Mutations of the breast cancer susceptibility gene 1 (BRCA1), a tumor suppressor, confer an increased risk for breast, ovarian, and prostate cancers. To investigate the function of the BRCA1 gene, we performed DNA microarray and confirmatory reverse transcription-PCR analyses to identify BRCA1-regulated gene expression changes. We found that BRCA1 up-regulates the expression of multiple genes involved in the cytoprotective antioxidant response, including glutathione S-transferases, oxidoreductases, and other antioxidant genes. Consistent with these findings, BRCA1 overexpression conferred resistance while BRCA1 deficiency conferred sensitivity to several different oxidizing agents (hydrogen peroxide and paraquat). In addition, in the setting of oxidative stress (due to hydrogen peroxide), BRCA1 shifted the cellular redox balance to a higher ratio of reduced to oxidized glutathione. Finally, BRCA1 stimulated antioxidant response element-driven transcriptional activity and enhanced the activity of the antioxidant response transcription factor nuclear factor erythroid-derived 2 like 2 [also called NRF2 (NFE2L2)]. The ability of BRCA1 to stimulate antioxidant response element-dependent transcription and to protect cells against oxidative stress was attenuated by inhibition of nuclear factor erythroid-derived 2 like 2. These findings suggest a novel function for BRCA1, i.e., to protect cells against oxidative stress. This function would be consistent with the postulated role of BRCA1 as a caretaker gene in preserving genomic integrity.

Inherited mutations of the breast cancer susceptibility gene breast cancer susceptibility gene 1 (BRCA1) confer an increased risk for breast, ovarian, and prostate cancers (1, 2). In addition, BRCA1 expression is often decreased or absent in sporadic breast and ovarian cancers due, in part, to promoter methylation or other causes, suggesting a role for BRCA1 in nonhereditary tumors (3, 4). The specific functions of the BRCA1 gene that contribute to tumor suppression are unclear. However, established functional roles for BRCA1 include the regulation of cell cycle progression, DNA damage signaling and repair, maintenance of genomic integrity, and the regulation of various transcriptional pathways [reviewed by Rosen et al.(5)].

A role for BRCA1 in transcriptional regulation was first suggested by the finding that BRCA1 has a conserved acidic COOH-terminal transcriptional activation domain (6). Although BRCA1 is not known to bind to specific DNA sequences, it may regulate transcription through protein:protein interactions with components of the basal transcription factor (e.g., RNA helicase A and RNA pol II), transcriptional coactivators and corepressors [e.g., p300 and its functional homologue CBP (the cAMP-responsive element binding proteinbinding protein), retinoblastoma 1, retinoblastoma 1-associated proteins (RbAp46/48), and several histone deaceylases (HDAC-1/2)], and/or sequence-specific DNA-binding transcription factors (e.g., p53, c-Myc, estrogen receptor, and other proteins; refs. 7, 8, 9, 10, 11, 12).

Some of the functions of BRCA1 cited above may be due, in part, to regulation of specific transcriptional pathways by BRCA1, but the linkage of these functions to BRCA1-regulated transcription is not well understood. We used cell culture models of BRCA1 overexpression, underexpression, and mutational inactivation to identify patterns of BRCA1-regulated gene expression. The identification of antioxidant genes as transcriptional targets of BRCA1 led to the findings that BRCA1 regulates the activity of the antioxidant response transcription factor nuclear factor erythroid-derived 2 like 2 [also called NRF2 (NFE2L2)] and protects cells against oxidative stress.

Cell Lines and Culture

Human prostate (DU-145, LNCaP) and breast (MCF-7, T47D) cancer cell lines were obtained from the American Type Culture Collection (Manassas, VA) and cultured as described before (12, 13). The stable wild-type BRCA1 (wtBRCA1) and control (Neo) DU-145 cell clones were isolated and characterized earlier (14, 15). A mouse embryonic fibroblast (MEF) cell line homozygous for a deletion of Brca1 exon 11 and the control wild-type (Brca1+/+) MEFs (16) were provided by Dr. Chuxia Deng (National Institutes of Diabetes, Digestive and Kidney Diseases, Bethesda, MD). All of the above cell types were grown in DMEM supplemented with 5% (DU-145) or 10% (all other cell types) v/v fetal calf serum, l-glutamine (5 mmol/L), nonessential amino acids (5 mmol/L), penicillin (100 units/mL), and streptomycin (100 μg/mL; all obtained from BioWhittaker, Walkersville, MD).

EBV-immortalized peripheral blood lymphocyte cell lines R794 and R1041 were derived from a female BRCA1 (185delAG) and BRCA2 (6174delT) mutation carrier, respectively. These lymphoblastoid cell lines were provided by the Tissue Culture Shared Resource of the Lombardi Comprehensive Cancer Center. The genotypes of the cells were confirmed by the Familial Cancer Registry of the Lombardi Comprehensive Cancer Center.

BRCA1 Expression Vectors and Transfections

For transient expression experiments, cells were transfected with a wild-type BRCA1 expression vector (wtBRCA1) consisting of the full-length BRCA1 cDNA within the pcDNA3 mammalian expression vector (Invitrogen, Carlsbad, CA) or within the pCMV-Tag2B vector (Stratagene, La Jolla, CA), which allows expression of the full-length protein containing a NH2-terminal FLAG epitope tag. Both the untagged and the FLAG-tagged proteins are expressed well and exhibit identical biological activities (13). Methodologies used for transient transfections have been reported previously (13, 15) and are also briefly described below.

Small Interfering (si) RNAs

The BRCA1 and control (scrambled-sequence) siRNAs were described earlier (15). All siRNAs were chemically synthesized by Dharmacon, Inc. (Lafayette, CO). For siRNA treatments, subconfluent proliferating cells were treated with each siRNA (50 nmol/L), with siPORT Amine reagent (Ambion, Austin, TX). The cells were incubated with siRNA for 72 hours (to reduce BRCA1 protein levels to <25% of control) before the start of the experiment. The control siRNA has no effect on BRCA1 levels (15), and neither siRNA is toxic to the cells under these experimental conditions, as determined by the use of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays.

Isolation of RNA

The total cellular RNA was extracted with TRIzol Reagent (Life Technologies, Inc., Rockville, MD), according to the manufacturer’s instructions, additionally purified with chloroform and precipitated with 95% etomidate before cDNA synthesis. The quality of isolated RNA was verified by electrophoresis through 1.0% agarose-formaldehyde gels, and its quantity was determined from absorbance measurements at 260 and 280 nm.

DNA Microarray Analyses

cDNA Spotted Microarrays.

cDNA-spotted slides corresponding to 9216 human genes (including expressed sequence tags) and 9568 mouse genes (including expressed sequence tags) were prepared at the Albert Einstein College of Medicine microarray facility (Bronx, NY). cDNA synthesis, hybridizations, scanning, gridding, and analysis have been described earlier (ref. 17; also see web site).4 On the basis of our experience suggesting that cDNA spotted microarrays often underestimate differences in gene expression (17), ratios of gene expression were considered to be significant if they were ≥1.5 or ≤ 0.7 in at least two independent experiments.

