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Advances in Brief |
Department of Carcinogenesis, University of Texas, M. D. Anderson Cancer Center, Smithville, Texas 78957
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ABSTRACT |
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3-fold by 3 h
post-E2 treatment. We cloned five novel genes
(E2IG1-5), which were observed
up-regulated by the hormonal treatment. Of these the most highly
induced transcript, E2IG1, appears to be a novel member
of the family of small heat shock proteins. The E2IG4
gene is a new member of the large family of leucine-rich
repeat-containing proteins. On the basis of architectural and domain
homology, this gene appears to be a good candidate for secretion in the
extracellular environment and, therefore, may play a role in breast
tissue remodeling and/or epithelium-stroma interactions. Several
interesting genes with a potential role in the regulation of cell cycle
progression were also identified to increase in expression, including
Pescadillo and chaperonin CCT2. Two
putative paracrine/autocrine factors of potential importance in the
regulation of the growth of breast cancer cells were identified to be
highly up-regulated by E2: stanniocalcin 2, a
calcium/phosphate homeostatic hormone; and inhibin-ß B, a
TGF-ß-like factor. Interestingly, we also determined that
E2IG1 and stanniocalcin 2 were
exclusively overexpressed in estrogen-receptor-positive breast cancer
lines, and thus they have the potential to serve as breast cancer
biomarkers. This data provides a comprehensive view of the changes
induced by E2 on the transcriptional program of
human E2-responsive cells, and it also identifies novel and
previously unsuspected gene targets whose expression is affected by
this hormone. |
Introduction |
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TopABSTRACTIntroductionMaterials and MethodsResultsDiscussionREFERENCES |
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It is known that the effect of E2 is mediated
through its ability to bind the ERs, 
and ß, which are basically
ligand-activated transcription factors. Recently, numerous
ER-associated proteins, coactivators, and repressors have been
identified that are of importance in regulating the ER interaction with
the basal transcription machinery (2)
. The mitogenic
effects of E2 have been in large part attributed
to its ability to increase the expression of key cell cycle regulatory
genes (3)
. However, regulation of cell proliferation is
just one aspect of interest in E2 studies. Of
much importance is the identification of "novel" downstream
E2 effectors, regardless of their association
with proliferation. Furthermore, the potential exists for such newly
identified E2 targets to become biomarkers of
relevance in the monitoring of estrogen-related disease conditions such
as breast cancer and osteoporosis.
In this report we describe a comprehensive gene expression analysis of the effects of E2 using a classical E2-responsive human model. To perform the comparative gene expression profiling we used SAGE, a powerful global gene expression technique that allows for the quantitative evaluation of all cellular mRNA populations (i.e., the transcriptome; Ref. 4 ). As a result of this study, various novel E2 targets, both known and previously unknown, were identified, which will stimulate additional studies into the mechanisms of E2 action.
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Materials and Methods |
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TopABSTRACTIntroductionMaterials and MethodsResultsDiscussionREFERENCES |
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The MCF-7 cell line batch used in these studies is derived directly from the original MCF-7 cell line. The ability of E2 to induce cell proliferation was verified by fluorescence-activated cell sorting analysis and cell counts. MCF-7 cells were maintained in Iscove’s MEM (Biofluids) without phenol red and supplemented with glutamine, 50 µg/ml gentamicin, and 10% FBS (BioWhittaker). Other breast cancer cell lines used included ZR-75-1, SKBR3, MDA-MB-157, MDA-MB-435, MDA-MB-453, and T47D grown in10% FBS/DMEM, and UACC-812 grown in 10%FBS/L-15. We also used normal human mammary epithelial cells (HME-87), normal mammary organoids (B43), and normal bulk breast tissues (HMG), as described previously (5) .
SAGE.
To obtain mRNA samples for SAGE, MCF-7 cells were seeded into 150-mm
plates (1.5 x 106 cells/plate)
and allowed to reach a logarithmic growth phase in culture media
supplemented with FBS. At 40% confluency, cells were incubated for
48 h in culture media supplemented with 10% charcoal stripped
serum (Hyclone). Cells were then treated with
10-8 M 17ß-estradiol (Sigma) or
vehicle control (equivalent amounts of ethanol). Samples were collected
at time 0 (i.e., untreated), 3, and 10 h after starting
treatment. Total RNA was isolated using the Qiagen total RNA Maxi kit
(Qiagen) and mRNA was purified using the Oligotex mRNA mini kit
(Qiagen) following the manufacturer’s protocol. SAGE library
generation and sequencing was performed as described previously by
Velculescu et al. (4)
. Statistical analysis of
and comparison between different time points and controls were
performed as described by Zhang et al. (6)
and
by using statistical functions available in the SAGE 3.0 software
(kindly provided by Dr. K. Kinzler, The John Hopkins University) for
P calculations and Monte Carlo simulations.
Northern Blot Analysis.
Samples for Northern blot analysis were obtained from MCF-7 cells
handled as described for SAGE and treated with
10-8 M E2 for
0, 3, 6, 10, 15, and 24 h and with vehicle control for 24 h
before harvesting. RNA isolation and Northern blotting was performed
following standard procedures. Probes for hybridization were obtained
by RT-PCR from breast cDNA libraries and their sequence was confirmed
before use. Expression of ER- mRNA was confirmed using RT-PCR.
