Data on HepG2 cells changes following exposure to cadmium sulphide quantum dots (CdS QDs)

The data included in this paper are associated with the research article entitled "Markers for toxicity to HepG2 exposed to cadmium sulphide quantum dots; damage to mitochondria" (Paesano et al.) [1]. The article concerns the cytotoxic and genotoxic effects of CdS QDs in HepG2 cells and the mechanisms involved. In this dataset, changes in expression levels of candidate genes are reported, together with details concerning synthesis and properties of CdS QDs, additional information obtained through literature survey, measures of the mitochondrial membrane potential and the glutathione redox state.


a b s t r a c t
The data included in this paper are associated with the research article entitled "Markers for toxicity to HepG2 exposed to cadmium sulphide quantum dots; damage to mitochondria" (Paesano et al.) [1]. The article concerns the cytotoxic and genotoxic effects of CdS QDs in HepG2 cells and the mechanisms involved. In this dataset, changes in expression levels of candidate genes are reported, together with details concerning synthesis and properties of CdS QDs, additional information obtained through literature survey, measures of the mitochondrial membrane potential and the glutathione redox state.

Subject area
Biology More specific subject area

Toxicogenomics, transcriptomics
Type of data HepG2 cells were exposed to a toxic acute dose of CdS QDs corresponding to the IC 50 , and to two sub-toxic doses for different time periods Experimental features Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (v/v) fetal bovine serum (FBS), 50 U mL À 1 penicillin/streptomycin and 1% (w/v) L-glutamine in an incubator at 37°C and 5% CO 2 Data source location

Parma, Italy
Data accessibility Data are available within this article

Value of the data
The dataset provides a list of candidate genes useful for comparing effects of nanomaterials in other cell systems.
The data may be useful for other researchers analysing mitochondrial dysfunctionalities in stressed cells.
The literature survey may be useful for planning additional experiments on risk assessment of cadmium-based quantum dots.
1. Data Table 1 shows a survey of the most recent literature on experimentation with animal cell lines and cadmium-based quantum dots. It details the main parameters which can be assessed to estimate the functionality and viability of cells and describes the main changes detected in cells. Particular reference has been made to instances of oxidative stress, apoptosis and autophagy. In addition Table 2 reports a comparison of the effects of exposure to CdS QDs and Cd 2þ ions. Table 3 reports in details the experimental conditions chosen for treating HepG2 cells with CdS QDs. Table 4 lists the changes in gene expression of candidate genes upon exposure to toxic and subtoxic doses of CdS QDs. Genes are grouped according to their involvement in relevant cellular processes. Table 5 lists the changes in gene expression determined after quantitative reverse transcriptase PCR (qRT-PCR) for specific genes chosen on the basis of their involvement in relevant cellular processes.

Synthesis and characterization of CdS QDs
The method 1 used to synthesize CdS QDs followed Villani et al. [28], and the synthesis was performed by IMEM-CNR (Parma, Italy). X-ray diffraction (XRD) was carried out using an ARL-X'Tra device (Thermo Fisher Scientific, Waltham, MA, USA). A field emission high resolution (Scherzer resolution of $ 0.19 nm) JEM-2200 FS transmission electron microscope (JEOL Ltd., Tokyo, Japan)  Most of the induced genes belonged to one of the three major functional categories "apoptosis", "autophagy" and "stress response" CdS QDs did not induce a rapid ROS generation, causing only mild increase in reactive oxygen species (ROS) levels Exposure to CdS QDs generated, in HepG2 cells, a minor degree of DNA damage; after a major exposure, the extent of the damage was almost indistinguishable from that shown by the non-treated control The data suggest that mitochondriamediated intrinsic apoptosis pathway were activated by CdS QDs exposure, but did not arrive at the extreme point (mtDNA distruption, cell death)

Cadmium
Cadmium induces at least two types of genes: (1) genes coding for detoxifying and other cytoprotective proteins, i.e. metallothioneins, enzymes of glutathione synthesis, heat shock proteins, zinc transporter proteins; and (2) early genes response proto-oncogenes related to cell proliferation control (c-FOS, c-JUN, c-MYC, EGR-1) [22] Cadmium induces a rapid and transient ROS generation [23], causing formation of superoxide ion and hydrogen peroxide [24]. The major toxic effects of increasing doses of Cd concentration involve decreased antioxidant enzyme levels (superoxide dismutase and glutathione peroxidase) [25] Cadmium causes DNA fragmentation [23] Oh and Lim [23] demonstrated that Cdinduced cell death was caspasedependent Several authors report the view that genotoxicity induced by Cd is not a direct effect of the metal, but rather due to the generation of reactive oxygen free radicals and the resulting oxidative stress [26] Cd exhibits remarkable potential to inhibit DNA damage repair, and this has been identified as a major mechanism underlying the carcinogenic potential of Cd      Multifunctional transcription factor in ER stress response. Plays an essential role in the response to a wide variety of cell stresses and induces cell cycle arrest and apoptosis in response to ER stress DNAJB9 (HSP40) DnaJ homolog subfamily B member 9 Involved in endoplasmic reticulum-associated degradation (ERAD) of misfolded proteins. Acts as a co-chaperone with an Hsp70 protein

LONP1
Lon protease homolog, mitochondrial ATP-dependent serine protease that mediates the selective degradation of misfolded, unassembled or oxidatively damaged polypeptides as well as certain short-lived regulatory proteins in the mitochondrial matrix. May also have a chaperone function in the assembly of inner membrane protein complexes. Participates in the regulation of mitochondrial gene expression and in the maintenance of the integrity of the mitochondrial genome. Binds to mitochondrial promoters and RNA in a single-stranded, sitespecific, and strand-specific manner. May regulate mitochondrial DNA replication and/ or gene expression using site-specific, single-stranded DNA binding to target the degradation of regulatory proteins binding to adjacent sites in mitochondrial promoters 3.157 3.041