Microarray Comparisons.

For DU-145 cells, we compared gene expression in two different wtBRCA1 versus Neo clone pairs, with two independent experiments per clone pair, for a total of n = 4 independent experiments. For MCF-7 cells, subconfluent proliferating cells were transiently transfected with wtBRCA1 or empty pcDNA3 vector (15) and postincubated for 24 hours to allow gene expression. Three independent experiments comparing wtBRCA1- versus pcDNA3-transfected cells were made after confirming that the wtBRCA1 gene was expressed in each experiment. For MEFs, we performed three independent comparisons of Brca1-deficient (Δ exon 11) versus wild-type MEFs. In each case, the ratios of gene expression were considered to be significant if they were ≥1.5 or ≤0.7 in at least two independent experiments.

Affymetrix Oligonucleotide Microarrays.

Affymetrix microarray analyses were performed at the North Shore-Long Island Jewish Research Institute core facility. RNA isolation, cRNA synthesis, gene chip hybridizations, and data analysis were performed as described earlier (18). We performed one experiment each comparing a DU-145 wtBRCA1 versus Neo clone pair and comparing Brca1-deficient MEFs versus wild-type MEFs. The gene chips used for these experiments were HG-U133A (which contains ∼16,000 human probe sets) and MG_U74Av2 (which contains ∼12,000 mouse genes plus expressed sequence tags). Differences in gene expression were considered to be significant if the log signal ratios were ≥ +1 or ≤ −1 and the P values were significant according to the Affymetrix algorithm. These log signal ratio cutoffs correspond to ratios of ≥2.0 or ≤0.5, respectively.

Semiquantitative Reverse Transcription-PCR Analysis

Rigorously controlled semiquantitative reverse transcription-PCR assays were performed as described before (15, 17). The PCR primers, reaction conditions, and cycle numbers are shown in Tables 1 and 2. The PCR reactions were individually optimized so that each reaction fell within the linear range of product amplification. The first-strand cDNA template was generated from 1 μg of total RNA in a final volume of 20 μL, with SuperScript II reverse transcriptase (Life Technologies, Inc.) and oligo(dT) primers. One microliter (of 20 μL) of 1:2.5-diluted cDNA template was amplified in a total volume of 50 μL, containing 200 μmol/L each of all four deoxynucleoside triphosphates, 2 μmol/L each of specific primers, and 1 unit of Tag DNA polymerase (Perkin-Elmer, Norwalk, CT). β-Actin, whose expression is unaffected by BRCA1, was used as a control for loading. The PCR products were analyzed by electrophoresis through 1.0% agarose gels containing ethidium bromide (0.1 mg/mL) and photographed under UV illumination.

Assays of Oxidant Sensitivity

MTT Dye Reduction.

Subconfluent proliferating cells in 96-well dishes were treated with different doses of H2O2 or paraquat (Sigma Chemical Co., St. Louis, MO) for 24 hours (or for different time intervals) and then assayed for MTT dye reduction, a measure of mitochondrial viability (14, 19). Cell viability was normalized to 0 dose control cells. Cell viability values were calculated as means ± SE of n = 10 replicate wells or as means ± SE for three independent experiments, each of which used n = 10 replicate wells per cell type per assay condition.

Trypan Blue Dye Exclusion.

This assay measures the ability of intact cell membranes of viable cells to exclude trypan blue dye. Subconfluent proliferating DU-145 cells in 100-mm plastic Petri dishes were transfected overnight using Lipofectamine with a FLAG-wtBRCA1 expression vector or the empty pCMV-Tag2B vector (15 μg of plasmid DNA per dish), washed, and allowed to recover and express the transgene for 24 hours. wtBRCA1-transfected, empty vector-transfected, and untransfected control cells were harvested, plated into 2-cm2 wells (8 × 104 cells per well in quadruplicate wells), allowed to attach, and exposed to different doses of H2O2 for T = 24 hours at 37°C. The cells were then collected, suspended in a solution containing 0.4% trypan blue, and counted with a hemocytometer. For each experiment and dose of H2O2, at least 200 cells were counted per well. Three independent experiments were performed; and the cell viability values were expressed as means ± SE.

Assays of the Cellular Redox State

Subconfluent proliferating cells in 24-well dishes were transfected overnight with wtBRCA1 or empty pcDNA3 vector (0.25 μg per well) with Lipofectamine, washed, and postincubated in fresh culture medium for 24 hours to allow gene expression. The cells were then treated with different doses of H2O2 for T = 24 hours and assayed for reduced (GSH) or oxidized (GSSG) forms of glutathione using a kit from Oxis, Inc. (Portland, OR).

Transcriptional Assays

The wild-type NRF2 vector, dominant negative NRF2 vector (DN-NRF2), NQO1-ARE-Luc reporter, and mutant or truncated BRCA1 expression vectors have been described earlier (12, 20). The NQO1-ARE-Luc reporter contains the antioxidant response element (ARE) of NAD(P)H dehydrogenase quinone 1 (NQO1), driving a minimal promoter upstream of the luciferase gene. Transient transfection assays were performed to measure transcriptional activity, as described earlier (12, 15). Briefly, subconfluent proliferating cells in 24-well dishes were transfected overnight with the indicated expression vector(s) (0.25 μg per well) and luciferase reporter (0.25 μg per well), with Lipofectamine. The cells were washed and postincubated for 24 hours to allow luciferase expression. Luciferase values (minus background) were normalized to the control (reporter only) and expressed as means ± SE of quadruplicate wells. Transfection efficiency was monitored using the control plasmid pRSV-β-gal (15).

Western Blotting

Whole cell lysates were prepared and subjected to Western blotting, as described earlier (14, 15). Briefly, equal aliquots of total cellular protein (50 μg per lane) were electrophoresed on a 4 to 13% SDS-polyacrylamide gradient gel, transferred to nitrocellulose membranes (Millipore, Bedford, MA), and blotted with primary antibodies directed against human BRCA1 (C-20, rabbit polyclonal, 1:200; Santa Cruz Biotechnology, Santa Cruz, CA) and α-actin (I-19, goat polyclonal, 1:500; Santa Cruz Biotechnology). After incubation with the appropriate horseradish peroxidase conjugated secondary antibody (Amersham Lifescience), immune complexes were visualized by using an enhanced chemiluminescence detection system (Amersham Lifescience, Buckinghamshire, UK), with colored markers (Bio-Rad, Hercules, CA) as molecular size standards.

Statistical Methods

Where appropriate, statistical comparisons were made using the two-tailed Student’s t test.

Microarray Analysis of BRCA1-overexpressing Cell Lines.

