A Toxicogenomics Approach To Identify New Plausible Epigenetic Mechanisms of Ochratoxin A Carcinogenicity in Rat
A Toxicogenomics Approach To Identify New Plausible Epigenetic Mechanisms of Ochratoxin A Carcinogenicity in Rat
doi:10.1093/toxsci/kfj017
Advance Access publication October 26, 2005
Since the carcinogenic mechanism remains obscure, there period of the study, animals were housed in cages on absorbent paper under
is still significant debate about the best model for human tightly controlled conditions (21 ± 1C, 55 ± 10% relative humidity, air-
exchange, 12-h light-dark cycle). Animal growth and welfare were monitored
risk assessment. Knowledge of the extent of a toxicant’s by regular weighing and daily surveillance. For the gene expression study, five
genotoxicity is vital in evaluating its potency as a carcinogen. time points were selected to represent early (7 and 21 days) and later (4, 7, and
At present, the genotoxic status of OTA is still unclear 12 months) responses. At each time point, four control and treated animals were
(Manderville, 2005; Turesky, 2005), mainly due to contradic- randomly chosen for tissue harvest. Kidneys and liver from these rats were im-
tory experimental evidence. (1) Applying 32P-postlabelling, mediately snap-frozen in liquid nitrogen. All handling and procedures were
carried out in accordance with the UK Animals (Scientific Procedures) Act 1986.
some authors have found low levels of DNA lesions in organs
of animals treated with OTA (Castegnaro et al., 1998; Faucet RNA isolation. Homogenates from liver and kidney tissue samples were
prepared with the FastPrep system (Q.BIOgene, Germany). Total RNA was
et al., 2004; Pfohl-Leszkowicz et al., 1993). These lesions have isolated using the Clontech Atlas Pure Total RNA Labeling System (BD
been interpreted as OTA-specific covalent DNA adducts, Biosciences, Switzerland) following the manufacturer’s protocol. Total RNAs
suggesting that OTA is a genotoxin sensu stricto. Such were treated with DNase I to remove genomic DNA contamination. RNA
a compound would require dose-response modeling for concentration was measured with the RiboGreen RNA quantification Kit
quantitative risk assessment. It has, however, also been (Molecular Probes, Eugene, OR) according to the manufacturer’s instruction.
Assessment of RNA quality and measurement of the 28S to 18S ratio were
suggested that OTA-mediated DNA lesions detected by 32P- performed by dynamic gel electrophoresis using the Agilent Bioanalyser
postlabelling may have arisen through indirect mechanisms (Agilent Biotechnologies, Germany).
rather than direct DNA-binding (Gautier et al., 2001b). (2) In
kidney and liver. The vertical axis of each dendrogram shows individually the gene expression study originated. The body weight of
selected probes, whereas the horizontal axis represents the clustering level at treated animals did not differ significantly from that of control
the time points studied (7 days, 21 days, 4 months, 7 months, and 12 months).
animals. All tumors that were found before the 2-year end point
Single value decomposition. The variability of gene modulation induced of the carcinogenicity study were from animals that had been
by OTA during the time was also investigated by a matrix factorization
technique equivalent to Principal Component Analysis (PCA), the singular
euthanized because of loss of condition. The first renal tumor
value decomposition (SVD) method (Alter et al., 2003). SVD method provides was found 75 weeks after OTA treatment commenced (Fig. 1).
a low-dimensional projection of the original dataset by its decomposition in The total incidence of animals with a renal tumor reached 25%
three quantities—the matrices containing the left- and right-singular vectors of (n ¼ 64) at the end of the study. At least 75% of these animals
the original data matrix, and the diagonal matrix containing the singular values. had unilateral renal carcinoma as determined by tumor size,
Clusters formed by the SVD method can be interpreted as the relative
frequencies with which a given gene is modulated at every one of the original
proliferating and disorganized histopathology, and abundance
single time points which, when combined, form the temporal modes of gene of metastasis (Mantle et al., in press).
