doi:10.1093/humrep/dem129
Human Reproduction Vol.22, No.8 pp. 2093–2102, 2007
Advance Access publication on June 11, 2007
A system-wide analysis of differentially expressed
genes in ectopic and eutopic endometrium
Jonathan D. Wren1,3, Yan Wu2 and Sun-Wei Guo2
1
Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, 825 N.E. 13th Street, Room W313, Oklahoma
City, OK 73104-5005, USA; 2Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, PO Box 26509,
Milwaukee, WI 53226, USA
3
Correspondence address. Tel: þ1-405-271-6989; Fax: þ1-405-271-4110; E-mail: [email protected]
BACKGROUND: Decades of research suggest that endometriosis is a complex disorder, with varying severity, onset
and progression. Many genes have been associated with endometriosis through a number of studies and now microarray analyses have added to the list of perturbed or differentially regulated genes. Thus, it is difficult to see ‘the big
picture’ without first integrating these multiple, heterogeneous sources of high-quality information for analysis.
METHODS: The goal of this study was to infer correlative and/or causal trends by combining empirical microarray
analysis with a historical knowledge base of genetic relationships in endometriosis via a program called IRIDESCENT. RESULTS: Importantly, we found a number of genes, which may have a central role in endometriosis,
despite the fact that few or no past studies have reported these associations. CONCLUSIONS: Several genes listed
as non-responders on the microarray were found to be regulated post-transcriptionally, illustrating the importance
of integrating multiple data sources.
Keywords: data mining; endometriosis; gene expression; microarray
Introduction
In the last five years, gene expression microarrays have become
synonymous with genome-wide or near genome-wide analysis
of gene expression patterns and changes in many diseases. In
endometriosis, close to a dozen gene expression profiling
studies have been published so far (Eyster et al., 2002;
Lebovic et al., 2002; Arimoto et al., 2003; Kao et al., 2003;
Matsuzaki et al., 2004; Smith, 2004; Fan et al., 2005; Matsuzaki
et al., 2005a; Matsuzaki et al., 2005b; Kato et al., 2006; Wu
et al., 2006a), differing by focus, study design, microarray platform, quality control measure, data analysis, cell type used for
RNA extraction, and patients. The number of differentially
expressed genes identified in these studies varies from a few
to hundreds. Typically, for previously identified genes, their
roles in the pathogenesis of endometriosis are further discussed
and for genes that have not been identified, their roles are
speculated. Only one study went one step further to classify
subtypes of endometriosis based on expression patterns and
to identify possible pathways involved in endometriosis (Wu
et al., 2006a). It is the sheer size of these gene datasets that
makes it difficult to conduct a thorough and complete analysis
in the initial report of the study. Even linking dataset genes to
gene ontology (GO) categories is only useful to get a general
idea of the processes involved, as GO annotation and GO
development are both far from complete. Furthermore, GO
analysis of microarray responders only includes associations
with GO categories, and does not identify associations with diseases, chemical compounds, metabolites or phenotypic information, all of which are highly relevant to disease etiology.
In this paper, using the list of 904 differentially expressed
genes identified by comparing eutopic and ectopic endometrium of women with endometriosis, we re-analysed this
dataset to identify associations with genes, diseases, phenotypes, chemical compounds and pharmaceuticals based upon
what has been reported in the published literature. After discarding 337 expressed sequence tags (ESTs) from this set
that were not reported in the published literature, we performed
a shared relationship analysis of the remaining 567 genes/
ESTs. We found a number of genes experimentally implicated
as having a central role in the progression of endometriosis,
despite the fact that few or no past studies have reported
these associations. Several genes listed as non-responders on
the microarray, yet linked to many of the responding genes,
have been reported as post-transcriptionally regulated, such
as STAT1, ERK2 and IGF2, illustrating the importance of
integrating multiple data sources.
Materials and Methods
In the experiments previously described (Wu et al., 2006a), 904 genes
were identified to be differentially expressed between ectopic and
# The Author 2007. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology.
All rights reserved. For Permissions, please email: [email protected]
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Wren et al.
eutopic endometrium of 12 women with endometriosis, using cDNA
microarrays containing 9600 genes/ESTs. Since the microarrays
used in the study were house-made and contained a substantial
number of ESTs, not all gene symbols/names appear in MEDLINE.
Therefore, after removing clone names and accession numbers
that would not be found in the literature (e.g. LOC0101023,
FLJ1dkad19327, etc.), the list contained 567 gene symbols. A software package called IRIDESCENT (Wren, 2004; Wren et al., 2004)
was used to identify commonalities among the genes in the list
(Wren and Garner, 2004). In brief, IRIDESCENT works by searching
every published MEDLINE abstract for associations between objects.
Objects encompass genes, diseases, phenotypes, chemical compounds, drugs and ontology categories. The more frequently two
objects mentioned together and whether they are mentioned in the
same sentence or abstract determines their relative strength of association. Integrating microarray data with published associations is a
useful way to examine microarray data (Mizumoto et al., 2005; Xu
et al., 2005) beyond a simple analysis of ontology categories.
At the time of this analysis, MEDLINE contained approximately 16
million records, which highlights the need for a computational means
of assimilating this information. Objects co-mentioned in the same
sentence are weighted higher (0.8 per co-mention) than objects
co-mentioned in the same abstract (0.5 per co-mention). These
values were obtained from previous studies on the probability of significance for an association of co-mentioned objects (Wren et al.,
2004) and reflect strength of association. Once a network of associations has been constructed, then given a list of objects such as microarray responders, IRIDESCENT can identify what objects they have in
common based upon previous publications. Fig. 1 depicts this process
— a set of responding genes is analysed for what they have in
common. Each of these commonalities is then weighted for its potential significance based upon how frequently they are mentioned within
the literature (i.e. if something is mentioned frequently in the literature, then the fact that several genes have been mentioned with it is
unexceptional) (Somech et al., 2004). Each association is weighted
by the ratio of how frequently it is observed (Obs) with a set of
Figure 1: Given a set of genes (grey circles on the left side, G1–G6),
our goal is to effectively identify common relationships that more than
one gene in the list shares (circles on the right side, R1 –R4).
Each commonality is scored based upon how many connections would
be expected by chance, given the relative connectivity of each object
in the network as a whole. For example, note that five genes are related
to R2. The relevance of this observation depends upon how many
relationships R2 has — if it is connected to 90% of the objects in
the network, then this observation is unexceptional even if it is true.
Even though R4 is related to fewer genes (3), if R4 and each gene
(G2, G3, G5) are connected to relatively few objects in the network,
then this commonality is more statistically noteworthy. In this
way, we can identify relevant commonalities among microarray
responders
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genes to how many times we would expect (Exp) to observe it by
chance alone (i.e. based upon how frequently it is mentioned with
any gene).
Results
For the 567 gene symbols analysed, the average Obs/Exp for
the entire list of associations was high (1.34) compared to
what would be expected of a randomly assembled set of
genes (0.67 + 0.06), indicating that the microarray data contains a great deal of previously documented and informative
interactions.
Table 1 lists the top 40 literature-based commonalities found
among the microarray responders, ranked in order of their Obs/
Exp ratio. Intriguingly, many of the top hits had little or no
documented relationships to endometriosis, suggesting a rich
base for knowledge discovery and for generating new hypotheses. Rather than enumerate each of these connections one by
one, we have identified three interrelated themes that are contained within this list and will instead summarize what this
analysis reveals about differential gene expression in endometriosis. The three themes are: cellular growth and division,
nuclear import and export, and cellular adhesion and growth.
Each theme has elements already anchored in the endometriosis literature as well as several novel associations revealed by
our analysis of this experimental dataset.
Cellular growth and division
Many genes in the differentially expressed (De and Hardy,
1990) list have been linked to tumor suppression (131 genes).