To determine the effect of BRCA1 overexpression on the transcriptosome, we compared the gene expression profiles of DU-145 human prostate cancer cell clones stably expressing a wild-type BRCA1 gene (wtBRCA1) with control (Neo) clones with cDNA spotted microarrays. These wtBRCA1 and Neo cell clones have been described and extensively characterized in previous studies (13, 14, 15). A partial list of genes up-regulated in the wtBRCA1 clones, categorized by function, is shown in Table 3 (see Supplemental Material for complete list). The wtBRCA1 cells showed up-regulation of various types of genes, including those involved in transcription, stress responses, DNA replication and repair, signal transduction, metabolism, differentiation, and RNA and protein processing. As a check on the methodology, a separate experiment revealed that a large number of genes identified by the cDNA-spotted arrays were concordantly up-regulated with an Affymetrix oligonucleotide microarray (Table 3).

Noticeably, the wtBRCA1 cell lines overexpressed many genes that protect against oxidative stress, including microsomal glutathione S-transferases (GSTs; MGST1 and MGST2), cytoplasmic GSTs (GSTT1 and GSTZ1), a glutathione peroxidase (GPX3), and various oxidoreductases [e.g., NQO1, alcohol dehydrogenase 5 (ADH5), and malic enzyme (ME2)]. wtBRCA1 also up-regulated other potential antioxidant genes, including paraoxonase 2 (PON2), an enzyme that hydrolyzes toxic organophosphates (e.g., pesticides) and oxidized lipids (e.g., oxidized low density lipoprotein; ref. 21), the Klotho gene (KL), a deficiency of which causes oxidative brain damage and a shortened life span in mice (22), and ubiquitin carboxyl-terminal esterase L1 (UCHL1), an oxidation-sensitive ubiquitin recycling enzyme that has been implicated in Parkinson’s disease (23). A number of these genes are involved in xenobiotic and drug metabolism: e.g., GSTs, NQO1, PON2, and member of PAS protein 2 (MOP2, also called HIF2α), an aryl hydrocarbon receptor (AhR) family gene.

Somewhat fewer genes were down-regulated by wtBRCA1 than were up-regulated (see Table 4 for a partial list and see Supplemental Material for the complete list). Again, an Affymetrix microarray experiment identified many of the same genes found with cDNA spotted arrays (Table 4). Only one GST, GSTP1, was decreased in wtBRCA1 clones. Interestingly, the overexpression of this particular isoform of GST in cancer cell lines is associated with cellular chemoresistance (24). Various genes involved in cell cycle regulation and DNA repair were down-regulated, including the retinoblastoma susceptibility gene retinoblastoma 1, which is known to be down-regulated by wtBRCA1 (13).

On the basis of previous experience with cDNA-spotted microarrays, we expected a low rate of false positivity with the selected filtering criteria (ref. 17; see Materials and Methods). To confirm this expectation, we tested n = 15 genes with rigorously controlled semiquantitated reverse transcription-PCR assays (14, 15, 17) of RNA samples from parental DU-145 cells and three clones each of Neo and wtBRCA1 cells. β-Actin, which is unaffected by BRCA1, was used as a control gene. The expression of BRCA1 in the wtBRCA1 relative to control cell lines is shown in Fig. 1,A. For all 15 genes, the expected increases (Fig. 1,B) or decreases (Fig. 1,C) in gene expression were confirmed. In some cases, the fold changes (determined by densitometry and expressed relative to β-actin) were greater by reverse transcription-PCR than by microarray assays, consistent with our impression that cDNA spotted arrays often underestimate gene expression changes. We tested the effect of BRCA1 knockdown with a previously validated siRNA (15) on the expression of three antioxidant response genes that were up-regulated by wtBRCA1 (MGST1, NQO1, and GSTZ1). In each case, the mRNA levels were decreased by BRCA1-siRNA but not by control-siRNA (Fig. 1 D). These findings suggest that BRCA1 regulates the expression of some antioxidant response genes over a very wide range of intracellular BRCA1 protein levels.

We also examined the effect of overexpression of wtBRCA1 on gene expression in MCF-7 human breast cancer cells. In these studies, gene expression was compared in MCF-7 cells transiently transfected with wtBRCA1 versus empty pcDNA3 vector. Gene expression was compared in wtBRCA1 versus control (pcDNA3)-transfected cells in the absence (−E2) or presence (+E2) of exogenous estrogen (17β-estradiol, 1 μmol/L × 24 hours). Although the cell types and duration of BRCA1 expression differed, we identified >40 genes concordantly regulated by wtBRCA1 in DU-145 versus MCF-7 cells (Table 5). These include MGST1, ANX1, ADH5, DSS1, MOP2, IGFBP3, GNG10, NOV, G6PD, KRT19, IFRD2, and others. In the absence and/or presence of E2, wtBRCA1 up-regulated expression of genes involved in the oxidative stress response or the detoxification of xenobiotics and drugs in MCF-7 cells, including MGST1, MOP2, ADH5, ALDH8, an epoxide hydrolase (EPHX2), several selenoproteins (SEPHS1 and SEPW1), and several other antioxidant proteins (PRDX4 and TSA).

Microarray Analysis of Brca1 Mutant Cell Lines.

Next, we determined the effect of loss of the endogenous full-length Brca1 protein on gene expression. Thus, we compared gene expression in Brca1-deficient (exon 11-deleted) versus wild-type (Brca1+/+) MEFs. The Brca1 Δ exon 11 MEFs express a Mr 92,000 Brca1 protein that is defective in DNA repair function (25). Examples of genes down-regulated in Brca1-deficient MEFs are listed in Table 6 (see Supplemental Material for the full list.) Categories of genes underexpressed in the Brca1-deficient cells included those involved in transcription, stress responses, cell cycle regulation, DNA replication and repair, signal transduction, and other processes. Stress response genes up-regulated in Brca1-deficient cells included a GST (Gsta2), a glutathione peroxidase (Gpx3), the antioxidant response transcription factor Nfe2l2 (also called Nrf2), a Nrf2 binding partner [activating transcription factor 2 (Atf2)], a superoxide dismutase (Sod1), a selenoprotein (Sepp1), the aryl hydrocarbon receptor (Ahr), several etomidate-responsive genes, and several heat shock proteins. In contrast, very few genes were up-regulated, and the magnitude of the increases was small (see Supplemental Material). Examples of genes concordantly increased in BRCA1-overexpressing (DU-145 or MCF-7) cells and decreased in Brca1-deficient MEFs include PROS1, GPX3, BNIP3, and TGFB2 (see Table 7 A).

We compared our findings with published microarray studies of gene regulation by BRCA1 in 293T cells (26), colon cancer cells (27), and Brca1-deficient mouse embryonic stem cells (28). Examples of genes concordantly regulated in our study versus published studies are provided in Table 7 B. These include (a) genes commonly induced by wtBRCA1 in 293T and in DU-145 and/or MCF-7 cells (MGAT2, CCNG2, FSTL1, LAMA3, and KCNK1), (b) genes induced by wtBRCA1 in 293T cells and decreased in Brca1-deficient MEFs (SEPP1, ZNF148, and ENPP2), (c) genes induced by wtBRCA1 in colon cancer cells and decreased in Brca1-deficient MEFs (TOP1 and SOD1), (d) genes decreased by wtBRCA1 in colon cancer and DU-145 cells (CD59), (e) genes decreased in Brca1-deficient embryonic stem cells and MEFs (Rock2, Qk, and Nfl), and (f) genes decreased in Brca1-deficient embryonic stem cells and up-regulated in DU-145 wtBRCA1 cells (CKB, SYHUQT, and PSMC2).