modulation. Average from each SVD-generated cluster was performed in order
to evaluate the profile of the gene expression during the time. Gene Selection and Clustering
Real-time polymerase chain reaction (PCR). Several key genes, each of
which represents a category of genes found to be modulated by OTA, were
Applying the stringency criteria for selection of significantly
selected to validate the microarray data. RNA preparation, quantification, and differentiated genes, statistical analysis revealed that the
quality control were conducted as described above. RNA was converted to expression of 470 genes in the kidney and 233 genes in the
(Alpha Diagnostic, San Antonio, TX). Each blot was subsequently probed with
10
horseradish peroxidase linked to the specific secondary antibody. Chemilumi-
8
nescence of the immunoblots was detected using ECL solution (Pierce,
6
Rockford, IL). Membranes were wrapped in polythene film and exposed to
Kodak films. 4
2
0
70 75 80 85 90 95 100 105 110
RESULTS
Weeks of OTA-treatment
OTA treatment was generally well tolerated throughout the FIG. 1. Cumulative renal tumor incidence during the last quarter of live in
2-year carcinogenicity study from which the tissue samples for rats given OTA-contaminated diet continuously for up to 2 years.
OCHRATOXIN A CARCINOGENICITY 123
the predominant effect, with 60% and 56% of genes down- time (Figs. 2C and 2D). In both organs, eight clusters with
regulated in kidney and liver, respectively. differentiated time-dependent expression profile were identi-
Further analysis of the gene expression profile in kidney fied. The modulation of OTA-induced gene expression was
and liver was performed by application of a single value generally less than two-fold. The two main clusters include
decomposition (SVD) method along the time coordinate. The only genes that, over the five time points, are either continu-
mean fold-expression values were plotted as a function of ously up-regulated (31% in kidney, 25% in liver) or
124 MARIN-KUAN ET AL.
Glutathione metabolism
Cytochrome P450
Xenobiotics metabolism
Oxidoreductase activity
Apoptosis
Cell cycle
Biological function
Cell differentiation/development
Binding
Cell adhesion
Transporters
Regulation of transcription
Immune response
Metabolism
Miscellaneous
0 5 10 15 20 25 30 35 40 45
Number of genes
FIG. 3. Biological function clustering. Genes exhibiting at least 1.5-fold up- or down-regulation in kidney (white columns) and liver (black columns), plotted
as a function of the total number of genes in each category.
continuously down-regulated (47% in kidney, 27% in liver). No as being under transcriptional control of HNF4a (Table 2). Of
other clear and easily interpretable time-dependent trends, such interest was the finding that the mRNA specific for HNF4a
as an early and/or late response, could be observed. itself was down-regulated.
Grouping of genes modulated by OTA was performed Expression of many transporter genes was down-regulated in
according to their biological functions. For this analysis, a gene the kidney (Table 3). Several genes known as markers of kidney
ontology approach was applied to genes exhibiting at least 1.5- injury, cell regeneration, and oncogenesis were significantly
fold expression values. The number of genes attributed to each modulated by OTA. For example, the kidney injury molecule
functional class is depicted in Figure 3, showing a wide (KIM-1, 4.4-fold) and the survival markers c-myc (3.7-fold),
diversity of highly tissue-selective biological responses. In the Akt-1 (1.7-fold), Polo-like kinase (Plk, 1.5-fold), and Cdkn1a
kidney, genes involved in xenobiotic metabolism and oxida- alias p21 (2.3-fold) were up-regulated. The regucalcin (REG),
tive stress response were generally down-regulated by OTA, also known as the senescence marker protein 30 (Smp30), was
whereas this group of genes was much less modulated in the down-regulated more than 10-fold by OTA.
liver. Interestingly, many of these genes share the antioxidant Only small changes occurred in expression of genes known
regulatory element (ARE) as a regulatory motif (Table 1). to be involved in DNA synthesis and repair or in genes induced
Other gene classes, such as several enzymes involved in fatty as a result of DNA damage. Few genes associated with DNA
acid metabolism and cytochrome P450, were also selectively repair were slightly down-regulated. Similarly, very little or no
down-regulated in the kidney of OTA-treated animals. Many of effects were found on expression of apoptosis-related genes.