Besides tumor suppressors, other genes involved in cell
growth and division such as the cyclins or CDK cell cycle
genes, transcription factors, post-translational modification
(94 genes), c-JUN, PPARg, NF-kB, histone deacetylase and
hypermethylation, also have been identified. There are
several non-responding genes on this dataset that are linked
to many of the responding genes — almost all of these are
involved in cell growth, differentiation and/or organ development. Bear in mind that many but not all genes are regulated
at the transcriptional level and thus their involvement in some
processes will not be observable from microarray experiments
alone. One study reported that approximately three-fourths of
reported regulatory events took place at the transcriptional
level (Wren and Conway, 2006). Taken together, this suggests
that genes that ordinarily suppress cell division and growth are
being turned off or genes that induce it are turned on.
The second on the list is CDC42, a gene that, as of this
writing, has only been identified in the original profiling
study as Rac (Wu et al., 2006a) for its role in either endometriosis or endometrium based on our MEDLINE search.
CDC42 belongs to the Rho-family of GTPases that regulate
various aspects of cellular functions, including morphogenesis
(actin cytoskeleton, a theme identified with 83 genes connected), polarity, trafficking regulation, and cell division
(Jaffe and Hall, 2005). Interestingly, #26 and #40 on the list
are GSTase and RhoA, respectively, where RhoA is a gene
in the same family. Members of the Rho family of small
GTPases are key regulators of actin reorganization, cell
Data-mining genes differentially expressed in endometriosis
Table 1: Analysis of what the differentially regulated microarray genes have in common within MEDLINE
Shared relationship
Number of genes sharing
relationship
Expect
Tumor suppressor
CDC42
Nuclear export
GRB2
RNA interference
E2F-1
c-SRC
STAT5
BMP4
Nuclear import
STAT1
RAC1
STAT3
JAK2
MYOD
Drosophila
CDK2
IGF2
ERK2
Nuclear translocation
Proline-rich
GTPase-activating protein
Cyclin A
p19
GTPase
Cyclin D1
ERK1
HER-2
c-ABL
Protein complex
Raf-1
Protein tyrosine kinases
b-Catenin
Antigen receptor
FGF-1
Ubiquitin
CDK4
Alternative splicing
RHOA
Focal adhesion kinase
131
60
51
44
98
40
52
41
41
49
53
49
56
42
44
198
60
41
63
91
81
45
49
76
91
77
41
59
50
118
52
60
67
52
43
98
46
174
51
43
35.3
17.0
14.0
12.8
29.0
12.7
15.8
12.7
12.6
14.0
17.3
15.8
18.2
13.6
14.3
63.0
19.4
13.6
20.9
30.1
26.0
14.4
16.4
26.3
30.9
27.1
13.5
20.4
16.1
39.8
18.1
20.3
25.0
17.6
15.2
34.9
16.5
58.9
17.8
16.0
Obs/Exp
3.036
3.030
2.949
2.917
2.910
2.844
2.784
2.773
2.767
2.766
2.722
2.699
2.671
2.645
2.636
2.623
2.557
2.557
2.556
2.545
2.526
2.504
2.497
2.467
2.461
2.444
2.431
2.429
2.429
2.411
2.403
2.402
2.401
2.401
2.394
2.391
2.379
2.377
2.375
2.348
Relationship strength
with endometriosis
3.3
#N/A
#N/A
#N/A
#N/A
#N/A
#N/A
#N/A
#N/A
#N/A
#N/A
#N/A
1.5
#N/A
#N/A
#N/A
#N/A
#N/A
#N/A
1.5
1.3
#N/A
1.3
1
#N/A
2
3
2.3
#N/A
#N/A
#N/A
#N/A
20.9
#N/A
#N/A
5.8
#N/A
1
#N/A
#N/A
The rightmost column shows the relative strength of the relationship between endometriosis and the object in the leftmost column. Where positive, this indicates
the two have been co-mentioned in MEDLINE abstracts. Where ‘#N/A’, this indicates that no relationship with endometriosis was found in the literature (with
the caveat that not all gene name synonyms are in the database. For example, IGF2 and endometriosis are listed as #N/A, but there are six articles that refer to
IGF-II and endometriosis). The observed to expected ratio (Obs/Exp) is a statistical ranking of how exceptional the relationship is (see Methods). Shaded rows
are differentially regulated genes from the microarray.
motility, cell –cell and cell – extracellular matrix (ECM)
adhesion as well as of cell cycle progression, gene expression
and apoptosis (Fritz and Kaina, 2006). The Rho GTPases are
thought to be promising cellular targets for novel anticancer
drugs (Fritz and Kaina, 2006).
The identification of the theme of transcription factors is also
not surprising, since several sex steroid receptor genes such
as estrogen receptors and progesterone receptors known to be
involved in endometriosis belong to the nuclear receptor
gene family of transcription factors. In addition, other genes
linked to the dataset, such as c-Jun and NF-kB, are also transcription factors.
We also found many cell-cycle genes/themes on the list:
CDK2 (60 genes), cyclin A (49 genes), cyclin D1 (77 genes),
CDK4 (46 genes), cyclin B1 (48 genes), p21/WAF1
(46 genes), cyclin E (75 genes), cell cycle arrest (80 genes),
p53 (137 genes), C-kit (50 genes), cell cycle (197 genes),
cyclin-dependent kinase (67 genes), M phase (59 genes), cell
cycle control (58 genes), S phase (87 genes), G1 phase (64
genes). This strongly suggests that the cell cycle was disturbed
in the endometriotic cells, echoing the finding that these cells
have greater anti-apoptotic capability (Beliard et al., 2004),
even in the face of apoptosis-inducing drugs (Izawa et al.,
2006).
Consistent with the involvement of cell cycle disturbance,
several genes/themes on cell growth and apoptosis were identified: IGF2 (41 genes), c-met (39 genes), c-Jun 106 genes),
HGF (67 genes), FGFR1 (40 genes), caspase (84 genes),
platelet-derived growth factors or PDGFs (86 genes), induction
of apoptosis (85 genes), caspase 3 (86 genes), cell growth (197),
fibroblast growth factor (68 genes), bcl-xl (45 genes), Ki-67
(54 genes), apoptosis (226 genes), c-fos (84 genes), Bcl-2
(94 genes), mitosis (96 genes), CD95/Fas (43 genes),
caspase activation (44 genes), PCNA (65 genes), cell
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proliferation (192 genes), nerve growth receptor (87 genes),
apoptotic (142 genes), cell death (171 genes), Fas ligand (47
genes), growth factors (160 genes), IGF2 (Giudice et al.,
1994; Sbracia et al., 1997; Kim et al., 2000), HER-2, c-Met
and HGF (Khan et al., 2003; Yoshida et al., 2004; Khan
et al., 2005), PCNA (a proliferation index) (Khan et al.,
2003), PDGF (Surrey and Halme, 1991; Munson et al., 1995;
Garcia-Velasco et al., 1999), Fas and FasL (Garcia-Velasco
et al., 2002; Selam et al., 2002; Garcia-Velasco and Arici,
2003; Harada et al., 2004; Eidukaite et al., 2006), Bcl-2
(Nezhat and Kalir, 2002; Harada et al., 2004; Nishida et al.,
2005), Bcl-xl (Nishida et al., 2005), FGFs and their receptors
(Di Blasio et al., 1995; Mihalich et al., 2003; Wing et al.,
2003; Bourlev et al., 2006), caspase (Wang et al., 2005;
Izawa et al., 2006), and c-Jun (Shazand et al., 2004). c-fos
has been recently reported to be upregulated in a baboon
model of induced endometriosis (Hastings et al., 2006). It
should be noted that c-Fos and c-Jun are two members of the
AP-1 transcription family, which plays a critical role in the
life and death of cells (Shaulian and Karin, 2002).