BRCA1 Protects against Oxidative Stress and Restores Cellular Redox Balance.

To determine whether the ability of BRCA1 to stimulate the expression of antioxidant response genes has functional consequences, we measured the effects of BRCA1 on the cellular sensitivity to two different oxidizing agents, hydrogen peroxide (H2O2), and paraquat. DU-145 wtBRCA1 or Neo clones were exposed to different doses of H2O2 for 24 hours, after which, the cell viability was determined by using MTT assays. The wtBRCA1 cells were significantly more resistant to H2O2 over a wide range of doses (P < 0.001, two tailed t tests; Fig. 2,A). In concordance with these findings, pretreatment of parental DU-145 cells with a BRCA1-siRNA caused significant sensitization to H2O2 (P < 0.001; Fig. 2,B). Please note that the experiments shown in Fig. 2, A and B, are representative of two or three independent experiments of each type that showed similar results. These results suggest that both exogenous and endogenous BRCA1 protects DU-145 cells against oxidative stress due to H2O2.

We also tested the ability of endogenous Brca1 to protect MEFs against H2O2 induced cytotoxicity. Consistent with the results obtained with DU-145 cells, Brca1-deficient MEFs were more sensitive than control (Brca1+/+) MEFs to H2O2 (P < 0.001 to 0.01; Fig. 2,C). The cell viability values shown in Fig. 2,C are means ± SE of three independent experiment, each of which used 10 replicate wells per dose of H2O2. The herbicide paraquat induces cytotoxicity by causing the generation superoxide ions (O2), which are detoxified by a mechanism distinct from H2O2. Brca1-deficient MEFs were more sensitive to paraquat than wild-type MEFs (P < 0.001 to 0.01; Fig. 2,D). A DU-145 wtBRCA1 clone was less sensitive than the Neo clone, whereas BRCA1-siRNA conferred increased sensitivity to paraquat (P < 0.001 to 0.05; Fig. 2 E). These findings suggest that exogenous and endogenous BRCA1 protects cells against several distinct forms of oxidative stress.

The assays shown in Fig. 2 A–E used a 24-hour exposure to H2O2 or paraquat. We performed additional studies to rule out the possibility that the effects of BRCA1 are limited to short-term assays. Thus, DU-145 wtBRCA1 or Neo cell clones were incubated with H2O2 for different time intervals from T = 16 to 96 hours and then tested for cell viability with MTT assays. Because of the prolonged exposure times, lower doses of H2O2 (either 10 or 25 nmol/L) were tested. These studies revealed persistent and significant increases in viability of the wtBRCA1 cell clones. Thus, at the lower dose of H2O2, cell viability increases of up to ∼20% were observed, whereas at the higher doses, increases of up to 30 to 35% were found (P < 0.001 to 0.05, two-tailed t tests).

Finally, we tested the effect of transient expression of wtBRCA1 on the response of DU-145 cells to H2O2 with a different end point, trypan blue dye exclusion. MTT assays assess the ability of mitochondria to reduce a tetrazolium salt to formazan, a measure of mitochondrial viability, whereas trypan blue exclusion assesses the ability of an intact plasma membrane to exclude the dye. At H2O2 doses of 300 to 500 nmol/L, we found significant increases (11 to 40%) in the proportion of wtBRCA1-transfected cells that excluded trypan blue dye, as compared with empty vector transfected cells or untransfected cells (P < 0.001; Fig. 2,G). Values in Fig. 2 G are means ± SE of three independent experiments. Although there is some variability from experiment to experiment, the cell viability values tended to be higher with the trypan blue assay than the MTT assay. This may reflect the fact that loss of membrane integrity is a late end point; thus, cells that have lost mitochondrial function (MTT end point) may not yet have lost their membrane integrity. Regardless, it seems clear that overexpression of BRCA1 (by either stable or transient transfection) protects and inactivation of BRCA1 (by either knockdown or gene deletion) sensitizes cells against oxidative stress.

The response to oxidative stress depends upon the ability of the cell to maintain its redox balance (i.e., the ratio of reduced to oxidized glutathione) in the setting of stress. We examined the effect of exogenous wtBRCA1 on the redox balance of prostate (DU-145 and LNCaP) and breast (MCF-7) cancer cell lines after treatment with different doses of H2O2 for 24 hours. The end point was the ratio of GSH to GSSG. BRCA1-transfected cells showed a mostly similar basal redox balance to vector-transfected and untransfected control cells (Fig. 3). H2O2 caused a dose-dependent shift in the redox state to increased GSSG and decreased GSH levels. However, wtBRCA1-transfected cells were able to maintain significantly higher ratios of GSH/GSSG than control cells, especially at high doses of H2O2 (P < 0.001, two tailed t tests). These findings suggest that BRCA1 enhances the production of GSH in response to oxidative stress.

BRCA1 Regulates ARE-driven Transcription.

The cytoprotective antioxidant response is mediated, in part, by the nuclear factor (erythroid-derived 2)-like factors NFE2L2 (NRF2) and NFE2L1 (NRF1) via the ARE (29). In this regard, BRCA1 appears to regulate a subset of genes that are known to be regulated by NRF2 [NQO1, MGST2, G6PD, malic enzyme (ME2), and Gsta1/2] and/or that are known to contain AREs in their promoters (NQO1, MGST1/2, and Gsta1/2; refs. 30, 31). This finding suggests that BRCA1 protection against oxidants may be mediated, in part, by NRF2. To test this hypothesis, we performed transient transfection assays using an NRF2-responsive reporter driven by the ARE of NQO1 (NQO1-ARE-Luc).

wtBRCA1 increased the basal activity of the NQO1-ARE-Luc reporter in DU-145, T47D, and MCF-7 cells by 1.6 to 6.6-fold, as compared with empty pcDNA3 vector or no vector (Fig. 4,A). In these assays, MCF-7 cells showed larger wtBRCA1-induced increases in ARE-Luc activity than DU-145 or T47D cells, but all cell types showed significant increases in ARE-Luc activity (P < 0.01). Co-expression of wtBRCA1 with NRF2 caused a modest but significant increase in NRF2-stimulated NQO1-ARE-Luc activity in DU-145 and T47D cells (36 to 50%; P < 0.01) but caused a much larger increase in NRF2-stimulated activity (4.3-fold) in MCF-7 cells (P < 0.001; Fig. 4,B). In plasmid dose-response studies of MCF-7 cells, increases in NQO1-ARE-Luc reporter activity were detectable at 10 to 50 ng per well of wtBRCA1 and were half maximal by 100 ng per well (Fig. 4 C). An 8-fold stimulation of reporter activity was achieved at our standard plasmid dose (0.25 μg per well), and the stimulation reached a maximum of 11-fold at 2.5 μg of plasmid per well.

