, interrupting DNA replication and transcription
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NPs can bind to single-stranded DNA and then merge into a double-strand structure [43] In addition,
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NPs can disrupt mitosis or chromosomes by mechanical or chemical binding, leading to some
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vertebrate diseases. NPs can also induce primary genotoxicity by indirect contact with DNA, via
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interaction with nuclear proteins involved in DNA replication, transcription, and repair processes,
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or by interfering with cell cycle checkpoint functions and generating mitochondrial reactive
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oxygen species. Oxidative stress has been proposed as a mechanism of MO-NP toxicity in various
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organisms
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epithelial cells
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with acidic conditions (pH 4.5) that can dissolve MOs and release them as metal ions
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possible that CuO NPs may easily cross the cell membrane, and once inside the cell, may release
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Cu2+ and induce the production of reactive oxygen species or directly affect intracellular proteins.
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Cu2+ may also decrease cell viability by binding to DNA directly, resulting in DNA damage and
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cell death [47].
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[40-42]
. During DNA replication, carbon
[44]
. Studies have shown that MO-NPs can cross the cell membrane of respiratory [45]
. MO-NPs entering the cell will be transported to the lysosome, an organelle [46]
. It is
Several studies have suggested that the toxicity of MO-NPs is associated with oxidative stress,
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leading to DNA damage
and constant activation of DNA repair processes. DNA damage
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from environmental stressors typically includes double-strand breaks (DSBs). Homologous
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recombination is critical for the accurate repair of DSBs, and is a process of nucleotide sequence
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exchange between two identical or similar DNA molecules. Cells usually repair DSBs rapidly by
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homologous recombination. Recombinases are key rate-limiting enzymes in the homologous
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recombination process, and the RecA recombinase protein family is thought to have been inherited
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from a common ancestral recombinase. RecA is a 38-KDa recombinase necessary for repairing
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DNA damage and maintaining DNA integrity, and a functional and structural homolog of RecA
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has been identified in multiple species. Investigations into the evolutionary relationships between
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these recombinases in bacteria, eukaryotes, and archaea have indicated that they are monophyletic
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and may have originated from a common ancestor. Several recA-like genes have been identified in
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D. rerio, and all are essential for cell division, differentiation, and proliferation. In the present
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study, the RecA-like genes RAD51B, RAD52, RAD54, and XRCC2 were significantly
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down-regulated following exposure to MO-NPs. The protein encoded by RAD51B is a member of
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the RAD51 family, evolutionarily conserved proteins responsible for homologous recombination
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in DNA damage repair. RAD51B can interact with RAD51C to form a stable heterodimer, which
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can interact with other members of this protein family to effect DNA single-strand invasion.
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Moreover, RAD54 can closely interact with RAD51s to form a complex that participates in
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homologous recombination and DNA damage repair. Alterations in the expression of these genes
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are known to delay the G1 phase and cell apoptosis, suggesting a role for these proteins in DNA
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damage-sensing. RAD52 is a key regulator in DSB repair and homologous recombination via
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binding to the ends of single-stranded DNA, a process crucial to annealing complementary DNA
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strands. RAD52 can also interact with the DNA recombination protein RAD51, suggesting an
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underlying role of this complex in RAD51-related DNA recombination and repair.
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Down-regulating the expression of these genes can reduce the levels of the response proteins,
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affect the stability of the DNA strand and the single-strand invasion process during repair, and
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prevent efficient repair of damaged DNA. The comet assay results showed that the DNA tail
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moment increased significantly following exposure to MO-NPs, indicating that DNA damage
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occurred. DNA damage from environmental stressors can often be repaired effectively by
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homologous recombination. In this study, the MO-NPs not only influenced the cell cycle and
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DNA replication processes, but also suppressed homologous recombination, amplifying the effects
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on DNA replication and the cell cycle because the DSBs could not be effectively repaired by
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homologous recombination.
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Our analysis indicated effects on the Fanconi anemia pathway, suggesting that in addition to
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DSB damage, MO-NP exposure may also lead to DNA cross-link damage in D. rerio. DNA
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cross-link damage can block the formation of the DNA replication fork and affect the replication
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process. The DNA cross-link repair process is relatively complex, and the Fanconi anemia
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pathway is one effective repair method. Fanconi anemia is a rare genetic disease that can cause an
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impaired response to DNA damage, and each of its subtypes corresponds to a gene mutation. At
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least 12 protein families encoded by Fanconi anemia genes have been described. In the present
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study, the proteins FANCB, FANCC, FANCF, FANCG, and FANCI, as well as their interacting
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centromere protein MHF, core complex-associated protein FAAP24, and downstream target
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replication protein RPA, were down-regulated following exposure to MO-NPs. This indicates that
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the Fanconi anemia pathway was significantly inhibited by the exposure, hindering the repair of
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DNA cross-link damage. In particular, the decrease in RPA expression can establish a relationship
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between the Fanconi anemia pathway and homologous recombination or the repair of DSBs.