The identification of the AP-1 theme actually ties together
several genes that were identified in the original study such
as PDGF, PDGFR, Raf1 (which also happened to be a gene
identified in this study), ERK, MKP, cPLA2, MNK1/2, and
RSK2 (Wu et al., 2006a), which are all in the ERK signalling
pathway, leading to activation of c-Fos, which, in turn, is
responsible for cellular proliferation and differentiation. Raf1
can be regulated by Ras. Interestingly, GRB2 (related to 44
genes), fourth on the list in Table 1, happens to be the downstream gene for PDGF-PDGFR, FGF-FGFR, and EGF-EGFR
(all have been identified in this analysis, see also Fig. 3 in
(Wu et al., 2006a)), and the upstream gene for SOS, which activates Ras (Chardin et al, 1995). Ras, in turn, activates Raf1,
which, through MEK1/MEK2, activates ERK. This is consistent with the mounting evidence that suggests the involvement
of MAPK pathway in general and ERK pathway in particular in
endometriosis (Yoshino et al., 2004; Deura et al., 2005; Hirota
et al., 2005; Matsuzaki et al., 2005b; Wu et al., 2006a).
Nuclear import and export
Among the high-ranking associations were found nuclear translocation (91 genes), nuclear export (51 genes), and nuclear
import (49 genes), which are relevant since steroid hormone
receptor genes including estrogen receptor genes and progesterone receptor genes, as transcription factors, go through
nuclear import and export processes as part of the activation
or inactivation processes. These transcription factors are, in
most cases, nuclear proteins that undergo a continuous nucleocytoplasmic shuttling (Guiochon-Mantel et al., 1991; Dauvois
et al., 1993; Madan and DeFranco, 1993). For example, progesterone receptor activation involves multiple steps, including
a conformational change, dissociation from a multiprotein
sequestering complex consisting of protein chaperones, translocation into nucleus and dimerization, and binding to specific
DNA sequences (Leonhardt and Edwards, 2002). The signal
involved in the transport of these receptors from the cytoplasm
to the nucleus has been studied extensively, which includes a
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basic type nuclear localization signal NL1 (LaCasse and
Lefebvre, 1995).
Visualizing the entire co-citation network is not easily
achieved due to the sheer number of interconnections, thus
we opted to use a subset of genes for analysis based on a
recent finding that NF-kB and AP-1 (c-JUN) transcription
factors are involved in endometriosis (Wu and Guo, unpublished data), shown in Fig. 2. As expected, proinflammatory
cytokines and chemokines IL-1, IL-6, IL-8 and RANTES
have been well-documented to be involved in endometriosis
(Garcia-Velasco and Arici, 1999a,b; Hornung et al., 2001;
Lebovic et al., 2001; Arici, 2002; Wu and Ho, 2003; Lebovic
et al., 2004; Luk et al., 2004; Wieser et al., 2005), as have
matrix metalloproteinases (MMPs) (Osteen et al., 2003; Zhou
and Nothnick, 2005). The involvement of IL-2 and IL-10 in
endometriosis has also been documented (Szyllo et al., 2003;
Tabibzadeh et al., 2003; Lee et al., 2005). In fact, IL-1 (Mori
et al., 1992; Hiscott et al., 1993), IL-2 (Hoyos et al., 1989;
Serfling et al., 1989; Lai et al., 1995), IL-6 (Libermann and
Baltimore, 1990; Shimizu et al., 1990), IL-8 (Kunsch and
Rosen, 1993), IL-10 (Xu and Shu, 2002), RANTES (Moriuchi
et al., 1997; Wickremasinghe et al., 2004), MMP-2 (Yeh et al.,
2005), and MMP-3 (Schulze-Tanzil et al., 2004) are all known
to be NF-kB target genes. The expression of c-Jun has been
shown to be increased in endometriosis (Shazand et al.,
2004). The upregulation of c-Fos has been recently reported
in a baboon model of induced endometriosis (Hastings et al.,
2006). It is interesting to note that in c-Fos transformed cells,
DNMT1 is upregulated (Bakin and Curran, 1999). Perhaps
not so coincidental, DNMT1 and the other two genes coding
for DNA methyltransferases that are responsible for DNA
methylation have been shown recently to be upregulated in
endometriosis (Guo et al., 2005), and promoter hypermethylation of PR-B in endometriosis also has been found recently
(Wu et al., 2006b).
Fig. 3 examines the same data in terms of ‘cliques’ or highly
interconnected neighbourhoods (Adamcsek et al., 2006). As
can be seen in the graph, most of the responding genes have
not been reported to be related to endometriosis, yet are differentially regulated between normal and endometriotic cells.
Especially the green coloured genes, which are largely implicated in cellular growth and tumorigenesis. This integration
and visualization of experimental data with literature-based
relationships helps us to better understand what processes are
implicated in endometriosis by the data, but largely unexplored
in the literature
Cellular adhesion and growth
Several genes/themes identified in this study, such as
b-catenin (67 genes), E-cadherin (59 genes), cell migration
(94 genes), MMP-9 (60 genes), retinoic acid (107 genes),
Matrigel (45 genes), cell differentiation (119 genes), PAI-1
(44 genes), and vimentin (77 genes) strongly suggest that the
invasiveness phenotype is involved with endometriosis,
which has been reported previously (Gaetje et al., 1995;
Zeitvogel et al., 2001). Cadherin is a large family of transmembrane glycoproteins responsible for mediating calciumdependent cell – cell adhesion in normal cells (Jiang et al.,
Data-mining genes differentially expressed in endometriosis
Figure 2: Shared relationships between selected target genes identified to be differentially expressed between ectopic and eutopic endometrium
of women with endometriosis.
The number on each line connecting any two gene symbols or themes represents the strength of such connection
1998) and also involved in contact inhibition of cell growth by
inducing cell-cycle arrest (Feeley and Wells, 2001). Mounting
evidence indicates that the modulation of this complex, which
acts as an invasion suppressor and as a major growth and
proliferation suppressor through a variety of mechanisms,
plays an important role in the initiation and progression of
human cancer (Boling et al., 1988). E-cadherin expression in
endometriosis has been a bit controversial. Some investigators
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Wren et al.
Figure 3: Shared relationship ‘cliques’ or highly interconnected subnetwork groupings, shown by colour.
Note that many of these genes have been studied with one another in
the literature, but only a few have been directly studied in terms of
endometriosis. The microarray experiment indicates these genes are
involved in endometriosis and the graph shows how such novel connections might be better understood within the context of what is
already known. Genes such as p75, N-myc and Raf-1 are well
studied in terms of their connections to many of the differentially
expressed genes.
found increased expression of E-cadherin in endometriosis
(Beliard et al., 1997; Ueda et al., 2002), but a preponderance
of studies found its expression decreased (van der Linden
et al., 1994; Gaetje et al., 1997; Scotti et al., 2000; Poncelet
et al., 2002). Gaetje et al. (1997) have shown that E-cadherin
negative epithelial cells from peritoneal endometriosis biopsies
were invasive in vitro. Recent data showed that the promoter
region of E-cadherin in the endometriotic cell lines studied in
(Gaetje et al., 1997) is hypermethylated and that E-cadherin
can be reactivated by a histone deacetylase inhibitor, trichostatin A (Y. Wu and S.-W. Guo, unpublished observations). Ecadherin has been shown to be silenced by aberrant methylation of the promoter in various cancers (Herman et al.,
1996; Graff et al., 1997; Corn et al., 2000; Esteller, 2003),
and loss of E-cadherin expression has been found to be widespread in sporadically occurring epithelial tumors (Strathdee,
2002).
b-Catenin functions in cell adhesion at the plasma membrane, by linking E-cadherin to a-catenin. Loss of intercellular
adhesion mediated by the cadherin/catenin complex plays a
key role in the precondition for loss of cell polarity and the
onset of cell invasion leading to tumor metastasis (Aberle
et al., 1996). b-catenin expression has been reported to be
reduced in endometriotic cells (Scotti et al., 2000), suggesting
some defects in the E-cadherin/b-catenin complex in
endometriosis.