SIRT1
NAD-dependent protein deacetylase sirtuin-1 NAD-dependent protein deacetylase that links transcriptional regulation directly to intracellular energetics and participates in the coordination of several separated cellular   3 lg mL À 1 7 lg mL À 1 14 lg mL À 1 Apoptosis AIFM2 Apoptosis-inducing factor 2 Oxidoreductase, which may play a role in mediating a p53/TP53-dependent apoptosis response. Probable oxidoreductase that acts as a caspase-independent mitochondrial effector of apoptotic cell death Calcium/calmodulin-dependent serine/threonine kinase involved in multiple cellular signaling pathways that trigger cell survival, apoptosis, and autophagy. Regulates both type I apoptotic and type II autophagic cell deaths signal, depending on the cellular setting. The former is caspase-dependent, while the latter is caspase-independent and is characterized by the accumulation of autophagic vesicles

LONP1
Lon protease homolog, mitochondrial ATP-dependent serine protease that mediates the selective degradation of misfolded, unassembled or oxidatively damaged polypeptides as well as certain short-lived regulatory proteins in the mitochondrial matrix. May also have a chaperone function in the assembly of inner membrane protein complexes. Participates in the regulation of mitochondrial gene expression and in the maintenance of the integrity of the mitochondrial genome. Binds to mitochondrial promoters and RNA in a singlestranded, site-specific, and strand-specific manner. May regulate mitochondrial DNA replication and/or gene expression using site-specific, single-stranded DNA binding to target the degradation of regulatory proteins binding to adjacent sites in mitochondrial promoters  200 kV, was used to examine QD structure. The aggregation of a group of QDs following solvent evaporation (Fig. 1a) was due to the lack of capping molecules at the QD surface. The corresponding reduced Fourier transform (FT) in the inset confirms the hexagonal structure (greenockite, P63mc) of as-synthesized CdS QDs (d ¼ 0.36 nm in agreement with standard card JCPDS no. 80-0006). The FT of the whole high resolution transmission electron microscope (HRTEM) image is presented in Fig. 1b. The expected ring feature arising from the random orientation of CdS crystals is clear, as is the overlap of (100), (002) and (101) reflections of the wurtzite structure (at high d values) due to low dimension peak broadening. Such features are in agreement with the XRD pattern shown in Fig. 1c. All peaks have been indexed according to the structure of greenockite and no other reflections arising from possible impurities are observed. A Scherrer calculation based on the FWHM (full width at half maximum) of the three main peaks produced an estimated mean size of $ 6 nm. An ESEM (environmental scanning electron microscopy) Quanta 250FEG (FEI Co., Hillsboro, OR, USA) together with a QUANTAX EDS (energy-dispersive systems) XFlash s 6T detector series and the ESPRIT 2 analytical methods interface (Bruker, Berlin, Germany) was used to determine CdS QDs morphology and elemental content. Single 1 mL drops containing 80 mg L À 1 CdS QDs were left to dry on an scanning electron microscopy (SEM) stub covered with carbon tape in a protected environment. Seven stubs were analysed during one round of experiments. The working parameters for SEM imaging and X-ray spectra acquisition were: pressure: 70 Pa, working distance: 9.9 mm, acceleration voltage: 20 KeV. SEM images of a CdS QDs drop at 29,750x magnification (Fig. 2a) and at 130,802x magnification (Fig. 2b) show the nanocrystals are grouped into small agglomerates of 50-100 nm. The energydispersive X-ray analysis (EDX) (Fig. 2c)

Cytotoxicity assay
The cytotoxicity of the CdS QDs (Fig. 4) was evaluated by CellTiter 96 s AQ ueous One Solution Cell Proliferation Assay (Promega, Madison, WI, USA) according to the manufacturer's protocol. In this assay, cell viability was assumed to be proportional to the quantity of formazan generated by the reduction of MTS. Data obtained were also used in Paesano et al. [1].

Assay on mitochondrial integrity
HepG2 cells were exposed to a range of CdS QDs concentrations and were subsequently stained for 30 min in 40 nM rhodamine B hexyl ester (ThermoFisher Scientific, Waltham, MA, USA), rinsed in PBS, harvested by centrifugation (800 g, 5 min) and re-suspended in PBS with 1% (v/v) FBS. The suspension was analyzed using a FC500 flow cytometer (Beckman Coulter Inc.) (Fig. 6).

Analysis of transcriptomic data
The data reported in Table 4 were analysed to build a heat map (Fig. 7) depicting the hierarchical clustering of genes according to their expression profile. Moreover, data were summarized in a scheme that highlights the interactions between the different cellular processes involved (Fig. 8). Fig. 8. Scheme of the interaction between the intrinsic apoptosis, autophagy and stress response pathways governing the HepG2 response to CdS QDs. Up-regulation is indicated by red arrows and down-regulation by green arrows. Mitochondrial dysfunction is linked to oxidative stress, as the mitochondria are both generators of, and targets for ROS. CdS QDs may undergo autophagic sequestration and then selective compartmentalization in autophagosome, leading to a dysfunctional autophagic pathway due to the inhibition of autophagic flux. The effect could also be associated with an accumulation of ubiquitinated proteins.

Transparency document. Supplementary material
Transparency document associated with this paper can be found in the online version at http://dx. doi.org/10.1016/j.dib.2016.12.051.