Cloning and Computer Analysis of Novel Transcripts.
Novel transcripts were cloned from a human placenta cDNA library (Rapid
Screen; Origene Technologies). To screen this library we used the same
primers as for generating Northern probes. Each cDNA clone was
sequenced in its entirety, and the SAGE tag was confirmed. The
predicted amino acid sequence for each transcript was analyzed using
BLASTP and PSIBLAST algorithms, and the identification of protein
family domains was determined using the Pfam domain
models.4
For protein cellular localization analysis we used the PSORT
algorithm (7)
.
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Results |
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TopABSTRACTIntroductionMaterials and MethodsResultsDiscussionREFERENCES |
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MCF-7 cells were cultured in conditions devoid of E2 for 48 h before the start of the experiments. mRNA was then collected for SAGE at time points of 3 (E2 3 h) and 10 (E2 10 h) h after E2 treatment. The sampled time points allowed us to analyze changes occurring in the transcriptome of the MCF-7 cells prior to entry into S phase, as determined by fluorescence-activated cell sorting (data not shown).
The SAGE profiles for E2-treated cells (E2 3 h and E2 10 h), were compared with SAGE profiles from untreated MCF-7 cells (E2 0 h) and a 3-h, vehicle-treated control. A total of 188,367 transcript tags (approximately 61,000 tags for each E2 0 h, E2 3 h, and E2 10 h) plus additional tags from vehicle control were sequenced and analyzed. These tags identified a total of 12,550 different transcripts. Of these, the vast majority (83%) showed matches in GB databases to either known genes or anonymous ESTs. The remaining 17% of the tags (i.e., 2,100 transcripts) showed no database matches.
Comparison of the SAGE tag libraries from MCF-7 treated and untreated
cells demonstrated a remarkable similarity between expression profiles.
Fig. 1A
illustrates scatter plots representing the relative
expression of all transcripts analyzed, derived from pairwise
comparisons of the three SAGE libraries. The excellent correlation
coefficients illustrates both the reproducibility of SAGE using three
different samples and RNA isolates as well as the close similarity of
the samples under analysis in this particular study. The vast majority
of transcripts did not change in expression; 81.4% of them (
10,214
transcripts) exhibited a <2-fold difference in expression upon
E2 treatment (Fig. 1B)
.
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3-fold at the P <0.001 level of significance. Of these
transcripts, 37 tags identified known genes, 8 corresponded to
anonymous EST clusters, 2 matched more than one sequence, and 3
transcripts showed no reliable matches in the GB databases (Table 1)
. One transcript (the arginino succinate synthase gene) was
also observed to increase in the vehicle control-treated cells.
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Cloning and Characterization of Novel
E2-induced Genes
As indicated, several of the transcript tags shown in Table 1
identified anonymous EST clusters or had no matches in GB databases. On
our follow-up studies to the SAGE analysis, we first focused on those
transcript tags that increased >10-fold upon E2
treatment. As a result, we isolated a series of five novel cDNAs from a
human placenta cDNA library using transcript-specific PCR primers. We
named these novel genes "E2IGs" 1–5, for
"E2-induced genes." Full-length
cDNA sequences for each of the novel transcripts have been reported to
the GB databases of the National Center for Biotechnology Information
under accession nos. AF191017, AF242180, AF191018, AF191019, and
AF191020 for E2IG1, E2IG2, E2IG3,
E2IG4, and E2IG5, respectively.
The gene cloned from tag CCTGGCCTAA, which increased in number from 0
to 18 tags, was named E2IG1. The corresponding cDNA is 2007
bp long containing a predicted open reading frame of 588 bp. The
central portion of this 196AA protein is homologous to a highly
conserved HSP- crystalline domain common to all HSP20 family members
(10)
. Furthermore, E2IG1 shows a 54% homology
to HSP27, suggesting that E2IG1 is a novel member of the
small HSP family. On the basis of matching sequence with sts
TIGR–A002J47, we can predict that this gene maps to chromosome 12
(D12S366–D12S340 interval).
E2IG4 corresponds to the SAGE tag GGCATCAGGG, which
increased from 0 tags to 12 tags by 3 h
post-E2 exposure in MCF7 cells. This cDNA is 2542
bp long, showing a 1059-bp open reading frame encoding for a 353AA
protein. This protein is characterized by the presence of a
leucine-rich repeat in the NH2-terminal
domain and eight additional leucine-rich repeats (Fig. 2)
. Interestingly, E2IG4 demonstrates domain and structural homology to
extracellular matrix leucine-rich proteoglycans such as decorin (PGS2)
and biglycan (PGS1). The E2IG4 protein is likely to reside in the cell
membrane or extracellular compartments (57% probability; Ref.
7
). E2IG4 also contains a typical cleavable signal peptide
at AA 1–16, which makes it a candidate protein for intracellular
transport and extracellular secretion. In addition, E2IG4
contains various potential phosphorylation sites throughout its amino
acid sequence. On the basis of matching DNA sequence from sts
AA009735 to E2IG4, it is possible to predict the mapping of
this gene to human chromosome 11, (D11S911–D11S4172 interval).
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E2-Induced Expression of Previously Known Genes
Chaperones.