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The plasminogen-activating system, which consists of plasminogen activators (PAs) and their inhibitors (PAIs) and the
urokinase plasminogen activator receptor (uPAR), are involved
in tissue degradation and remodelling under both physiological
and pathological conditions (Dano et al., 1985). In endometriosis, dysregulated uPA and PAI expression was noted a decade
ago (Fernandez-Shaw et al., 1995), and has been consistently
reported (Bruse et al., 1998; Kobayashi, 2000; Guan et al.,
2002; Gilabert-Estelles et al., 2003; Bruse et al., 2004; Bruse
et al., 2005). Increased mRNA and protein levels of uPA in peritoneal fluid and the eutopic endometrium of women with endometriosis also have been reported (Edelstam et al., 1998;
Sillem et al., 1998; Bruse et al., 2004; Ramon et al., 2005),
suggesting that they may facilitate the attachment of endometrial tissue to the peritoneum and ovarian surface, as well
as the invasion of the extracellular matrix. Similarly, dysregulated MMP expression in endometriosis has been welldocumented (Osteen et al., 2003; Ramon et al., 2005; Zhou
and Nothnick, 2005). In particular, upregulation of MMP-9
in endometriotic cells has been reported by several groups
(Chung et al., 2001; Liu et al., 2002; Ueda et al., 2002; Collette
et al., 2004).
Vimentin is an intermediate filament that cross-links other
cytoskeletal proteins and is normally expressed by cells of
mesenchymal origin, but is a feature of highly invasive, ER
negative, breast cancer cell lines (Thompson et al., 1992).
Given the genes/themes such as b-catenin, E-cadherin, cell
migration, and MMP-9 that are identified, it is perhaps no coincidence that endometriosis has been proposed as a disease of
de-differentiation with invasive phenotypes (Starzinski-Powitz
et al., 2001). This is further buttressed by the two more
themes identified, retinoic acid and Matrigel, the former
playing an important role in cell differentiation and transformation (Chambon, 1996) and the latter being an extract
from tumors, containing all of the components present in the
basement membrane, very biologically active and used to
measure the invasive activity of tumor cells (Kleinman and
Martin, 2005).
The themes histone deacetylase (63 genes), ubiquitin (98
genes), hyperphosphorylation (47 genes), hypermethylation
(48 genes), transcriptional regulation (143 genes), histone (81
genes), post-translational modifications (94 genes), chromatin
(130 genes), and acetyltransferase (85 genes) strongly
suggest the possibility of epigenetic regulation of gene
expression in endometriosis. It has been recently reported by
our group that the promoter region of PR-B is hypermethylated
in endometriosis (Wu et al., 2006b), which may be responsible
for PR-B downregulation (Attia et al., 2000). Interestingly,
histone deacetylase inhibitors have been shown to suppress
proliferation of endometrial and endometriotic cells (Wu and
Guo, 2006).
The themes, post-translational modification and histone
deacetylase, may refer to the post-translational modification
of histones which is one of two major mechanisms that foster
epigenetic changes (the other being DNA methylation at cytosine bases within a CpG dinucleotide) (Issa, 2002). Posttranslational modification of histone modifications include
methylation, acetylation, phosphorylation, and ubiquitination
Data-mining genes differentially expressed in endometriosis
(Li, 2002; Jaenisch and Bird, 2003). Histone deacetylase is an
enzyme involved in the deacetylation of histones.
Discussion
This analysis highlights the importance of several issues that
have not been addressed in endometriosis research, yet have
now been strongly linked to it by experimental data. First,
what role does NF-kB play in endometriosis? Second, what
role does nuclear translocation/import/export play in endometriosis? Third, many genes implicated in the growth/development cycle were differentially expressed in the microarray
dataset. Some such as RAC1, Raf-1 and FGFR1 also play
central roles and are related to many of the themes. RAC1,
for example, is a critical upstream signalling molecule that
can cause stem cells to divide (Benitah et al., 2005), whereas
Raf-1 regulates cellular differentiation, proliferation and apoptosis (Ziogas et al., 2005). Does interfering with these genes
induce or prevent endometriosis?
The astounding complexity of the interconnections of the
567 genes underscores several points that have not been
appreciated fully in the past. First, piecemeal approaches may
be necessary to dissect individual components of the system
but, to understand endometriosis as a phenomenon, a systemwide approach is necessary, especially since endometriosis
appears to be a system-wide disease affecting many aspects
of reproductive health and well-being (Leyendecker, 2000;
Vinatier et al., 2000). As in complex systems, “while in
many cases properties of individual components can be well
characterized in a laboratory, these isolated measurements are
typically of relatively little use in predicting the behaviour of
large-scale interconnected systems or mitigating the cascading
spread of damage due to the seemingly innocuous breakdown
of individual parts” (Carlson and Doyle, 1999). The heterogeneity observed in endometriosis is to be expected, since, like
tumors, heterogeneity among endometriotic lesions may be a
result of “a high level of redundancy, and hence increased
chances of survival and growth” (Kitano, 2003) and may be
generated by complex genetic and epigenetic changes. Since
the female reproductive system itself is very complex, involving several organs, a more fundamental, system or near
system-wide approach is needed (Schadt and Lum, 2006).
Second, perhaps as a corollary, any brazen claim that a single
gene, or protein, that plays a vital role either in disease
initiation or progression and that its activation/inhibition
would be effective to treat endometriosis should be carefully
scrutinized. This is especially true when, say, a putative novel
gene is identified from a gene profiling study or a putative
novel protein is identified from a 2D electrophoresis or other
high-throughput proteomic technologies. In these cases hundreds, if not thousands, of genes/proteins can be differentially
expressed between the uteri and ectopic uterine implants, and
the chance of picking up the causal protein is slim to none.
As an example, the two proteins identified by this method,
so-called ENDO-1 and ENDO-2 (Sharpe et al., 1993), turned
out to be two known proteins: one is a variant of hepatic haptoglobin (Piva and Sharpe-Timms, 1999), and the other, tissue
inhibitor of metaloproteinase-1 (TIMP-1) (Sharpe-Timms
et al., 1995). Not surprisingly, the promise of providing alternative methods of therapeutic management for endometriosis
based on these two proteins have so far not been materialized.
Finally, the data-mining of the large data sets arising from
gene expression profiling has shown its use here in generating
feed-forward hypotheses regarding the pathogenesis of endometriosis. While most, if not all, gene expression profiling
studies of endometriosis have discussed and speculated about
the roles of differentially expressed genes, none so far has
linked these genes to the current knowledge base regarding
the disease. This study demonstrates that this type of literaturebased data mining not only helps corroborate that the experimental data is consistent with established knowledge, but can
also identify new areas of research where future efforts are
likely to yield a greater understanding.
It is worth noting several limitations of this study. First, this
study is based on a gene expression profiling of the difference
between eutopic and ectopic endometrium of women with
endometriosis. Due to the cross-sectional nature of the study,
many identified changes or differences are likely the consequences, rather than the causes, of endometriosis. Second,
the literature-based analysis is based upon the presumption
that co-mentioned objects in MEDLINE abstracts represent
meaningful relationships. While this has been examined in
the original IRIDESCENT studies, and found to be generally
true, there is nonetheless a false-positive rate that diminishes
with the frequency of co-mentions (i.e. the more two things
are mentioned together, the less likely it is a trivial relationship). There are also false-negatives, whereby due to nomenclature difficulties, certain relationships are not detected,
such as when the gene name is identical to a common
English word (e.g. red, basket, arrow). Third, the nature of
some identified relationships can have multiple interpretations.
A more in-depth examination of the references will tell, but the
number of genes so linked makes this a non-trivial task. Lastly,
some discussions on the possible roles of certain genes or
themes are, by necessity, mostly speculative, based on circumstantial evidence or data. Speculative as it may be, however, the
weight of evidence provided by the general themes identified
should yield some educated guess about the pathogenesis of
endometriosis and help generate novel hypotheses that can be
tested in future studies.