In contrast to wtBRCA1, BRCA1-siRNA (but not a control-siRNA) significantly decreased basal and NRF2-stimulated NQO1-ARE-Luc activity (Fig. 4, D and E). Decreases in basal and NRF2-stimulated activity ranged from 60 to 100% (P < 0.001). These findings suggest that BRCA1 regulates NRF2 activity through the ARE over a wide range of intracellular BRCA1 protein levels. Next, we determined the BRCA1 structural requirements for stimulation of ARE activity with a series of previously described expression vectors encoding truncated or mutant BRCA1 proteins (Fig. 4,F; refs. 12, 14, 15). These studies revealed that COOH-terminal truncations (Δ BamHI, Δ KpnI, and Δ EcoRI) or mutations (5382insC and C5365G) of BRCA1 retained the ability to stimulate reporter activity, but a point mutation in the NH2-terminal RING domain (T300G) or a NH2-terminal truncation abrogated the ability of BRCA1 to stimulate activity (Fig. 4 F). These findings suggest that the NH2 terminus of BRCA1 is both necessary and sufficient to stimulate NQO1-ARE-Luc activity.

Fig. 4,G shows BRCA1 protein levels in MCF-7 and DU-145 cells experimentally manipulated to over- or underexpress BRCA1. As noted earlier (14), DU-145 cells show low basal BRCA1 expression that is significantly increased by stable (Fig. 1,A) or transient (Fig. 4,G) expression of exogenous wtBRCA1. In this (Fig. 4,G) and a prior study (15), basal BRCA1 protein levels in MCF-7 cells were significantly higher than in DU-145 cells were similar to or slightly less than those observed in wtBRCA1-transfected DU-145 cells. By way of comparison, BRCA1 levels in lymphoblastoid cell lines derived from a BRCA1 (185delAG) [R794] and a BRCA2 (6174delT) [R1041] mutation carrier were generally similar to the BRCA1 levels observed in untransfected MCF-7 cells or in wtBRCA1-transfected DU-145 cells (Fig. 4 G). For both MCF-7 and DU-145 cells, BRCA1-siRNA abolished or nearly abolished BRCA1 protein expression, whereas the control-siRNA had little or no effect on protein expression. The physiologic significance of these findings is considered in the Discussion.

We used a dominant negative NRF2 expression vector (20) to determine whether the endogenous NRF2 protein is required for BRCA1 to stimulate the antioxidant response. Here, we found that co-expression of DN-NRF2 ablated basal NQO1-ARE-Luc activity (some of which is dependent upon endogenous BRCA1), as well as wtBRCA1-stimulated activity (P < 0.001; Fig. 5,A). Consistent with these findings, transient expression of the DN-NRF2 sensitized MCF-7 cells to H2O2 and abrogated the ability of wtBRCA1 to protect MCF-7 cells against to H2O2 (P < 0.01; Fig. 4 B).

DNA microarray analyses of BRCA1 overexpressing and Brca1-mutant cells identified various categories of genes positively regulated by BRCA1, including genes involved in transcription, stress responses, signal transduction, DNA replication and repair, cell proliferation, metabolism, and other processes. A number of these findings were confirmed by using independent mRNA assays. We identified potential BRCA1-regulated genes consistent with its known functions in DNA repair and cell cycle regulation, e.g., deleted in split hand/split foot syndrome 1 (DSS1) [a BRCA2-interacting protein required for homologous recombination (32)], a DNA cross-link repair gene (Dclre1a, also called SNM1), and several cell cycle regulatory genes [e.g., CDKN2C (p18), G0S2, and Gspt1]. Brca1-deficient cells, which exhibit a defect in centrosome function (16), showed decreased expression of a major centrosome protein, centrosomin A (Csma), three mitotic kinases (Stk2, Stk10, and Clk), and a chromosome segregation gene (Ttc3).

Although the functional categorization of genes is somewhat arbitrary (many genes fit into more than one category), it appeared that overexpression (mutation) of BRCA1 led to increased (decreased) expression of a sizeable group of genes involved in the response to stress, including the antioxidant response, detoxification of xenobiotics, and drug metabolism. Genes up-regulated in BRCA1 overexpressing cells include GSTs and peroxidases (e.g., MGST1/2, GSTT1, GSTZ1, and GPX3), oxidoreductases (e.g., NQO1 and ME2), alcohol and aldehyde dehydrogenases (e.g., ADH5 and ALDH7), a paraoxonase (PON2), an AhR-like protein (MOP2), and other antioxidant proteins.

Consistent with these findings, Brca1-deficient MEFs showed decreased expression of stress-response genes, including Gsta2, Gpx3, Nrf2, Sod1, Ahr, and Sepp1, a selenoprotein that mediates protection against oxidative stress (33). Mice deficient for the major antioxidant response transcription factor Nrf2 exhibited increased susceptibility to hyperoxic lung damage, a reduced expression of several ARE-dependent phase II drug-metabolizing enzymes, increased sensitivity to carcinogens, and decreased protection against carcinogenesis by chemoprevention agents (34, 35). Our findings suggest that BRCA1 regulates the expression of several genes that are known to be regulated by NRF2 and/or to contain AREs in their regulatory regions. A recent study identified Nrf2-regulated genes for which basal and/or inducible expression was increased in the small intestine of Nrf2+/+ relative to Nrf2−/− mice (31). BRCA1 increased the expression of some of these Nrf2-regulated genes (NQO1, MGST1/2, Gsta2, G6PD, and ME2). BRCA1 also induced (and Brca1 mutation inhibited) expression of a glutathione peroxidase (GPX3), other isoforms of which are down-regulated in Nrf2−/− cells (31, 34). These results suggest an overlap in the genes regulated by BRCA1 versus NRF2.

Consistent with its ability to up-regulate antioxidant gene expression, BRCA1 overexpression conferred resistance, whereas BRCA1 mutation or underexpression conferred sensitivity to two different oxidizing agents (H2O2 and paraquat). Because peroxides and superoxide, which is generated by paraquat, are detoxified by distinct enzymatic pathways (e.g., those involving catalase versus superoxide dismutase, respectively), these findings suggest that BRCA1 may stimulate more than one antioxidant defense pathway. However, this remains to be demonstrated. BRCA1 is classified as a caretaker gene based on the findings that BRCA1 mutations lead to chromosomal instability and defects in DNA repair (reviewed in ref. 5). The ability of BRCA1 to protect against oxidative stress may contribute to its caretaker function because reactive oxygen species (e.g., H2O2, O2, and hydroxyl radicals) generated endogenously in mitochondria and other organelles can cause DNA damage (oxidation). In addition to endogenous reactive oxygen species, which contribute to carcinogenesis (36), many DNA-damaging agents and xenobiotics cause oxidative stress, resulting in DNA damage, protein oxidation, and lipid peroxidation. Some of these lesions are detoxified by BRCA1-regulated genes (e.g., GSTs, GPXs, oxidoreductases, and paroxonases).