In addition to the novel genes described above, we show in Table 1
all
genes that were found to increase in expression at 3-fold with
E2 treatment at the P < 0.001-level
of significance. Among these transcripts we found abundant
representation of protein members of a large class of molecular
chaperones known as HSPs. In our studies, the most significant
increases in gene expression were observed for HSP90 (both
and ß chains), HSP60 (chaperonin), CCT2,
HSC71 (HSP70 family), FKBP4
(immunophilin/p59/HSP56), and the
E2-induced gene described in this report,
E2IG1 (HSP20 family; Table 1
).
Cell Cycle Progression-related Genes.
SAGE tags identifying CCT2 were found to increase from 0 to
10 tags by 10 h post-E2 treatment. This
chaperone complex plays a fundamental role in cell cycle progression
because it is in charge of the proper folding and maturation of cyclin
E molecules (12)
.
Among well-known critical cell cycle targets of E2, the tags identifying cyclin D1 were observed to increase from 32 to 113 SAGE tags (i.e., 3.5-fold) by 3 h of hormonal treatment.
The tag identifying the human homologue to the zebrafish developmental
gene PES1 also demonstrated a marked increase in expression
after E2 treatment (from 0 to 14 tags; Table 1
).
PES1 is predicted to encode a protein of 582AA that is
highly conserved from yeast to humans (13)
. On the basis
of the presence of a BRCT (BRCA1 COOH terminus) domain in
PES1, we can speculate that PES1 may be of
relevance in cell cycle regulation (14)
.
Ran/TC4, another transcript up-regulated by the treatment, is a small GTP-binding protein member of the Ras superfamily, which is essential for the translocation of RNA and proteins through the nuclear pore complex. This GTPase may play a role in releasing steroid receptors from the nuclear pore complex and in connecting DNA synthesis with the onset of mitosis (15 , 16) .
Tags identifying other relevant cell cycle progression modulators
include those identifying calmodulin subunits, CALM1 and
CALM2. CALM1 expression increased from 30 to 50
tags (data not shown), and CALM2 increased from 12 to 40
tags (P < 0.001) upon
E2 treatment (Table 1)
. It is known that this
important calcium-binding protein plays an essential role for quiescent
cells to enter the cell cycle (17)
. Calmodulin also
regulates phosphorylation and induces conformational changes of the ER
(18
, 19)
.
We also observed an increase in tag numbers identifying subunits of the proteasome complex, a multicatalytic intracellular protease system that targets key proteins for degradation (20) . The ubiquitin-proteasome pathway also appears to be a major mechanism implicated in the turnover of the ER in an E2-dependent manner, which would agree with our findings (21) .
Paracrine-Autocrine Factors.
Among interesting gene targets not associated previously with
E2 effects, we observed a 10-fold increase in
expression for STC2 (Table 1)
. STC2 (also known as
stanniocalcin-related peptide STCrP) has amino acid sequence homology
to the previously identified STC1 (22
, 23)
. However, the
SAGE tag matching STC1 did not increase in numbers, nor did
we observe up-regulation by Northern analysis (data not shown).
An additional autocrine/paracrine factor, INHBB
(activin-ß-b subunit) was identified to increase >15-fold
upon E2 treatment (Table 1)
. Originally inhibin
was identified as a gonadal hormone that inhibits the secretion of
follicle-stimulating hormone (whereas activin stimulates the
secretion of follicle-stimulating hormone) by the pituitary gland
(24)
. Activins/inhibins belong to the TGF-ß
superfamily (25)
. The only inhibin-related transcript tag
found up-regulated by E2 treatment was that of
the INHBB subunit.
Tumor-associated Genes.
SAGE identified an increase in expression for various tumor associated
proteins, RFP (ret finger protein),
D52L1 (D53 tumor protein), Trefoil
factor (TFF1 or PS2), CAV1, and
NDKA, among others (Table 1)
.
RFP was first identified for its elevated expression in a variety of rodent tumor cell lines (26) . This protein is located in the nucleus and because of its zinc finger domain is believed to bind DNA. However the function of this protein is, at present, unknown.
Tumor protein D52L1, also known as D53, increased from 7 tags in untreated cells to 27 tags in the 3-h E2-treatment profile. D53 was originally cloned from a breast carcinoma cDNA library and has a 52% homology to D52 (27) . Interestingly, and in agreement with our SAGE findings, previous studies have shown that both D52 and D53 transcription in breast carcinoma cells are dependent upon E2 presence in MCF-7 cells (27) .
The well-known E2 regulated gene PS2 (Trefoil factor; Ref. 28 ) was also detected to increase 14-fold by SAGE from 13 tags at 0 h to 186 tags by 10-h-post-E2 treatment.
Interestingly, we observed a significant increase in tags identifying the putative metastasis suppressor gene NDKA/Nm23H1 (2.5-fold increase; P = 0.000003). It is likely that such an increase in expression is related to its fundamental housekeeping role in maintaining the nucleoside diphosphate/nucleotide triphosphate cellular balance (29) .
The tags identifying CAV1 were also shown to increase
4-fold (Table 1)
. CAV1 is an integral membrane protein and the main
component of caveolae membranes (a plasma membrane specialization). It
was recently shown that CAV1 functions as a membrane adaptor to link
integrin subunits to the tyrosine kinase FYN (30)
.
Validation of SAGE Findings.