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DSBs in Fanconi anemia have been shown to occur in response to cross-linking agents
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indicating that the Fanconi anemia pathway is involved in repairing DSBs by homologous
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recombination. The Fanconi anemia, DNA replication, cell cycle, and homologous recombination
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pathways may therefore be closely related to the normal physiological processes in D. rerio, and
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impairment of these pathways may explain the toxic effects of MO-NPs at the molecular level.
[36]
,
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In this study, MO-NPs mainly affected nucleic acid metabolism in the nucleus via alterations in
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nucleic acid binding. The DEGs were mainly classified into the genotoxicity-related pathways
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“cell cycle”, “Fanconi anemia”, “DNA replication”, and “homologous recombination”. These
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results will help us to understand the nature of aquatic toxicity of NPs with different properties
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and have important scientific significance. In order to reduce the toxicity, the interaction and
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integration of NPs should be paid more attention in the future research.
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ASSOCIATED CONTENT
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Supporting Information Available: File S1 lists differentially expressed genes for CuO NPs, ZnO
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NPs, and NiO NPs. File S2 lists 4792 differentially expressed genes co-expressed in CuO NPs,
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ZnO NPs, and NiO NPs treatments. File S3 lists of enrichment GO terms for CuO NPs, ZnO NPs,
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and NiO NPs. File S4 lists of enriched KEGG pathways for CuO NPs, ZnO NPs, and NiO NPs.
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The Supporting Information is available free of charge on the ACS Publications website at DOI:
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10.1021/acs.est.XXXXX.
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AUTHOR INFORMATION
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* Corresponding authors:
[email protected] (Shiguo Li);
[email protected] (Xiangke Wang).
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Tel(Fax):+86-10-61772890
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Conflict of Interest: The authors declare no competing financial interest.
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Acknowledgments. Financial support from NSFC (21607043), the Youth Innovation Promotion
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Association, Chinese Academy of Sciences (2018054), the Open Project of Key Laboratory of
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Environmental Biotechnology, CAS (kf2016009), the Fundamental Research Funds for the
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Central Universities (2016ZZD06, 2018ZD11) are acknowledged.
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Table 1. The mean hydrodynamic diameter and zeta potential of copper oxide (CuO), zinc oxide
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(ZnO), and nickel oxide (NiO) nanoparticles (NPs) at baseline (0 h) and 96 h. Hydrodynamic diameter (nm)
ζ-potential (mV)
0h
96 h
0h
96 h
CuO NPs
45±11
348±33
-18.2±3.3
-36.6±5.6
ZnO NPs
55±9
686±59
-19.6±3.8
-29.6±4.8
NiO NPs
60±12
1225±96
-13.6±2.6
-23.9±4.9
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Figure 1. Survival curves of Danio rerio exposed to copper oxide (CuO), zinc oxide (ZnO), and
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nickel oxide (NiO) nanoparticles (NPs) for 96 h.
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Figure 2. Volcano plots illustrating the distribution of differentially expressed genes (DEGs) in
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Danio rerio treated with (A) copper oxide (CuO) nanoparticles (NPs), (B) zinc oxide (ZnO) NPs,
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and (C) nickel oxide (NiO) NPs relative to the control. The x axis indicates the fold-change of
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each gene on a log2 scale (fold change > 2). The y axis indicates the statistical significance of each
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gene on a log10 scale (p < 0.05). Each dot represents one gene. Green dots
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represent down-regulated DEGs. Red dots represent up-regulated DEGs. Black dots represent
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genes that were not differentially expressed. (D) Venn diagram illustrating the overlap of DEGs
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between the three treatments.
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Figure 3. Gene ontology (GO) enrichment analysis of differentially expressed genes (DEGs). The
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top 30 GO terms were sorted by p-value. The x-axis represents p-value on a log10 scale, and the
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y-axis is the GO functional classification. The GO enrichment analysis is divided into three
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categories: Biological processes, cellular components, and molecular functions.
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Figure 4. Three-dimensional principal component analysis score plot of Danio rerio exposure to
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copper oxide (CuO), zinc oxide (ZnO), and nickel oxide (NiO) nanoparticles (NPs). Each color
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represents an exposure and each point represents a replicate sample.
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Figure 5. Fifteen genes that were differentially expressed following exposure to (A) copper oxide,
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(B) zinc oxide, and (C) nickel oxide nanoparticles were selected at random for RT-qPCR analysis
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to verify the accuracy of microarray data. Each dot represents a gene.
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Figure 6. Effects of copper oxide (CuO), zinc oxide (ZnO), and nickel oxide (NiO) nanoparticles
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(NPs) on DNA damage in Danio rerio cells, detected by the comet assay.
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