these genes possess a common promoter targeted by the Three genes involved in the regulation of protein synthesis
transcription factor hepatocyte nuclear factor alpha (HNF4a). were modulated by OTA. The prostaglandin F2 receptor nega-
Several genes, which belong to different functional classes and tive regulator (Ptgfrn) and the eukaryotic translation initia-
were down-regulated following OTA-treatment, were identified tion factor 4E binding protein 1 (Eif4ebp1) were up-regulated
OCHRATOXIN A CARCINOGENICITY 125
TABLE 1
Genes Modulated by OTA under Transcriptional Control of Nrf2
Accession no. Gene title Symbol Folda Fold 7D Fold 21D Fold 4M Fold 7M Fold 12M
Xenobiotic metabolism
X65296 carboxylesterase 3 Ces3 3.4* 1.5 9.8* 4.2* 3.3* 2.0*
M33747 UDP-glucuronosyltransferase 2 family, member 5 Ugt2b5 2.7* 2.5 1.3 5.2* 3.1 3.0
X81395 carboxylesterase 1 Ces1 1.9* 2.0 2.2 2.7 1.8 1.3
S81433 Heme-oxygenase 2/5# region HMOX2 1.6* 2.4 3.0* 1.1 1.0 1.6
AF045464 aflatoxin B1 aldehyde reductase Akr7a3/ Afar 1.5* 1.0 2.0* 2.1* 1.2 1.4
J02722cds heme oxygenase 1 Hmox1 2.1* 1.4 4.4 1.6* 1.3 3.2*
Carbon metabolism
AI008020 malic enzyme 1 Me1 1.8* 1.3 2.8* 3.2* 1.0 1.7
AJ005046 fructose bisphosphatase 2 Fbp2 2.6* 1.8 1.8 2.9 4.1 3.2
Glutathionerelated genes
J05181 glutamate-cysteine ligase catalytic subunit Gclc 4.8* 3.4* 8.0* 6.0* 2.7* 5.8*
S65555 glutamate cysteine ligase, modifier subunit Gclm 3.1* 3.5* 3.4* 4.1* 1.7 3.5*
L38615 glutathione synthetase Gss 1.9* 1.1 2.5* 2.7* 1.8* 1.8
a
Average fold-change in gene expression from the five time points (7D and 21D days and 4M, 7M, and 12M months).
*Statistical significance represented by the alpha risk <0.001.
(3.2- and 1.5-fold, respectively), while the Elongation factor nephrotoxicity and nephrocarcinogenicity in rat (NTP, 1989).
1-alpha 1 (eEF1A-1) was down-regulated (3.3-fold). There is significant debate on the use of rat carcinogenicity data
to assess the potential carcinogenic risk to humans. A very
Confirmation of Microarray Expression Data relevant question with respect to OTA-mediated carcinogenic-
ity and risk assessment is whether the toxin acts through
In order to confirm the microarray data, selected gene
genotoxic or epigenetic mechanisms. For human safety
products assigned to various functional classes were analyzed
assessment, a nongenotoxic mechanism of OTA would trigger
by quantitative real-time PCR (TaqMan-PCR). As with the
the use of a health-based guidance value established by the
microarray data, TaqMan RT-PCR data is presented as fold-
application of uncertainty factors to the pivotal No Observed
expression value of OTA-treated samples as compared to
Adverse Effect Level obtained in animal studies (WHO, 2001).
controls. As shown in Figure 4, expression values obtained
The present work was aimed to generate data relevant to
with RT-PCR are highly comparable to the data generated by
understanding the mechanism of OTA action and should help to
microarray technology.
select the most appropriate risk assessment procedure. This
Protein expression of six genes was measured from samples
study was intended better to reflect the pattern of human
taken at the early and late time-points (21 days and 12 months)
exposure, and therefore, for the first time, oral feeding was
by Western blot analysis. A good correlation was observed be-
chosen as the route of administration. This allowed ingestion of
tween microarray data and measured protein expression (Fig. 5).