The effects of E2 treatment on the expression of
specific genes were confirmed by means of Northern analysis. To this
end, MCF-7 cells were grown in conditions devoid of
E2 for 48 h and then exposed to
E2 treatment for various lengths of time as shown
in Fig. 3
. These representative transcripts demonstrated different patterns of
expression. Some transcripts increased and remained high for the entire
course of treatment, whereas others increased rapidly in early time
points and then tapered off in later time points (Fig. 3)
. As can be
observed, E2IG1 and E2IG4 already increased
considerably by 3 h of E2 treatment.
E2IG5 showed only a modest increase in expression levels as
detected by total RNA Northern blot analysis (data not shown). The
reason for the apparent discrepancy between the fold values of
increased expression detected by SAGE versus those detected
by Northern analysis in this last case is unclear.
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, and Northern blot analysis
confirmed this fold difference with remarkable accuracy to a 2.5-fold
change. In addition, SAGE also identified a 3.5-fold increase in
cyclin D upon E2 treatment in close
agreement with Northern and Western data reported previously
(3)
.
Transcript Expression in ER+ and ER- Breast Cancer Cell Lines
Northern blot analysis was also used to assess the level of
expression for E2IG1, E2IG2, E2IG3,
E2IG4, and STC2 in a small panel of ER+ and ER-
cell lines. The expression of ER- for each of the cell lines was
confirmed by RT-PCR (Fig. 4)
. Both E2IG1 and STC2 demonstrated selective
expression in ER+ cell lines (Fig. 4)
, whereas E2IG2,
E2IG3, and E2IG4 demonstrated varied expression
in the different cell lines (data not shown). The selective expression
in ER+ cell lines for STC2 and E2IG1 suggests
their expression is dependent on the presence of a functional ER.
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Discussion |
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TopABSTRACTIntroductionMaterials and MethodsResultsDiscussionREFERENCES |
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Our cloning effort was focused on those SAGE tags identifying anonymous
ESTs which increased above 10-fold upon E2
treatment. Among these, E2IG1 was identified as a putative
small HSP and which bears 54% homology to HSP27.
Interestingly, the HSP27 expression has been associated with
the presence of ER in breast and endometrial carcinomas
(31)
. It was remarkable in our study that there was
selective overexpression of E2IG1 in ER+ breast cancer cell
lines (Fig. 4)
. These findings suggests that E2IG1
expression is dependent on the presence of a functional ER. On the
basis of these observations and on the rapid and dramatic up-regulation
of E2IG1 after E2 treatment, we can
speculate that this gene is a prime candidate to be a direct effector
of E2. Because E2IG1 is a putative new
member of the small HSP family, it may play a specific chaperonic role
related to either the ER itself or to some point downstream of the
E2-induced signaling cascade. In addition, the
described selective overexpression of E2IG1 in ER+ breast
tumor cells make it a good potential marker for
E2-dependent breast carcinomas.
A second very intriguing novel target of E2 treatment is the E2IG4 protein. This putative protein is a new member of the large family of leucine-rich repeat-containing proteins. On the basis of sequence homology and motif distribution analysis, it is possible to speculate that E2IG4 may constitute a novel extracellular matrix component. Analysis of the E2IG4 amino acid sequence showed some moderate homology to GAC1, a leucine-rich protein amplified in gliomas (32) . E2IG4 also showed domain and leucine-repeat distribution homology, as well as general features of similarity, to several cleaved extracellular proteins such as: platelet glycoprotein V precursor; PGS2 (bone proteoglycan II precusor), also known as decorin; and PGS1 (biglycan). Both decorin and biglycan belong to the small interstitial proteoglycans family and are found in the extracellular matrix. Interestingly in rat, decorin has been isolated from cervix uteri, and it appears to be hormonally regulated (33) .
The presence of a typical signal peptide cleavage site in the AA sequence of E2IG4 also makes this protein a good candidate for transport to the cell membrane and secretion to the extracellular environment. The combination of the described E2IG4 structural features and homologies plus the observed up-regulation induced by E2 suggests that this protein could play a role in hormonally regulated, extracellular matrix remodeling and/or epithelium-stromal interactions in breast tissue.
Among the SAGE tags increasing in abundance upon E2 treatment, several identified various members of large families of proteins with chaperonic function. There is evidence to suggest that the expression of HSPs may play a role in breast cancer and in E2 regulation, however the induced expression of HSPs is not unique to E2 (34, 35, 36) . HSP90 also functions as a stabilizer of critical signal transducers, including cell cycle and developmental regulators. These include Src-family-kinases, raf serine/threonine kinases, calmodulin, dioxin-receptor, cyclin-dependent kinases, and steroid-hormone receptors (37) . HSP90 together with HSP70 play important roles in the maturation of the steroid receptor in achieving a hormone-binding competent state as well as in regulating the receptor cytoplasmic-nuclear trafficking (15) . The HSP90-binding protein, FKBP4, was also observed increasing in expression upon E2 treatment. Both HSP90 and FKBP4 are known to bind unliganded, steroid receptor complexes (38) .
Interestingly SAGE also identified up-regulation of CCT2, a chaperone protein which has recently been shown to bind newly synthesized cyclin E, mediating its maturation (folding) into a form that can associate with cyclin-dependent kinase 2 (12) . The important function of cyclin E as a key player promoting the G1-to-S phase transition in breast cancer cells has been shown (39) . The demonstrated ability of CCT2 to control in turn the maturation of cyclin E, and hence its critical function in the cell cycle, appears to provide an additional layer of influence in cell cycle progression by E2.