References
Aberle H, Schwartz H, Kemler R. Cadherin-catenin complex: protein
interactions and their implications for cadherin function. J Cell Biochem
1996;61:514– 523.
Adamcsek B, Palla G, Farkas IJ, Derenyi I, Vicsek T. CFinder: locating cliques
and overlapping modules in biological networks. Bioinformatics
2006;22:1021–1023.
Arici A. Local cytokines in endometrial tissue: the role of interleukin-8 in the
pathogenesis of endometriosis. Ann N Y Acad Sci 2002;955:101–109;
discussion 118, 396–406.
Arimoto T, Katagiri T, Oda K, Tsunoda T, Yasugi T, Osuga Y, Yoshikawa H,
Nishii O, Yano T, Taketani Y, Nakamura Y. Genome-wide cDNA
microarray analysis of gene-expression profiles involved in ovarian
endometriosis. Int J Oncol 2003;22:551–60.
Attia GR, Zeitoun K, Edwards D, Johns A, Carr BR, Bulun SE. Progesterone
receptor isoform A but not B is expressed in endometriosis. J Clin
Endocrinol Metab 2000;85:2897– 2902.
2099
Wren et al.
Bakin AV, Curran T. Role of DNA 5-methylcytosine transferase in cell
transformation by fos. Science 1999;283:387– 390.
Beliard A, Donnez J, Nisolle M, Foidart JM. Localization of laminin,
fibronectin, E-cadherin, and integrins in endometrium and endometriosis.
Fertil Steril 1997;67:266–272.
Beliard A, Noel A, Foidart JM. Reduction of apoptosis and proliferation in
endometriosis. Fertil Steril 2004;82:80– 85.
Benitah SA, Frye M, Glogauer M, Watt FM. Stem cell depletion through
epidermal deletion of Rac1. Science 2005;309:933– 935.
Boling RO, Abbasi R, Ackerman G, Schipul AH Jr, Chaney SA. Disability
from endometriosis in the United States Army. J Reprod Med 1988;
33:49– 52.
Bourlev V, Larsson A, Olovsson M. Elevated levels of fibroblast growth
factor-2 in serum from women with endometriosis. Am J Obstet Gynecol
2006;194:755–759.
Bruse C, Bergqvist A, Carlstrom K, Fianu-Jonasson A, Lecander I, Astedt B.
Fibrinolytic factors in endometriotic tissue, endometrium, peritoneal fluid,
and plasma from women with endometriosis and in endometrium and
peritoneal fluid from healthy women. Fertil Steril 1998;70:821–826.
Bruse C, Radu D, Bergqvist A. In situ localization of mRNA for the fibrinolytic
factors uPA, PAI-1 and uPAR in endometriotic and endometrial tissue. Mol
Hum Reprod 2004;10:159– 166.
Bruse C, Guan Y, Carlberg M, Carlstrom K, Bergqvist A. Basal release of
urokinase plasminogen activator, plasminogen activator inhibitor-1, and
soluble plasminogen activator receptor from separated and cultured
endometriotic and endometrial stromal and epithelial cells. Fertil Steril
2005;83(Suppl 1):1155– 1160.
Carlson JM, Doyle J. Highly optimized tolerance: a mechanism for power laws
in designed systems. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip
Topics 1999;60(2 Pt A):1412– 1427.
Chambon P. A decade of molecular biology of retinoic acid receptors. FASEB J
1996;10:940– 954.
Chardin P, Cussac D, Maignan S, Ducruix A. The Grb2 adaptor. FEBS Lett
1995;369:47– 51.
Chung HW, Wen Y, Chun SH, Nezhat C, Woo BH, Lake Polan M. Matrix
metalloproteinase-9 and tissue inhibitor of metalloproteinase-3 mRNA
expression in ectopic and eutopic endometrium in women with
endometriosis: a rationale for endometriotic invasiveness. Fertil Steril
2001;75:152– 159.
Collette T, Bellehumeur C, Kats R, Maheux R, Mailloux J, Villeneuve M,
Akoum A. Evidence for an increased release of proteolytic activity by the
eutopic endometrial tissue in women with endometriosis and for
involvement of matrix metalloproteinase-9. Hum Reprod 2004;19:1257–
1264.
Corn PG, Smith BD, Ruckdeschel ES, Douglas D, Baylin SB, Herman JG.
E-cadherin expression is silenced by 50 CpG island methylation in acute
leukemia. Clin Cancer Res 2000;6:4243– 4248.
Dano K, Andreasen PA, Grondahl-Hansen J, Kristensen P, Nielsen LS, Skriver L.
Plasminogen activators, tissue degradation, and cancer. Adv Cancer Res
1985;44:139– 266.
Dauvois S, White R, Parker MG. The antiestrogen ICI 182780 disrupts estrogen
receptor nucleocytoplasmic shuttling. J Cell Sci 1993;106(Pt 4):1377– 1388.
De AK, Hardy RE. Elucidation of sialyltransferase as a tumour marker. Indian
J Biochem Biophys 1990;27:452– 455.
Deura I, Harada T, Taniguchi F, Iwabe T, Izawa M, Terakawa N. Reduction of
estrogen production by interleukin-6 in a human granulosa tumor cell line
may have implications for endometriosis-associated infertility. Fertil Steril
2005;83(Suppl 1):1086– 1092.
Di Blasio AM, Centinaio G, Carniti C, Somigliana E, Vigano P, Vignali M.
Basic fibroblast growth factor messenger ribonucleic acid levels in eutopic
and ectopic human endometrial stromal cells as assessed by competitive
polymerase chain reaction amplification. Mol Cell Endocrinol 1995;
115:169–175.
Edelstam G, Lecander I, Larsson B, Astedt B. Fibrinolysis in the peritoneal
fluid during adhesions, endometriosis and ongoing pelvic inflammatory
disease. Inflammation 1998;22:341–351.
Eidukaite A, Siaurys A, Tamosiunas V. Aberrant expression of CD95 and
CD69 molecules among CD56 cells in women with endometriosis. Am J
Reprod Immunol 2006;55:276– 281.
Esteller M. Profiling aberrant DNA methylation in hematologic neoplasms: a
view from the tip of the iceberg. Clin Immunol 2003;109:80– 88.
Eyster KM, Boles AL, Brannian JD, Hansen KA. DNA microarray analysis of
gene expression markers of endometriosis. Fertil Steril 2002;77:38 –42.
2100
Fan Y, Chen BL, Ma XD, Su MQ. Detection of expression of
endometriosis-related cytokine and their receptor genes by cDNA microarray
technique. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2005;21:489–492.
Feeley KM, Wells M. Precursor lesions of ovarian epithelial malignancy.
Histopathology 2001;38:87–95.
Fernandez-Shaw S, Marshall JM, Hicks B, Barlow DH, Starkey PM.
Plasminogen activators in ectopic and uterine endometrium. Fertil Steril
1995;63:45 –51.
Fritz G, Kaina B. Rho GTPases: promising cellular targets for novel anticancer
drugs. Curr Cancer Drug Targets 2006;6:1– 14.
Gaetje R, Kotzian S, Herrmann G, Baumann R, Starzinski-Powitz A.
Invasiveness of endometriotic cells in vitro. Lancet 1995;346:1463–1464.
Gaetje R, Kotzian S, Herrmann G, Baumann R, Starzinski-Powitz A.
Nonmalignant epithelial cells, potentially invasive in human
endometriosis, lack the tumor suppressor molecule E-cadherin. Am J
Pathol 1997;150:461– 467.
Garcia-Velasco JA, Arici A. Interleukin-8 expression in endometrial stromal
cells is regulated by integrin-dependent cell adhesion. Mol Hum Reprod
1999a;5:1135–1140.
Garcia-Velasco JA, Arici A. Interleukin-8 stimulates the adhesion of
endometrial stromal cells to fibronectin. Fertil Steril 1999b;72:
336 – 340.