OTA in the most natural way for the experimental animals,
homogenized into feed and consumed as desired, mainly in the
DISCUSSION dark part of the diurnal cycle. The dose was chosen to produce
tumors, although avoiding overt nephrotoxicity, which could
OTA is a common trace contaminant of some foodstuffs. It interfere with the carcinogenic process. A previous acute study
produces various toxicological effects, the most relevant being had shown a marked difference between the toxicity of single
126 MARIN-KUAN ET AL.
TABLE 2
Genes Modulated by OTA under Transcriptional Control of HNF4a
Accession no. Gene title Gene symbol Folda Fold 7D Fold 21D Fold 4M Fold 7M Fold 12M
Glucose metabolism
X05684 pyruvate kinase, liver and RBC Pklr 1.6* 1.8 2.1* 1.8 1.6 1.1
Androgen and estrogen metabolism
L19998 sulfotransferase family 1A, Sult1a1 1.9* 1.3 2.0* 2.2* 2.0* 1.9*
phenol-preferring, member 1
Lipids and steroid metabolism
M73714 aldehyde dehydrogenase family 3, Aldh3a2 1.9* 1.6 1.2 4.4* 1.0 4.6*
subfamily A2
D90109 fatty acid Coenzyme A ligase Facl2 1.6* 2.2* 1.1 1.7 1.5 1.8*
Xenobiotic metabolism
J02657 cytochrome P450, subfamily IIC Cyp2c 10.0* 8.2* 7.5* 64.9* 1.8 13.5*
J02861 cytochrome P450 2c13 Cyp2c13 2.4* 2.5* 1.1 2.6* 4.8* 2.2*
M18335 cytochrome P450, 2c39 Cyp2c39 1.5* 1.3 1.2 1.1 3.0* 2.0*
a
Average fold-change in gene expression from the five time points (7D and 21D days and 4M, 7M, and 12M months).
*Statistical significance represented by the alpha risk <0.001.
daily doses by gavage and the same amount homogenized into incidence of carcinomas was significantly lower than that
feed (Miljkovic et al., 2003). In the initial phase of the study observed in the NTP study at the highest dose (Mantle et al.,
(until rats reached 333 g), the chosen dose used (300 lg/kg bw) in press). However, the development of renal cancer in this
was twice that estimated as the highest average daily intake in study makes it a suitable source for studying carcinogenic
the NTP study (NTP, 1989), in which the toxin was adminis- processes. The difference of cancer incidence between the two
tered by oral gavage. After rats reached 333 g, the dose was studies highlights the importance of the route of administration
held to 100 lg/rat, aimed to gradually reduce the two-fold for tumor outcomes.
difference in intake between the NTP and the present regime as OTA-modulated gene expression profiles were obtained in
the body weight further increased. This protocol was consid- both kidney, the toxin’s main target organ, and liver. Overall,
ered to better mimic the human intake pattern (Mantle et al., the effects observed were relatively modest. Real-time PCR
in press). Dosing adult rats according to body weight (as in the
data confirmed the results. The effect on abundance of certain
NTP study) would have resulted in an increasing exposure to
mRNAs correlated with the change in expression of respective
OTA (due to weight gain from fat accumulation), which would
not have reflected exposure of human adults. At a given proteins, suggesting that such OTA-induced changes could be
occurrence level of OTA, human intake is likely to be relatively of biological significance. The various clustering approaches
stable because of the limited expected age-dependent varia- showed the distinctive difference between kidney and liver
tions in body weight and food intake. The various selected time responses, consistent with the known organ selectivity of OTA
points represented early (7 and 21 days) and late (up to 12 carcinogenicity in the male rat. It is also possible that the
months) exposure stages. The treatment was well tolerated, and apparently higher susceptibility of kidney is due to a dose-
cumulative incidence of animals with a renal tumor of 25% had response effect from the elevated content and the prolonged
occurred by the 2-year end point of the experiment. This residence of OTA in that organ. Indeed, it is well documented
TABLE 3
Transporter-Related Genes Modulated by OTA
Renal proximal
Accession no. Gene title Gene symbol Folda Fold 7D Fold 21D Fold 4M Fold 7M Fold 12M tubule Function Regulation Ref.