PES1 was another gene observed to be up-regulated upon E2 treatment that also may play a role in cell cycle regulation. The highly conserved PES1 displays a region of approximately 100 amino acids (322–415) with homology to the BRCT domain superfamily. BRCT domains are usually found in proteins that play critical roles in cell cycle control and DNA repair (14) . The possibility that PES1 is playing a role in either of these processes is of interest and therefore deserves additional investigation.
Among the identification of novel targets of E2 action, it is important to stress the dramatic increase in expression observed for STC2. Although STC was initially thought to be unique to fish, the two mentioned homologues of STC have now been identified in mammalians (i.e., STC1, 61% homology, and STC2, 30–38% homology). In humans, the function of these hormones is unknown. However, in fish it was observed that STC functions as a potent regulator of calcium and phosphate homeostasis preventing hypercalcemia in a similar fashion to calcitonin in mammals (40) . It has been proposed that mammalian STCs act as regulators of calcium/phosphate homeostasis in a paracrine and/or autocrine, rather than endocrine, fashion, as suggested by their widespread expression in tissues (41, 42, 43) . Some evidence suggests that STC2 acts in a manner opposite to STC1 on regulating calcium/phosphate concentrations (23) . The fact that STC2 appears to be a secreted protein and is selectively overexpressed in ER+ cell lines suggests that it may have potential use as a serum-detectable prognostic marker for breast cancer. In addition, because of its potential role as a calcium/phosphate regulator and its wide expression, including in bone, STC2 becomes a prime target for additional study because it may provide a novel link between the effects of E2 and bone remodeling.
SAGE also identified another interesting
E2-regulated, autocrine/paracrine factor, INHBB.
This protein subunit functions either as a homodimer (activin B) or a
heterodimer with ß-A or - subunits (forming activin AB or inhibin
B, respectively). The elevation of inhibin subunits and ß-B,
after E2 treatment has been observed in granulosa
cells (44)
. It has also been shown that ER+ breast cancer
lines are growth-inhibited by activin B (45)
. Furthermore,
the expression of inhibin/activin subunits and corresponding receptors
has been detected in MCF-7 cells (46)
. Theoretically, the
increased expression of INHBB would tilt the homo/heterodimer balance
toward generation of activin B, inasmuch as INHBB was the only inhibin
subunit found to increase upon E2 treatment. This
appears to point to a paradoxical effect of E2
because activins, along with the rest of the TGF-ß family, are
thought to contribute to maintaining a negative-growth regulatory
function in ER+ breast cancer cells, which would be in opposition to
the ability of E2 to stimulate cell growth
(45)
. Additional study is therefore required to better
understand the role of modifications in the activin/inhibin homeostasis
in E2-responsive breast cancer cells and its
putative effect in regulating cell growth.
In this report we have summarized some of the most prominent effects induced by E2 affecting the transcriptional program of E2-responsive cells at a global level. As mentioned, several of the observed changes in gene expression will be common to those induced by other mitogens. On the other hand, numerous changes observed are likely to be directly induced by this important female steroid hormone. Follow-up studies on the mechanisms of expression regulation for the novel targets described, as well as for previously unsuspected effectors of E2, are now in order.
It is also important to stress that several of these genes have a very good potential to serve as diagnostic/prognostic tools for the monitoring of estrogen-related disease conditions such as breast cancer.
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FOOTNOTES |
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1 Supported in part by the Susan G. Komen Breast
Cancer Foundation, postdoctoral award to A. H. C., and National
Institute of Environmental Health Sciences Center Grant ES07784. 
2 To whom requests for reprints should be
addressed, at University of Texas, M. D. Anderson Cancer Center,
Science Park Research Division, P. O. Box 389, Smithville, TX 78957.
Phone: (512) 237-9530; Fax: (512) 237-2475; E-mail: maldaz{at}odin.mdacc.tmc.edu
3 The abbreviations used are: E2,
17ß estradiol; FBS, fetal bovine serum; SAGE, serial analysis of gene
expression; RT-PCR, reverse transcription-PCR; HSP, heat shock protein;
CCT2, chaperonin-containing
t-complex; STC, stanniocalcin; INHBB, inhibin-ß
B; ER, estrogen receptors; GB, GenBank; EST, expressed sequence tag;
CAV1, caveolin 1; NDKA, nucleoside diphosphate kinase A, or Nm23H1;
PES1, Pescadillo.
4 Internet address: http://pfam.wustl.edu.
5 Internet address:
http://sciencepark.mdanderson.org/ggeg.
Received 6/16/00. Accepted 9/15/00.