Consistent its ability to up-regulate antioxidant genes and protect against oxidants, wtBRCA1 attenuated the loss of GSH due to H2O2, thus helping stressed cells to maintain their redox balance. It is not clear how BRCA1 stimulates GSH production under oxidizing conditions. GSH is produced via two processes: (a) conversion of GSSG to GSH by glutathione reductase, which requires NADPH; and (b) de novo synthesis via γ-glutamylcysteine synthetase (31). Both glucose-6-phosphate dehydrogenase (G6PD) and malic enzyme (ME2), which are up-regulated by wtBRCA1, stimulate NADPH formation (process 1). Although γ-glutamylcysteine synthetase was not on the list of BRCA1-regulated genes, γ-glutamylcysteine synthetase in an NRF2/ARE-regulated gene, and BRCA1 stimulates NRF2/ARE activity. Finally, we reported recently that BRCA1 up-regulates the expression of the small heat shock protein HSP27 (19), which functions to maintain the redox balance, possibly by helping to maintain the activity of cellular redox enzymes (37). Small heat shock proteins such as HSP27 protect cells against oxidative stress, in part, by enhancing G6PD activity (37), which helps to generate the reducing power for conversion of GSSG to GSH. In this regard, our findings suggest that G6PD may be a transcriptional target of BRCA1. The role of HSP27 and other small heat shock proteins in the BRCA1-mediated protection against oxidative and generation of GSH in stressed cells is a subject for additional investigation.

We have established the principle that BRCA1 stimulates ARE signaling and NRF2 transcriptional activity, although the extent of stimulation varied in different cell lines. The stimulation of NQO1-ARE-Luc activity and protection against oxidative stress by wtBRCA1 were ablated by a DN-NRF2, suggesting that NRF2 may be downstream of BRCA1 in an antioxidant response pathway. Although DN-NRF2 also abolished basal ARE-Luc activity and sensitized cells to oxidative stress in the absence of exogenous wtBRCA1, the siRNA experiments suggest that endogenous BRCA1 contributes to basal ARE-Luc activity and resistance to oxidative stress. Hence, some of the effects of DN-NRF2 could be due to pathways downstream of the endogenous BRCA1.

The NH2 terminus of BRCA1, including the RING domain, was necessary and sufficient to stimulate ARE signaling. A similar pattern (i.e., requirement for the NH2 terminus but not the COOH-terminus of BRCA1) was observed for stimulation of the HSP27 promoter activity and TERT promoter activity by BRCA1 (15, 19). The siRNA studies suggest the relevance of our findings to sporadic cancers in which BRCA1 expression is reduced, but the implications for BRCA1 mutant cancers are unclear at present because we do not know the extent to which BRCA1 mutant proteins are expressed in human cancers. Although most cancer-associated BRCA1 mutations are protein truncating mutations that should retain the ability to stimulate ARE signaling, the ability to stimulate ARE signaling would be compromised if the mutant BRCA1 proteins are underexpressed or rapidly degraded. Moreover, one cancer-associated BRCA1 mutation, T300G (which affects the NH2-terminal RING domain), abrogated the ability of BRCA1 to stimulate ARE-Luc activity. Our previous work indicates that the BRCA1-T300G mutant protein is stable and is well expressed (12, 15).

The ability of BRCA1 to protect against oxidant toxicity may be due, in part, to stimulation of antioxidant defenses (e.g., increased expression of antioxidant genes, increased production of GSH, and stimulation of NRF2 transcriptional activity). However, because DNA is a major target of oxidizing agents, the ability of BRCA1 to stimulate DNA repair (5) could also contribute to its cytoprotective activity. The extent to which BRCA1 functions to prevent DNA damage by enhancing detoxification of peroxides and superoxides as opposed to repairing established DNA lesions remains to be determined.

Our studies used three different models to investigate BRCA1 function: (a) overexpression (via stable or transient expression of exogenous wtBRCA1); (b) underexpression (via RNA interference); and (c) inactivation via gene deletion (Δ exon 11, which removes most of the Brca1 protein). Relative to model 1 (overexpression), studies of mice indicate that Brca1 is particularly highly expressed in the mammary gland in proliferating cells undergoing differentiation during puberty and pregnancy (38, 39). It has been suggested that the BRCA1 may play a particularly important role in preventing tumors during specific windows of time (e.g., puberty and pregnancy) in which it is highly expressed. The BRCA1 overexpression model might reflect these time periods when BRCA1is normally overexpressed. This expression pattern may also be reflected in vitro because BRCA1 expression is greatly increased when cultured mammary epithelial cells are forced to undergo differentiation (e.g., by the use of a hormonal mixture; refs. 40, 41). It remains to be proved whether these periods in which BRCA1 is highly expressed are directly related to its tumor suppressor function.

The role of endogenous BRCA1 in mediating protection against oxidative stress and/or stimulating NRF2 activity was documented in two different models (deletion of exon 11 in MEFs and knockdown of BRCA1 protein levels with an siRNA). The exon 11 deletion model may reflect the situation in BRCA1 mutant cancers, where the wild-type BRCA1 is usually lost (5, 42). We also note that the BRCA1 Δ exon 11 protein corresponds to a naturally occurring splice variant of BRCA1 in humans and mice (25, 43). As noted earlier, BRCA1 expression is often decreased or absent in sporadic breast cancers that do not exhibit a BRCA1 mutation (3, 4). This loss of BRCA1 expression may be due, in part, to epigenetic causes (hypermethylation of the BRCA1 promoter) and/or haploinsufficiency (loss of one BRCA1 allele; refs. 4, 5, 44). Regardless of the etiology, model 3 (BRCA1-siRNA) may reflect the underexpression of BRCA1 commonly observed in sporadic breast and ovarian cancers. The finding that BRCA1 can modulate various aspects of antioxidant defense over a wide range of BRCA1 expression levels is consistent with a physiologic role for BRCA1 in this pathway.

Taken together, our findings suggest a novel mechanism by which BRCA1 may prevent cancer development by enhancing antioxidant defenses, thereby protecting cells against damage caused by exogenous and/or endogenous reactive oxygen species. However, a definitive linkage between BRCA1-mediated protection against oxidative stress and tumor suppression remains to be demonstrated. They also suggest that in addition to its established roles in the repair of DNA damage, BRCA1 may prevent DNA damage due to ionizing radiation and other sources through the detoxification of reactive oxygen species, although this needs to be proven. Finally, these studies suggest a collaboration between BRCA1 and a transcription factor (NRF2) that functions to mobilize the cell’s antioxidant machinery.

Fig. 1.