U15176 ATPase, Naþ/Kþ Atp1a4 4.3* 3.3 4.3 6.4* 4.6 3.6 basolateral Intracellular sodium PKC, ERK1/2 Khundmiri et al.,
and potassium balance 2005
AB004559 solute carrier Slc22a6/rOAT1 2.7* 2.7* 4.4* 3.6* 1.8 1.9 basolateral Endogenous and PKC, ERK1/2 Koepsell and Endou,
family 22, exogenous anions 2004
member 6 Ochratoxin A Tsuda et al., 1999
D79981 solute carrier Slc21a4/OAT-K1 2.5* 2.7 5.6* 3.0 1.2 1.8 apical Organic anions, Takeuchi et al., 2001
family 21, xenobiotics,
member 4 Ochratoxin A
L19031 solute carrier Slc21a1/Oatp1 2.5* 1.6 3.8* 2.9 3.9* 1.3 apical Organic anions PKC, Terlouw et al., 2003
family 21, Ochratoxin A testosterone Hagenbuch and
member 1 Meier, 2003
OCHRATOXIN A CARCINOGENICITY
AB005547 aquaporin 8 Aqp8 2.5* 4.6* 1.0 2.1 2.1 4.4* apical/ H2O, Urine Vasopressin, Verkman et al., 1996
basolateral concentration adenylate
cyclase
D13871 solute carrier Slc2a5/GLUT5 2.2* 1.5 2.6* 2.7* 2.4* 2.2* apical fructose transport Swissprot
family 2,
member 5
D86086 ATP-binding Abcc2, Mrp-2 2.1* 2.1 1.9 2.5* 1.9 2.2 apical Organic anions, Lee and Kim, 2004
cassette glutathione conjugated
AB013455 solute carrier Slc34a1, NaPi-2 1.8* 1.5 3.0* 1.9 1.6* 1.3* apical Na/Pi cotransport Dietary Pi Magagnin et al., 1993
family 34, intake and
member 1 parathyroid
hormone
D83044 solute carrier Slc22a2/Oct2 1.7* 1.0 3.0* 2.0 1.8* 1.4* basolateral Endogenous and >Male Koepsell and Endou,
family 22, exogenous cations 2004
member 2 Lee and Kim, 2004
M80804 solute carrier Slc3a1/NBAT 1.7* 1.5 2.4* 2.0* 1.6 1.2 apical Amino acid transport Wells and Hediger,
family 3, 1992
member 1
X67948 aquaporin Aqp1 1.7* 1.8 2.5* 1.5 1.5 1.4 apical/ H2O, Urine Vasopressin, Ma et al., 1998
basolateral concentration adenylate cyclase
U76379 solute carrier Slc22a1/OCT1A 1.5* 1.9* 1.3 1.7* 1.5 1.1 basolateral Organic cations, PKC/PKA, Koepsell and Endou,
family 22, anions, weak bases TK cGMP 2004
member 1 Lee and Kim, 2004
U28504 solute carrier Slc17a1/ NaPi-1 1.5* 1.3 2.3* 1.8 2.3* 1.5 apical Na/Pi co-transport Swissprot
family 17,
member 1
M81855 P-glycoprotein/ Mdr1/Pgy1 4.6* 1.0* 6.9 21.8* 6.5* 2.2 apical Removal of Lee and Kim, 2004
multidrug xenobiotics
127
resistance 1
Database (RGD)
2005; O’Brien and Dietrich, 2005; WHO, 2001).
Rat Genome
Ref.
Hierarchical clustering analysis resulted in the identification
Swissprot
Swissprot
of relatively complex and unexpected time-related responses.
RGD
For example, a cluster was noted between the early response (at
7 days) and the late response (at 12 months). Currently, this
Regulation
carrier
calcium
cations
1.5
1.6
1.4
1.2
1.6
1.5
1.9
1.2
1.7
Note. Underlined genes correspond to the genes under the regulation of HNF4a.
1.6
1.7
1.7
2.0*
Coley, 2003).