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M. C. Abba, H. Sun, K. A. Hawkins, J. A. Drake, Y. Hu, M. I. Nunez, S. Gaddis, T. Shi, S. Horvath, A. Sahin, et al. Breast Cancer Molecular Signatures as Determined by SAGE: Correlation with Lymph Node Status Mol. Cancer Res., September 1, 2007; 5(9): 881 - 890. [Abstract] [Full Text] [PDF]
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 I. Cohen, B. Maly, I. Simon, A. Meirovitz, E. Pikarsky, E. Zcharia, T. Peretz, I. Vlodavsky, and M. Elkin Tamoxifen Induces Heparanase Expression in Estrogen Receptor Positive Breast Cancer Clin. Cancer Res., July 15, 2007; 13(14): 4069 - 4077. [Abstract] [Full Text] [PDF]
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S. Esseghir, A. Kennedy, P. Seedhar, A. Nerurkar, R. Poulsom, J. S. Reis-Filho, and C. M. Isacke Identification of NTN4, TRA1, and STC2 as Prognostic Markers in Breast Cancer in a Screen for Signal Sequence Encoding Proteins Clin. Cancer Res., June 1, 2007; 13(11): 3164 - 3173. [Abstract] [Full Text] [PDF]
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M. C. Abba, V. T. Fabris, Y. Hu, F. S. Kittrell, W.-W. Cai, L. A. Donehower, A. Sahin, D. Medina, and C. M. Aldaz Identification of Novel Amplification Gene Targets in Mouse and Human Breast Cancer at a Syntenic Cluster Mapping to Mouse ch8A1 and Human ch13q34 Cancer Res., May 1, 2007; 67(9): 4104 - 4112. [Abstract] [Full Text] [PDF]
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C. Yang, S. Trent, V. Ionescu-Tiba, L. Lan, T. Shioda, D. Sgroi, and E. V. Schmidt Identification of Cyclin D1- and Estrogen-Regulated Genes Contributing to Breast Carcinogenesis and Progression Cancer Res., December 15, 2006; 66(24): 11649 - 11658. [Abstract] [Full Text] [PDF]
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M. Dolled-Filhart, L. Ryden, M. Cregger, K. Jirstrom, M. Harigopal, R. L. Camp, and D. L. Rimm Classification of breast cancer using genetic algorithms and tissue microarrays. Clin. Cancer Res., November 1, 2006; 12(21): 6459 - 6468. [Abstract] [Full Text] [PDF]
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 F. Stossi, V. S. Likhite, J. A. Katzenellenbogen, and B. S. Katzenellenbogen Estrogen-occupied Estrogen Receptor Represses Cyclin G2 Gene Expression and Recruits a Repressor Complex at the Cyclin G2 Promoter J. Biol. Chem., June 16, 2006; 281(24): 16272 - 16278. [Abstract] [Full Text] [PDF]
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G. P. Elvidge, L. Glenny, R. J. Appelhoff, P. J. Ratcliffe, J. Ragoussis, and J. M. Gleadle Concordant Regulation of Gene Expression by Hypoxia and 2-Oxoglutarate-dependent Dioxygenase Inhibition: THE ROLE OF HIF-1{alpha}, HIF-2{alpha}, AND OTHER PATHWAYS J. Biol. Chem., June 2, 2006; 281(22): 15215 - 15226. [Abstract] [Full Text] [PDF]
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J. Yao, S. Weremowicz, B. Feng, R. C. Gentleman, J. R. Marks, R. Gelman, C. Brennan, and K. Polyak Combined cDNA array comparative genomic hybridization and serial analysis of gene expression analysis of breast tumor progression. Cancer Res., April 15, 2006; 66(8): 4065 - 4078. [Abstract] [Full Text] [PDF]
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V X Jin, H Sun, T T Pohar, S Liyanarachchi, S K Palaniswamy, T H-M Huang, and R V Davuluri ERTargetDB: an integral information resource of transcription regulation of estrogen receptor target genes J. Mol. Endocrinol., October 1, 2005; 35(2): 225 - 230. [Abstract] [Full Text] [PDF]
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J. Laganiere, G. Deblois, C. Lefebvre, A. R. Bataille, F. Robert, and V. Giguere From the Cover: Location analysis of estrogen receptor {alpha} target promoters reveals that FOXA1 defines a domain of the estrogen response PNAS, August 16, 2005; 102(33): 11651 - 11656. [Abstract] [Full Text] [PDF]
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J. I. Risinger, G. L. Maxwell, G. V.R. Chandramouli, O. Aprelikova, T. Litzi, A. Umar, A. Berchuck, and J. C. Barrett Gene Expression Profiling of Microsatellite Unstable and Microsatellite Stable Endometrial Cancers Indicates Distinct Pathways of Aberrant Signaling Cancer Res., June 15, 2005; 65(12): 5031 - 5037. [Abstract] [Full Text] [PDF]
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T. Itoh, K. Karlsberg, I. Kijima, Y.-C. Yuan, D. Smith, J. Ye, and S. Chen Letrozole-, Anastrozole-, and Tamoxifen-Responsive Genes in MCF-7aro Cells: A Microarray Approach Mol. Cancer Res., April 1, 2005; 3(4): 203 - 218. [Abstract] [Full Text] [PDF]
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J. Xu, S. Fan, and E. M. Rosen Regulation of the Estrogen-Inducible Gene Expression Profile by the Breast Cancer Susceptibility Gene BRCA1 Endocrinology, April 1, 2005; 146(4): 2031 - 2047. [Abstract] [Full Text] [PDF]