Garcia-Velasco JA, Arici A, Zreik T, Naftolin F, Mor G. Macrophage
derived growth factors modulate Fas ligand expression in cultured
endometrial stromal cells: a role in endometriosis. Mol Hum Reprod
1999;5:642–650.
Garcia-Velasco JA, Mulayim N, Kayisli UA, Arici A. Elevated soluble Fas
ligand levels may suggest a role for apoptosis in women with
endometriosis. Fertil Steril 2002;78:855–859.
Garcia-Velasco JA, Arici A. Apoptosis and the pathogenesis of endometriosis.
Semin Reprod Med 2003;21:165–172.
Gilabert-Estelles J, Estelles A, Gilabert J, Castello R, Espana F, Falco C,
Romeu A, Chirivella M, Zorio E, Aznar J. Expression of several
components of the plasminogen activator and matrix metalloproteinase
systems in endometriosis. Hum Reprod 2003;18:1516–1522.
Giudice LC, Dsupin BA, Gargosky SE, Rosenfeld RG, Irwin JC. The
insulin-like growth factor system in human peritoneal fluid: its effects on
endometrial stromal cells and its potential relevance to endometriosis. J
Clin Endocrinol Metab 1994;79:1284– 1293.
Graff JR, Herman JG, Myohanen S, Baylin SB, Vertino PM. Mapping patterns
of CpG island methylation in normal and neoplastic cells implicates both
upstream and downstream regions in de novo methylation. J Biol Chem
1997;272:22322–22329.
Guan YM, Carlberg M, Bruse C, Carlstrom K, Bergqvist A. Effects of
hormones on uPA, PAI-1 and suPAR from cultured endometrial and
ovarian endometriotic stromal cells. Acta Obstet Gynecol Scand 2002;
81:389– 397.
Guiochon-Mantel A, Lescop P, Christin-Maitre S, Loosfelt H, Perrot-Applanat M,
Milgrom E. Nucleocytoplasmic shuttling of the progesterone receptor.
Embo J 1991;10:3851– 3859.
Guo S, Wu Y, Strawn E, Basir Z, Halverson G. Aberrant expression of DNA
methyltransferases DNMT1 and DNMT3B in endometriosis. Fertil Steril
2005;84(Suppl 1):S125.
Harada T, Kaponis A, Iwabe T, Taniguchi F, Makrydimas G, Sofikitis N,
Paschopoulos M, Paraskevaidis E, Terakawa N. Apoptosis in human
endometrium and endometriosis. Hum Reprod Update 2004;10:29 –38.
Hastings JM, Jackson KS, Mavrogianis PA, Fazleabas AT. The estrogen early
response gene, fos, is altered in a baboon model of endometriosis. Biol
Reprod 2006;75:176–182.
Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin SB.
Methylation-specific PCR: a novel PCR assay for methylation status of
CpG islands. Proc Natl Acad Sci USA 1996;93:9821– 9826.
Hirota Y, Osuga Y, Hirata T, Harada M, Morimoto C, Yoshino O, Koga K,
Yano T, Tsutsumi O, Taketani Y. Activation of protease-activated
receptor 2 stimulates proliferation and interleukin (IL)-6 and IL-8
secretion of endometriotic stromal cells. Hum Reprod 2005;20:3547–3553.
Hiscott J, Marois J, Garoufalis J, D’Addario M, Roulston A, Kwan I, Pepin N,
Lacoste J, Nguyen H, Bensi G et al. Characterization of a functional
NF-kappa B site in the human interleukin 1 beta promoter: evidence for a
positive autoregulatory loop. Mol Cell Biol 1993;13:6231– 6240.
Hornung D, Bentzien F, Wallwiener D, Kiesel L, Taylor RN. Chemokine
bioactivity of RANTES in endometriotic and normal endometrial stromal
cells and peritoneal fluid. Mol Hum Reprod 2001;7:163–168.
Data-mining genes differentially expressed in endometriosis
Hoyos B, Ballard DW, Bohnlein E, Siekevitz M, Greene WC. Kappa B-specific
DNA binding proteins: role in the regulation of human interleukin-2 gene
expression. Science 1989;244:457– 460.
Issa JP. Epigenetic variation and human disease. J Nutr 2002;132(8
Suppl):2388S– 2392S.
Izawa M, Harada T, Deura I, Taniguchi F, Iwabe T, Terakawa N. Drug-induced
apoptosis was markedly attenuated in endometriotic stromal cells. Hum
Reprod 2006;21:600–604.
Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome
integrates intrinsic and environmental signals. Nat Genet 2003;33:245–254.
Jaffe AB, Hall A. Rho GTPases: biochemistry and biology. Annu Rev Cell Dev
Biol 2005;21:247–269.
Jiang X, Morland SJ, Hitchcock A, Thomas EJ, Campbell IG. Allelotyping
of endometriosis with adjacent ovarian carcinoma reveals evidence of a
common lineage. Cancer Res 1998;58:1707– 1712.
Kao LC, Germeyer A, Tulac S, Lobo S, Yang JP, Taylor RN, Osteen K, Lessey
BA, Giudice LC. Expression profiling of endometrium from women with
endometriosis reveals candidate genes for disease-based implantation
failure and infertility. Endocrinology 2003;144:2870–2881.
Kato N, Sasou S, Motoyama T. Expression of hepatocyte nuclear factor-1beta
(HNF-1beta) in clear cell tumors and endometriosis of the ovary. Mod Pathol
2006;19:83– 89.
Khan KN, Masuzaki H, Fujishita A, Kitajima M, Hiraki K, Sekine I, Matsuyama
T, Ishimaru T. Interleukin-6- and tumour necrosis factor alpha-mediated
expression of hepatocyte growth factor by stromal cells and its involvement
in the growth of endometriosis. Hum Reprod 2005;20:2715–2723.
Khan KN, Masuzaki H, Fujishita A, Kitajima M, Sekine I, Ishimaru T.
Immunoexpression of hepatocyte growth factor and c-Met receptor in the
eutopic endometrium predicts the activity of ectopic endometrium. Fertil
Steril 2003;79:173– 181.
Kim JG, Suh CS, Kim SH, Choi YM, Moon SY, Lee JY. Insulin-like growth
factors (IGFs), IGF-binding proteins (IGFBPs), and IGFBP-3 protease
activity in the peritoneal fluid of patients with and without endometriosis.
Fertil Steril 2000;73:996–1000.
Kitano H. Cancer robustness: tumour tactics. Nature 2003;426:125.
Kleinman HK, Martin GR. Matrigel: basement membrane matrix with
biological activity. Semin Cancer Biol 2005;15:378–386.
Kobayashi H. Invasive capacity of heterotopic endometrium. Gynecol Obstet
Invest 2000;50(Suppl 1):26– 32.
Kunsch C, Rosen CA. NF-kappa B subunit-specific regulation of the
interleukin-8 promoter. Mol Cell Biol 1993;13:6137–6146.
LaCasse EC, Lefebvre YA. Nuclear localization signals overlap DNA- or
RNA-binding domains in nucleic acid-binding proteins. Nucleic Acids Res
1995;23:1647–1656.
Lai JH, Horvath G, Subleski J, Bruder J, Ghosh P, Tan TH. RelA is a potent
transcriptional activator of the CD28 response element within the
interleukin 2 promoter. Mol Cell Biol 1995;15:4260– 4271.
Lebovic DI, Chao VA, Martini JF, Taylor RN. IL-1beta induction of RANTES
(regulated upon activation, normal T cell expressed and secreted) chemokine
gene expression in endometriotic stromal cells depends on a nuclear
factor-kappaB site in the proximal promoter. J Clin Endocrinol Metab
2001;86:4759–4764.
Lebovic DI, Baldocchi RA, Mueller MD, Taylor RN. Altered expression of
a cell-cycle suppressor gene, Tob-1, in endometriotic cells by cDNA array
analyses. Fertil Steril 2002;78:849– 854.