Confirmation of DU-145 microarray results by semiquantitative reverse transcription-PCR. A, increased expression of BRCA1 in DU-145 wtBRCA1 cell clones. Semiquantitative reverse transcription-PCR and Western blot assays were carried out as described in Materials and Methods. B and C, genes increased (B) and decreased (C) in DU-145 wtBRCA1 cell clones. The amplified cDNA products were quantitated by densitometry and expressed relative to β-actin. Values are means ± SE for n = 3 wtBRCA1 clones and n = 4 control cell lines (parental cells and three Neo clones). See Table 1 for full names of genes. D, down-regulation of BRCA1-inducible genes by BRCA1-siRNA. Parental DU-145 cells were treated with no siRNA (transfection reagent only), control-siRNA, or BRCA1-siRNA (50 nmol/L × 72 hours) and harvested for semiquantitative reverse transcription-PCR analysis.

Fig. 1.

Confirmation of DU-145 microarray results by semiquantitative reverse transcription-PCR. A, increased expression of BRCA1 in DU-145 wtBRCA1 cell clones. Semiquantitative reverse transcription-PCR and Western blot assays were carried out as described in Materials and Methods. B and C, genes increased (B) and decreased (C) in DU-145 wtBRCA1 cell clones. The amplified cDNA products were quantitated by densitometry and expressed relative to β-actin. Values are means ± SE for n = 3 wtBRCA1 clones and n = 4 control cell lines (parental cells and three Neo clones). See Table 1 for full names of genes. D, down-regulation of BRCA1-inducible genes by BRCA1-siRNA. Parental DU-145 cells were treated with no siRNA (transfection reagent only), control-siRNA, or BRCA1-siRNA (50 nmol/L × 72 hours) and harvested for semiquantitative reverse transcription-PCR analysis.

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Fig. 2.

Exogenous and endogenous BRCA1 confer resistance to oxidative stress. A. DU-145 wtBRCA1 clones are resistant to H2O2. Two wtBRCA1 and two control (Neo) clones in 96-well dishes were incubated with different doses of H2O2 for 24 hours and assayed for cell viability using MTT assays. For each clone and H2O2 dose, n = 10 wells were tested. Because the two clones of each clonal type behaved similarly, the data were pooled and averaged. Cell viability values are means ± SE (relative to 0 dose control). Comparisons of wtBRCA1 versus Neo clones were statistically significant at each dose of H2O2 (P < 0.001, two-tailed t tests). Note: The data shown in A and B are representative of n = 2 to 3 independent experiments. B. BRCA1 knockdown confers sensitivity to H2O2. DU-145 cells were incubated with BRCA1 or control siRNA (50 nmol/L × 72 hours), exposed to different doses of H2O2 for T = 24 h, and tested for cell viability using MTT assays. Comparisons of BRCA1-siRNA– versus control-siRNA–treated cells were significant at all except the lowest dose of H2O2 (P < 0.001). C. Brca1-deficient MEFs are more sensitive than control MEFs to H2O2. Cell sensitivity to H2O2 was compared in Brca1 Δ exon 11 (Brca1−/−) versus wild-type (Brca1+/+) MEFs with MTT assays. Values of cell viability are means ± SE of n = 3 independent experiments. For each experiment and each dose of H2O2, n = 10 replicate wells were assayed, and the values were averaged. Brca1−/− MEFs were more sensitive to H2O2 at every dose tested (P < 0.001 to 0.01). D. Brca1-deficient MEFs are more sensitive to paraquat than control MEFs. Cells were treated with different doses of paraquat for T = 24 hours and then tested with MTT assays for their viability. The values of cell viability are means ± SE of n = 3 independent experiments. For each experiment and each dose of paraquat, n = 10 replicate wells were tested, and the cell viability values were averaged. Brca1−/− MEFs showed reduced survival rates relative to wild-type (Brca1+/+) MEFs at each dose of paraquat tested (P < 0.001 to 0.01). E. wtBRCA1 confers resistance and BRCA1-siRNA confers sensitivity to paraquat. (left). DU-145 wtBRCA1 and Neo cell clones were tested with MTT assays for sensitivity to paraquat. Cell viability values are means ± SE of n = 3 independent experiments. For each experiment and each dose, n = 10 replicate wells were assayed per clone × two clones per clone type = 20 wells per clone type, and the values were averaged. Comparisons of wtBRCA1 versus Neo clones were significant at all paraquat doses (P < 0.01 to 0.05) (right). DU-145 cells were treated with control-siRNA, BRCA1-siRNA (50 nmol/L × 72 hours) or vehicle only (Parental) and then assayed for paraquat sensitivity as above. BRCA1-siRNA–treated cells were more sensitive to paraquat than control-siRNA or vehicle-treated cells (P < 0.001 to 0.01). F, time course for wtBRCA1-mediated protection against H2O2. wtBRCA1 and Neo DU-145 cell clones were exposed to 25 nmol/L (left) or 10 nmol/L (right) of H2O2 for different time intervals ranging from T = 16 to 96 hours and then assayed for cell viability using MTT assays. Cell viability values are expressed relative to untreated cells (T = 0 hour) and represent means ± SE for three independent experiments. At 25 nmol/L H2O2, survival rates were higher for wtBRCA1 than Neo clones from T = 24 to 96 hours (P < 0.01 to 0.001, two-tailed t tests). At 10 nmol/L H2O2, survival was higher in wtBRCA1 cell clones from T = 24 to 96 hours (P < 0.01 to 0.05). G. Transient expression of wtBRCA1 protects DU-145 cells against H2O2, as indicated by trypan blue dye exclusion assays. Subconfluent proliferating cells were transfected overnight with FLAG-wtBRCA1, empty pCMVTag2B vector or no vector (parental), washed, postincubated for 24 hours to allow BRCA1 gene expression, and exposed to different doses of H2O2 for T = 24 hours. The cells were then harvested with trypsin, stained with trypan blue dye, and counted. Cell viability was determined by counting the trypan blue dye-excluding cells and expressed relative to untreated control cells. The values plotted are means ± SE of n = 3 independent experiments. For each experiment and each dose of H2O2, at least 200 cells were counted. At H2O2 doses of 300 to 500 nmol/L, cell viability was higher in wtBRCA1-transfected cells than in control cells (empty vector or untransfected; P < 0.001).

Fig. 2.