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Y. Jia, C. Qi, Z. Zhang, Y. T. Zhu, S. M. Rao, and Y.-J. Zhu Peroxisome Proliferator-activated Receptor-binding Protein Null Mutation Results in Defective Mammary Gland Development J. Biol. Chem., March 18, 2005; 280(11): 10766 - 10773. [Abstract] [Full Text] [PDF]
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 M. P.H.M. Jansen, J. A. Foekens, I. L. van Staveren, M. M. Dirkzwager-Kiel, K. Ritstier, M. P. Look, M. E. Meijer-van Gelder, A. M. Sieuwerts, H. Portengen, L. C.J. Dorssers, et al. Molecular Classification of Tamoxifen-Resistant Breast Carcinomas by Gene Expression Profiling J. Clin. Oncol., February 1, 2005; 23(4): 732 - 740. [Abstract] [Full Text] [PDF]
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C.-W. Luo, M. D. Pisarska, and A. J. W. Hsueh Identification of a Stanniocalcin Paralog, Stanniocalcin-2, in Fish and the Paracrine Actions of Stanniocalcin-2 in the Mammalian Ovary Endocrinology, January 1, 2005; 146(1): 469 - 476. [Abstract] [Full Text] [PDF]
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 M. Becker, A. Sommer, J. R. Kratzschmar, H. Seidel, H.-D. Pohlenz, and I. Fichtner Distinct gene expression patterns in a tamoxifen-sensitive human mammary carcinoma xenograft and its tamoxifen-resistant subline MaCa 3366/TAM Mol. Cancer Ther., January 1, 2005; 4(1): 151 - 170. [Abstract] [Full Text] [PDF]
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Y. Hu, H. Sun, J. Drake, F. Kittrell, M. C. Abba, L. Deng, S. Gaddis, A. Sahin, K. Baggerly, D. Medina, et al. From Mice to Humans: Identification of Commonly Deregulated Genes in Mammary Cancer via Comparative SAGE Studies Cancer Res., November 1, 2004; 64(21): 7748 - 7755. [Abstract] [Full Text] [PDF]
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C. Qi, P. Kashireddy, Y. T. Zhu, S. M. Rao, and Y.-J. Zhu Null Mutation of Peroxisome Proliferator-activated Receptor-interacting Protein in Mammary Glands Causes Defective Mammopoiesis J. Biol. Chem., August 6, 2004; 279(32): 33696 - 33701. [Abstract] [Full Text] [PDF]
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 S. A. K. Harvey, S. C. Anderson, and N. SundarRaj Downstream Effects of ROCK Signaling in Cultured Human Corneal Stromal Cells: Microarray Analysis of Gene Expression Invest. Ophthalmol. Vis. Sci., July 1, 2004; 45(7): 2168 - 2176. [Abstract] [Full Text] [PDF]
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V. Bourdeau, J. Deschenes, R. Metivier, Y. Nagai, D. Nguyen, N. Bretschneider, F. Gannon, J. H. White, and S. Mader Genome-Wide Identification of High-Affinity Estrogen Response Elements in Human and Mouse Mol. Endocrinol., June 1, 2004; 18(6): 1411 - 1427. [Abstract] [Full Text] [PDF]
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M.-J. Lee, J.-Y. Kim, K. Suk, and J.-H. Park Identification of the Hypoxia-Inducible Factor 1{alpha}-Responsive HGTD-P Gene as a Mediator in the Mitochondrial Apoptotic Pathway Mol. Cell. Biol., May 1, 2004; 24(9): 3918 - 3927. [Abstract] [Full Text] [PDF]
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D.-Y. Wang, R. Fulthorpe, S. N. Liss, and E. A. Edwards Identification of Estrogen-Responsive Genes by Complementary Deoxyribonucleic Acid Microarray and Characterization of a Novel Early Estrogen-Induced Gene: EEIG1 Mol. Endocrinol., February 1, 2004; 18(2): 402 - 411. [Abstract] [Full Text] [PDF]
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X. Sun, J.-M. Fontaine, J. S. Rest, E. A. Shelden, M. J. Welsh, and R. Benndorf Interaction of Human HSP22 (HSPB8) with Other Small Heat Shock Proteins J. Biol. Chem., January 23, 2004; 279(4): 2394 - 2402. [Abstract] [Full Text] [PDF]
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 M. Huber, I. Bahr, J. R. Kratzschmar, A. Becker, E.-C. Muller, P. Donner, H.-D. Pohlenz, M. R. Schneider, and A. Sommer Comparison of Proteomic and Genomic Analyses of the Human Breast Cancer Cell Line T47D and the Antiestrogen-resistant Derivative T47D-r Mol. Cell. Proteomics, January 1, 2004; 3(1): 43 - 55. [Abstract] [Full Text] [PDF]
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M. Elkin, I. Cohen, E. Zcharia, A. Orgel, Z. Guatta-Rangini, T. Peretz, I. Vlodavsky, and H. K. Kleinman Regulation of Heparanase Gene Expression by Estrogen in Breast Cancer Cancer Res., December 15, 2003; 63(24): 8821 - 8826. [Abstract] [Full Text] [PDF]
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 Y. Kun, L. C. How, T. P. Hoon, V. B. Bajic, T. S. Lam, A. Aggarwal, H. G. Sze, W. S. Bok, W. C. Yin, and P. Tan Classifying the estrogen receptor status of breast cancers by expression profiles reveals a poor prognosis subpopulation exhibiting high expression of the ERBB2 receptor Hum. Mol. Genet., December 15, 2003; 12(24): 3245 - 3258. [Abstract] [Full Text] [PDF]