Lebovic DI, Chao VA, Taylor RN. Peritoneal macrophages induce RANTES
(regulated on activation, normal T cell expressed and secreted) chemokine
gene transcription in endometrial stromal cells. J Clin Endocrinol Metab
2004;89:1397–1401.
Lee KS, Baek DW, Kim KH, Shin BS, Lee DH, Kim JW, Hong YS, Bae YS,
Kwak JY. IL-10-dependent down-regulation of MHC class II expression
level on monocytes by peritoneal fluid from endometriosis patients. Int
Immunopharmacol 2005;5:1699–1712.
Leonhardt SA, Edwards DP. Mechanism of action of progesterone antagonists.
Exp Biol Med (Maywood) 2002;227:969–980.
Leyendecker G. Redefining endometriosis: endometriosis is an entity with
extreme pleiomorphism. Hum Reprod 2000;15:4–7.
Li E. Chromatin modification and epigenetic reprogramming in mammalian
development. Nat Rev Genet 2002;39:662–673.
Libermann TA, Baltimore D. Activation of interleukin-6 gene expression through
the NF-kappa B transcription factor. Mol Cell Biol 1990;10:2327–2334.
Liu XJ, He YL, Peng DX. Expression of metalloproteinase-9 in ectopic
endometrium in women with endometriosis. Di Yi Jun Yi Da Xue Xue Bao
2002;22:467–469.
Luk J, Seval Y, Kayisli UA, Ulukus M, Ulukus CE, Arici A. Regulation of
interleukin-8 expression in human endometrial endothelial cells: a
potential mechanism for the pathogenesis of endometriosis. J Clin
Endocrinol Metab 2005;90:1805– 1811.
Madan AP, DeFranco DB. Bidirectional transport of glucocorticoid
receptors across the nuclear envelope. Proc Natl Acad Sci U S A 1993;90:
3588 – 3592.
Matsuzaki S, Canis M, Pouly JL, Dechelotte P, Okamura K, Mage G. The
macrophage stimulating protein/RON system: a potential novel target for
prevention and treatment of endometriosis. Mol Hum Reprod
2005a;11:345– 349.
Matsuzaki S, Canis M, Vaurs-Barriere C, Boespflug-Tanguy O, Dastugue B,
Mage G. DNA microarray analysis of gene expression in eutopic
endometrium from patients with deep endometriosis using laser capture
microdissection. Fertil Steril 2005b;84(Suppl 2):1180– 1190.
Matsuzaki S, Canis M, Vaurs-Barriere C, Pouly JL, Boespflug-Tanguy O,
Penault-Llorca F, Dechelotte P, Dastugue B, Okamura K, Mage G. DNA
microarray analysis of gene expression profiles in deep endometriosis
using laser capture microdissection. Mol Hum Reprod 2004;10:719– 728.
Mihalich A, Reina M, Mangioni S, Ponti E, Alberti L, Vigano P, Vignali M, Di
Blasio AM. Different basic fibroblast growth factor and fibroblast growth
factor-antisense expression in eutopic endometrial stromal cells derived
from women with and without endometriosis. J Clin Endocrinol Metab
2003;88:2853–2859.
Mizumoto N, Hui F, Edelbaum D, Weil MR, Wren JD, Shalhevet D, Matsue H,
Liu L, Garner HR, Takashima A. Differential activation profiles of multiple
transcription factors during dendritic cell maturation. J Invest Dermatol
2005;124:718–724.
Mori H, Sawairi M, Nakagawa M, Itoh N, Wada K, Tamaya T. Expression of
interleukin-1 (IL-1) beta messenger ribonucleic acid (mRNA) and IL-1
receptor antagonist mRNA in peritoneal macrophages from patients with
endometriosis. Fertil Steril 1992;57:535– 542.
Moriuchi H, Moriuchi M, Fauci AS. Nuclear factor-kappa B potently
up-regulates the promoter activity of RANTES, a chemokine that blocks
HIV infection. J Immunol 1997;158:3483–3491.
Munson L, Upadhyaya NB, Van Meter S. Platelet-derived growth factor
promotes endometrial epithelial cell proliferation. Am J Obstet Gynecol
1995;173:1820–1825.
Nezhat FR, Kalir T. Comparative immunohistochemical studies of endo
metriosis lesions and endometriotic cysts. Fertil Steril 2002;78:820– 824.
Nishida M, Nasu K, Ueda T, Fukuda J, Takai N, Miyakawa I. Endometriotic
cells are resistant to interferon-gamma-induced cell growth inhibition and
apoptosis: a possible mechanism involved in the pathogenesis of
endometriosis. Mol Hum Reprod 2005;11:29–34.
Osteen KG, Yeaman GR, Bruner-Tran KL. Matrix metalloproteinases and
endometriosis. Semin Reprod Med 2003;21:155– 164.
Piva M, Sharpe-Timms KL. Peritoneal endometriotic lesions differentially
express a haptoglobin-like gene. Mol Hum Reprod 1999;5:71– 78.
Poncelet C, Leblanc M, Walker-Combrouze F, Soriano D, Feldmann G,
Madelenat P, Scoazec JY, Darai E. Expression of cadherins and CD44
isoforms in human endometrium and peritoneal endometriosis. Acta Obstet
Gynecol Scand 2002;81:195–203.
Ramon L, Gilabert-Estelles J, Castello R, Gilabert J, Espana F, Romeu A,
Chirivella M, Aznar J, Estelles A. mRNA analysis of several components
of the plasminogen activator and matrix metalloproteinase systems in
endometriosis using a real-time quantitative RT-PCR assay. Hum Reprod
2005;20:272– 278.
Sbracia M, Zupi E, Alo P, Manna C, Marconi D, Scarpellini F, Grasso JA, Di
Tondo U, Romanini C. Differential expression of IGF-I and IGF-II in eutopic
and ectopic endometria of women with endometriosis and in women without
endometriosis. Am J Reprod Immunol 1997;37:326– 329.
Schadt EE, Lum PY. Thematic review series: systems biology approaches to
metabolic and cardiovascular disorders. Reverse engineering gene
networks to identify key drivers of complex disease phenotypes. J Lipid
Res 2006;47:2601–2613.
Schulze-Tanzil G, Mobasheri A, Sendzik J, John T, Shakibaei M. Effects of
curcumin (diferuloylmethane) on nuclear factor kappaB signaling in
interleukin-1beta-stimulated chondrocytes. Ann N Y Acad Sci
2004;1030:578–586.
Scotti S, Regidor PA, Schindler AE, Winterhager E. Reduced proliferation and
cell adhesion in endometriosis. Mol Hum Reprod 2000;6:610– 617.
Selam B, Kayisli UA, Garcia-Velasco JA, Arici A. Extracellular matrixdependent regulation of Fas ligand expression in human endometrial
stromal cells. Biol Reprod 2002;66:1– 5.
2101
Wren et al.
Serfling E, Barthelmas R, Pfeuffer I, Schenk B, Zarius S, Swoboda R, Mercurio F,
Karin M. Ubiquitous and lymphocyte-specific factors are involved in the
induction of the mouse interleukin 2 gene in T lymphocytes. Embo J
1989;8:465– 473.
Sharpe KL, Zimmer RL, Griffin WT, Penney LL. Polypeptides synthesized and
released by human endometriosis differ from those of the uterine endo
metrium in cell and tissue explant culture. Fertil Steril 1993;60:839–851.
Sharpe-Timms KL, Penney LL, Zimmer RL, Wright JA, Zhang Y, Surewicz K.
Partial purification and amino acid sequence analysis of endometriosis
protein-II (ENDO-II) reveals homology with tissue inhibitor of
metalloproteinases-1 (TIMP-1). J Clin Endocrinol Metab 1995;80:3784–3797.