Folda
1.7*
1.6*
3.0*
1.5*
Slc25a20/Cact
Gene symbol
solute carrier
Gene title
family 25,
member 2
family 2,
J04024
Fold-expression
Fold-expression
20 20
15 15
10 10
5 5
REG REG
0 0
Pgy1 KIM-1 c-Myc Akt1 Pgy1 KIM-1 c-Myc Akt1
-5 -5
-10 -10
-15 Genes -15 Genes
Fold-expression
Fold-expression
-15 -15
-20 -20
-25 -25
-50 -50
-100 -100
Fold-expression
-8 -8
-10 -10
-13 -13
-15 -15
-30 -30
-45 -45
Genes Genes
-2 -2
Fold-expression
Fold-expression
-4 -4
-6 -6
-8 -8
FIG. 4. Quantitation of gene expression changes for selected kidney genes as measured by TaqMan and Affymetrix methods at three time points: 21 days
(black), 4 months (white), and 12 months (grey). The relative quantities of TaqMan RT-PCR products were normalized to the 18S rat housekeeping gene. TaqMan
RT-PCR data are presented as the fold expression values as compared to those of control samples from technical replicates from pooled kidney mRNA (n ¼ 3).
(A–B) Nephrotoxicity markers. (C–D) HNF4a-regulated genes. (E–F) Transport-related genes. (G–H) Nrf2-regulated genes.
130 MARIN-KUAN ET AL.
(Sladek, 1993), and the depletion of HNF4a-pathway was tion factors. Previous investigations have provided evidence
previously associated with cancer development (Sel et al., that phase II enzymes may not be regulated exclusively by
1996). HNF4a-expression and activity was analyzed in human Nrf2-mediated mechanisms (Kang et al., 2003). For example,
renal carcinomas (Sel et al., 1996). The data indicated that in recent studies indicated that Nrf2 might not significantly
tumor samples both the expression and activity of HNF4a were contribute to the expression of Gsta1/2 in the mouse small
reduced as compared to normal tissue, suggesting that this intestine (McMahon et al., 2001). Our results show that some
pathway might be an important molecular mechanism in renal Nrf2-regulated genes are not down- but up-regulated, suggest-
carcinogenesis. However, the present analyses occurred well ing that OTA may also alter other signaling pathways that have
before any renal tumors were evident in the OTA-treated rats. not yet been identified.
In the kidney, OTA treatment resulted in an average 10-fold The toxicological consequences of the OTA-mediated down-
down-regulation of the expression of the male-specific, HNF4a- regulation of many Nrf2-regulated genes are likely to be
regulated cytochrome P450 CYP 2C11. CYP 2C11 is involved biologically significant. It is well documented that chemicals
in phase I metabolism of endogenous compounds (i.e., steroids) inducing an oxidative stress response through activation of
and several xenobiotics (Riddick et al., 2004). A potential role of Nrf2 are associated with chemoprotective properties (Chen and
CYP 2C11 in bioactivation of OTA was suggested (Pfohl- Kong, 2004; Zhang and Gordon, 2004). With OTA, the
Leszkowicz et al., 1998), but data indicating a strong down- inhibition of expression of genes involved in the biosynthesis
regulation of this gene do not support this hypothesis. of glutathione (including the rate-limiting Gclc) is likely to
Nrf2
Detoxication enzymes
OTA GCS
Nrf2 GCLC Inhibition of oxidative
A/G TGA C/T NNN GC A/G GST stress response
PKC AFAR
? ARE
Growth factors? HNF4α Malignant
Toxicity
Fatty acids tumors
Cell metabolism ?
? REG AGGTCA
(Ca2+) Cyp2c11
Lipid metabolism Disruption of
Nucleolus Cell transporters cell homeostasis
?
FIG. 6. Role of PKC in the response of kidney cells to OTA. Putative scheme of plausible mechanism of OTA toxicity, assembled from the gene expression
data. Effect of OTA on potential signaling molecules (growth factors, fatty acids, and/or Ca2þ) could disrupt PKC-regulated pathways downstream. Down-
regulation of genes under transcriptional control of Nrf2 may lead to a reduced oxidative stress response. In addition, OTA-induced down-regulation of genes under
HNF4a-control may affect key metabolic processes. This could make kidney cells more vulnerable to OTA-induced toxicity leading to tumor development. Dashed
lines: hypothetical effects (? inhibition). Solid lines: OTA-effects demonstrated in this study. Down-regulation is denoted by Y.
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