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H. E. Cunliffe, M. Ringner, S. Bilke, R. L. Walker, J. M. Cheung, Y. Chen, and P. S. Meltzer The Gene Expression Response of Breast Cancer to Growth Regulators: Patterns and Correlation with Tumor Expression Profiles Cancer Res., November 1, 2003; 63(21): 7158 - 7166. [Abstract] [Full Text] [PDF]
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T. Hayano, M. Yanagida, Y. Yamauchi, T. Shinkawa, T. Isobe, and N. Takahashi Proteomic Analysis of Human Nop56p-associated Pre-ribosomal Ribonucleoprotein Complexes: POSSIBLE LINK BETWEEN Nop56p AND THE NUCLEOLAR PROTEIN TREACLE RESPONSIBLE FOR TREACHER COLLINS SYNDROME J. Biol. Chem., September 5, 2003; 278(36): 34309 - 34319. [Abstract] [Full Text] [PDF]
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S. Oesterreich, W. Deng, S. Jiang, X. Cui, M. Ivanova, R. Schiff, K. Kang, D. L. Hadsell, J. Behrens, and A. V. Lee Estrogen-mediated Down-Regulation of E-cadherin in Breast Cancer Cells Cancer Res., September 1, 2003; 63(17): 5203 - 5208. [Abstract] [Full Text] [PDF]
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L. Pusztai, M. Ayers, J. Stec, E. Clark, K. Hess, D. Stivers, A. Damokosh, N. Sneige, T. A. Buchholz, F. J. Esteva, et al. Gene Expression Profiles Obtained from Fine-Needle Aspirations of Breast Cancer Reliably Identify Routine Prognostic Markers and Reveal Large-Scale Molecular Differences between Estrogen-negative and Estrogen-positive Tumors Clin. Cancer Res., July 1, 2003; 9(7): 2406 - 2415. [Abstract] [Full Text] [PDF]
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N. Yadav, J. Lee, J. Kim, J. Shen, M. C.-T. Hu, C. M. Aldaz, and M. T. Bedford Specific protein methylation defects and gene expression perturbations in coactivator-associated arginine methyltransferase 1-deficient mice PNAS, May 27, 2003; 100(11): 6464 - 6468. [Abstract] [Full Text] [PDF]
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 C. Depre, M. Hase, V. Gaussin, A. Zajac, L. Wang, L. Hittinger, B. Ghaleh, X. Yu, R. K. Kudej, T. Wagner, et al. H11 Kinase Is a Novel Mediator of Myocardial Hypertrophy In Vivo Circ. Res., November 29, 2002; 91(11): 1007 - 1014. [Abstract] [Full Text] [PDF]
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E. K. Lobenhofer, L. Bennett, P. L. Cable, L. Li, P. R. Bushel, and C. A. Afshari Regulation of DNA Replication Fork Genes by 17{beta}-Estradiol Mol. Endocrinol., June 1, 2002; 16(6): 1215 - 1229. [Abstract] [Full Text] [PDF]
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T. Bouras, M. C. Southey, A. C. Chang, R. R. Reddel, D. Willhite, R. Glynne, M. A. Henderson, J. E. Armes, and D. J. Venter Stanniocalcin 2 Is an Estrogen-responsive Gene Coexpressed with the Estrogen Receptor in Human Breast Cancer Cancer Res., March 1, 2002; 62(5): 1289 - 1295. [Abstract] [Full Text] [PDF]
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 K. Ishibashi and M. Imai Prospect of a stanniocalcin endocrine/paracrine system in mammals Am J Physiol Renal Physiol, March 1, 2002; 282(3): F367 - F375. [Abstract] [Full Text] [PDF]
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K. Iwao, R. Matoba, N. Ueno, A. Ando, Y. Miyoshi, K. Matsubara, S. Noguchi, and K. Kato Molecular classification of primary breast tumors possessing distinct prognostic properties Hum. Mol. Genet., January 1, 2002; 11(2): 199 - 206. [Abstract] [Full Text] [PDF]
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 C. A. Iacobuzio-Donahue, B. Ryu, R. H. Hruban, and S. E. Kern Exploring the Host Desmoplastic Response to Pancreatic Carcinoma : Gene Expression of Stromal and Neoplastic Cells at the Site of Primary Invasion Am. J. Pathol., January 1, 2002; 160(1): 91 - 99. [Abstract] [Full Text] [PDF]
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S. Gruvberger, M. Ringner, Y. Chen, S. Panavally, L. H. Saal, A. Borg, M. Ferno, C. Peterson, and P. S. Meltzer Estrogen Receptor Status in Breast Cancer Is Associated with Remarkably Distinct Gene Expression Patterns Cancer Res., August 1, 2001; 61(16): 5979 - 5984. [Abstract] [Full Text] [PDF]
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 L. O'Donnell, K. M. Robertson, M. E. Jones, and E. R. Simpson Estrogen and Spermatogenesis Endocr. Rev., June 1, 2001; 22(3): 289 - 318. [Abstract] [Full Text] [PDF]
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K. Polyak and G. J. Riggins Gene Discovery Using the Serial Analysis of Gene Expression Technique: Implications for Cancer Research J. Clin. Oncol., June 1, 2001; 19(11): 2948 - 2958. [Abstract] [Full Text] [PDF]
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