Shaulian E, Karin M. AP-1 as a regulator of cell life and death. Nat Cell Biol
2002;4:E131–E136.
Shazand K, Baban S, Prive C, Malette B, Croteau P, Lagace M, Racine JB,
Hugo P. FOXO1 and c-Jun transcription factors mRNA are modulated in
endometriosis. Mol Hum Reprod 2004;10:871–877.
Shimizu H, Mitomo K, Watanabe T, Okamoto S, Yamamoto K. Involvement of
a NF-kappa B-like transcription factor in the activation of the interleukin-6
gene by inflammatory lymphokines. Mol Cell Biol 1990;10:561–568.
Sillem M, Prifti S, Neher M, Runnebaum B. Extracellular matrix remodelling
in the endometrium and its possible relevance to the pathogenesis of
endometriosis. Hum Reprod Update 1998;4:730–735.
Smith SK. Study of the profile of gene expression in the endometrium.
J Gynecol Obstet Biol Reprod (Paris) 2004;33(6 Pt 2):3S15–3S18.
Somech R, Izraeli S, J Simon A. Histone deacetylase inhibitors – a new tool to
treat cancer. Cancer Treat Rev 2004;30:461– 472.
Starzinski-Powitz A, Zeitvogel A, Schreiner A, Baumann R. In search of
pathogenic mechanisms in endometriosis: the challenge for molecular cell
biology. Curr Mol Med 2001;1:655–664.
Strathdee G. Epigenetic versus genetic alterations in the inactivation of
E-cadherin. Semin Cancer Biol 2002;12:373–379.
Surrey ES, Halme J. Effect of platelet-derived growth factor on endometrial
stromal cell proliferation in vitro: a model for endometriosis? Fertil Steril
1991;56:672– 679.
Szyllo K, Tchorzewski H, Banasik M, Glowacka E, Lewkowicz P,
Kamer-Bartosinska A. The involvement of T lymphocytes in the
pathogenesis of endometriotic tissues overgrowth in women with
endometriosis. Mediators Inflamm 2003;12:131–138.
Tabibzadeh S, Becker JL, Parsons AK. Endometriosis is associated with
alterations in the relative abundance of proteins and IL-10 in the
peritoneal fluid. Front Biosci 2003;8:a70 –78.
Thompson EW, Paik S, Brunner N, Sommers CL, Zugmaier G, Clarke R,
Shima TB, Torri J, Donahue S, Lippman ME et al. Association of
increased basement membrane invasiveness with absence of estrogen
receptor and expression of vimentin in human breast cancer cell lines. J
Cell Physiol 1992;150:534–544.
Ueda M, Yamashita Y, Takehara M, Terai Y, Kumagai K, Ueki K, Kanda K,
Hung YC, Ueki M. Gene expression of adhesion molecules and matrix
metalloproteinases in endometriosis. Gynecol Endocrinol 2002;16:
391– 402.
van der Linden J, de Goeij AF, Dunselman GA, van der Linden EP, Ramaekers
FC, Evers JL. Expression of integrins and E-cadherin in cells from menstrual
effluent, endometrium, peritoneal fluid, peritoneum, and endometriosis.
Fertil Steril 1994;61:85– 90.
Vinatier D, Cosson M, Dufour P. Is endometriosis an endometrial disease?
Eur J Obstet Gynecol Reprod Biol 2000;91:113– 125.
Wang YC, Fu RH, Hsieh HJ, Chao HT, Kao SH. Polyglycolic acid/chitosan
glue and apoptosis of endometriotic cells. Fertil Steril 2005;84:75– 81.
Wickremasinghe MI, Thomas LH, O’Kane CM, Uddin J, Friedland JS.
Transcriptional mechanisms regulating alveolar epithelial cell-specific
2102
CCL5 secretion in pulmonary tuberculosis. J Biol Chem 2004;279:27199–
27210.
Wieser F, Vigne JL, Ryan I, Hornung D, Djalali S, Taylor RN. Sulindac
suppresses nuclear factor-kappaB activation and RANTES gene and
protein expression in endometrial stromal cells from women with
endometriosis. J Clin Endocrinol Metab 2005;90:6441–6447.
Wing LY, Chuang PC, Wu MH, Chen HM, Tsai SJ. Expression and mitogenic
effect of fibroblast growth factor-9 in human endometriotic implant is
regulated by aberrant production of estrogen. J Clin Endocrinol Metab
2003;88:5547– 5554.
Wren JD. Extending the mutual information measure to rank inferred literature
relationships. BMC Bioinformatics 2004;5:145.
Wren JD, Garner HR. Shared relationship analysis: ranking set cohesion and
commonalities within a literature-derived relationship network. Bioinform
atics 2004;20:191–198.
Wren JD, Bekeredjian R, Stewart JA, Shohet RV, Garner HR. Knowledge
discovery by automated identification and ranking of implicit relation
ships. Bioinformatics 2004;20:389–398.
Wren JD, Conway T. Meta-analysis of published transcriptional and
translational fold changes reveals a preference for low-fold inductions.
Omics 2006;10:15–27.
Wu MY, Ho HN. The role of cytokines in endometriosis. Am J Reprod Immunol
2003;49:285–296.
Wu Y et al. Transcriptional characterizations of differences between eutopic
and ectopic endometrium. Endocrinol 2006a;147:232–246.
Wu Y, Strawn E, Basir Z, Halverson G, Guo SW. Promoter hypermethylation
of progesterone receptor isoform B (PR-B) in endometriosis. Epigenetics
2006b;1:106–111.
Wu Y, Guo SW. Inhibition of proliferation of endometrial stromal cells by
trichostatin A, RU486, CDB-2914, N-acetylcysteine, and ICI 182780.
Gynecol Obstet Invest 2006;62:193– 205.
Xu LG, Shu HB. TNFR-associated factor-3 is associated with BAFF-R and
negatively regulates BAFF-R-mediated NF-kappa B activation and IL-10
production. J Immunol 2002;169:6883– 6889.
Xu Z, Patterson TA, Wren JD, Han T, Shi L, Duhart H, Ali SF, Slikker W, Jr.
A microarray study of MPPþ-treated PC12 cells: mechanisms of toxicity
(MOT) analysis using bioinformatics tools. BMC Bioinformatics 2005;
6(Suppl 2):S8.
Yeh CH, Lin YM, Wu YC, Lin PJ. Inhibition of NF-kappa B activation can
attenuate ischemia/reperfusion-induced contractility impairment via
decreasing cardiomyocytic proinflammatory gene up-regulation and matrix
metalloproteinase expression. J Cardiovasc Pharmacol 2005;45:301–309.
Yoshida S, Harada T, Mitsunari M, Iwabe T, Sakamoto Y, Tsukihara S, Iba Y,
Horie S, Terakawa N. Hepatocyte growth factor/Met system promotes
endometrial and endometriotic stromal cell invasion via autocrine and
paracrine pathways. J Clin Endocrinol Metab 2004;89:823– 832.
Yoshino O, Osuga Y, Hirota Y, Koga K, Hirata T, Harada M, Morimoto C,
Yano T, Nishii O, Tsutsumi O, Taketani Y. Possible pathophysiological
roles of mitogen-activated protein kinases (MAPKs) in endometriosis.
Am J Reprod Immunol 2004;52:306– 311.
Zeitvogel A, Baumann R, Starzinski-Powitz A. Identification of an invasive,
N-cadherin-expressing epithelial cell type in endometriosis using a new
cell culture model. Am J Pathol 2001;159:1839–1852.
Zhou HE, Nothnick WB. The relevancy of the matrix metalloproteinase system
to the pathophysiology of endometriosis. Front Biosci 2005;10:569–575.
Ziogas A, Moelling K, Radziwill G. CNK1 is a scaffold protein that regulates
Src-mediated Raf-1 activation. J Biol Chem 2005;280:24205–24211.
Submitted on January 9, 2007; resubmitted on March 13, 2007; accepted on
April 17, 2007