Exogenous and endogenous BRCA1 confer resistance to oxidative stress. A. DU-145 wtBRCA1 clones are resistant to H2O2. Two wtBRCA1 and two control (Neo) clones in 96-well dishes were incubated with different doses of H2O2 for 24 hours and assayed for cell viability using MTT assays. For each clone and H2O2 dose, n = 10 wells were tested. Because the two clones of each clonal type behaved similarly, the data were pooled and averaged. Cell viability values are means ± SE (relative to 0 dose control). Comparisons of wtBRCA1 versus Neo clones were statistically significant at each dose of H2O2 (P < 0.001, two-tailed t tests). Note: The data shown in A and B are representative of n = 2 to 3 independent experiments. B. BRCA1 knockdown confers sensitivity to H2O2. DU-145 cells were incubated with BRCA1 or control siRNA (50 nmol/L × 72 hours), exposed to different doses of H2O2 for T = 24 h, and tested for cell viability using MTT assays. Comparisons of BRCA1-siRNA– versus control-siRNA–treated cells were significant at all except the lowest dose of H2O2 (P < 0.001). C. Brca1-deficient MEFs are more sensitive than control MEFs to H2O2. Cell sensitivity to H2O2 was compared in Brca1 Δ exon 11 (Brca1−/−) versus wild-type (Brca1+/+) MEFs with MTT assays. Values of cell viability are means ± SE of n = 3 independent experiments. For each experiment and each dose of H2O2, n = 10 replicate wells were assayed, and the values were averaged. Brca1−/− MEFs were more sensitive to H2O2 at every dose tested (P < 0.001 to 0.01). D. Brca1-deficient MEFs are more sensitive to paraquat than control MEFs. Cells were treated with different doses of paraquat for T = 24 hours and then tested with MTT assays for their viability. The values of cell viability are means ± SE of n = 3 independent experiments. For each experiment and each dose of paraquat, n = 10 replicate wells were tested, and the cell viability values were averaged. Brca1−/− MEFs showed reduced survival rates relative to wild-type (Brca1+/+) MEFs at each dose of paraquat tested (P < 0.001 to 0.01). E. wtBRCA1 confers resistance and BRCA1-siRNA confers sensitivity to paraquat. (left). DU-145 wtBRCA1 and Neo cell clones were tested with MTT assays for sensitivity to paraquat. Cell viability values are means ± SE of n = 3 independent experiments. For each experiment and each dose, n = 10 replicate wells were assayed per clone × two clones per clone type = 20 wells per clone type, and the values were averaged. Comparisons of wtBRCA1 versus Neo clones were significant at all paraquat doses (P < 0.01 to 0.05) (right). DU-145 cells were treated with control-siRNA, BRCA1-siRNA (50 nmol/L × 72 hours) or vehicle only (Parental) and then assayed for paraquat sensitivity as above. BRCA1-siRNA–treated cells were more sensitive to paraquat than control-siRNA or vehicle-treated cells (P < 0.001 to 0.01). F, time course for wtBRCA1-mediated protection against H2O2. wtBRCA1 and Neo DU-145 cell clones were exposed to 25 nmol/L (left) or 10 nmol/L (right) of H2O2 for different time intervals ranging from T = 16 to 96 hours and then assayed for cell viability using MTT assays. Cell viability values are expressed relative to untreated cells (T = 0 hour) and represent means ± SE for three independent experiments. At 25 nmol/L H2O2, survival rates were higher for wtBRCA1 than Neo clones from T = 24 to 96 hours (P < 0.01 to 0.001, two-tailed t tests). At 10 nmol/L H2O2, survival was higher in wtBRCA1 cell clones from T = 24 to 96 hours (P < 0.01 to 0.05). G. Transient expression of wtBRCA1 protects DU-145 cells against H2O2, as indicated by trypan blue dye exclusion assays. Subconfluent proliferating cells were transfected overnight with FLAG-wtBRCA1, empty pCMVTag2B vector or no vector (parental), washed, postincubated for 24 hours to allow BRCA1 gene expression, and exposed to different doses of H2O2 for T = 24 hours. The cells were then harvested with trypsin, stained with trypan blue dye, and counted. Cell viability was determined by counting the trypan blue dye-excluding cells and expressed relative to untreated control cells. The values plotted are means ± SE of n = 3 independent experiments. For each experiment and each dose of H2O2, at least 200 cells were counted. At H2O2 doses of 300 to 500 nmol/L, cell viability was higher in wtBRCA1-transfected cells than in control cells (empty vector or untransfected; P < 0.001).

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Fig. 3.

BRCA1 attenuates loss of GSH in response to oxidative stress. For LNCaP and MCF-7, the cells were transfected overnight with wtBRCA1, empty vector, or vehicle, washed, treated with different doses of H2O2 for 24 hours, and assayed for GSH and GSSG. For DU-145, stable wtBRCA1 and Neo cell clones were tested. At doses of H2O2 ≥ 100 nmol/L for MCF-7 and LNCaP and ≥200 nmol/L for DU-145, wtBRCA1-transfected cells had significantly higher ratios of GSH/GSSG than control cells (P < 0.001, two-tailed t tests).

Fig. 3.

BRCA1 attenuates loss of GSH in response to oxidative stress. For LNCaP and MCF-7, the cells were transfected overnight with wtBRCA1, empty vector, or vehicle, washed, treated with different doses of H2O2 for 24 hours, and assayed for GSH and GSSG. For DU-145, stable wtBRCA1 and Neo cell clones were tested. At doses of H2O2 ≥ 100 nmol/L for MCF-7 and LNCaP and ≥200 nmol/L for DU-145, wtBRCA1-transfected cells had significantly higher ratios of GSH/GSSG than control cells (P < 0.001, two-tailed t tests).

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Fig. 4.

BRCA1 stimulates NRF2 activity through the AREs. A and B. wtBRCA1 stimulates basal (A) and NRF2-induced (B) NQO1-ARE-Luc reporter activity. Cells were transfected with the indicated vector(s), postincubated for 24 hours, and assayed for luciferase activity. The values are expressed relative to the control (reporter only) and are means ± SE of n = 4 wells. ∗Represents a significant difference (P < 0.01, two-tailed t test). C, plasmid dose response for wtBRCA1 stimulation of basal NQO1-ARE-Luc activity. The total transfected DNA content was kept constant by the addition of empty pcDNA3 vector. D and E. BRCA1-siRNA inhibits basal (D) and NRF2-stimulated (E) NQO1-ARE-Luc activity. The cells were pretreated with no siRNA (transfection reagent only), control-siRNA, or BRCA1-siRNA for 72 hours, and the transcriptional assays were performed as described above. F, structural determinants for stimulation of NQO1-ARE-Luc activity. MCF-7 cells were cotransfected with NQO1-ARE-Luc and a set of expression vectors encoding mutant or truncated BRCA1 proteins, postincubated for 24 hours, and assayed for luciferase activity. The luciferase values are expressed relative to control cells transfected only with NQO-ARE-Luc (= 100%). G, BRCA1 protein expression levels in different cell types and in response to experimental manipulation. Proliferating cell cultures were harvested and analyzed for BRCA1 and α-actin by Western blotting. Lanes 1 and 2 show BRCA1 protein expression in EBV-immortalized peripheral blood lymphocyte-derived cell lines from female BRCA1 (185delAG) [R794] and BRCA2 (6174delT) [R1041] mutation carriers. Lanes 3 to 12 show BRCA1 protein levels in MCF-7 or DU-145 cells that were untreated (parental), exposed to BRCA1 or control siRNAs (50 nmol/L × 72 hours), or transfected with FLAG-wtBRCA1 or empty pCMV-Tag2B vectors (overnight transfected followed by a 24-hour postincubation).

Fig. 4.

BRCA1 stimulates NRF2 activity through the AREs. A and B. wtBRCA1 stimulates basal (A) and NRF2-induced (B) NQO1-ARE-Luc reporter activity. Cells were transfected with the indicated vector(s), postincubated for 24 hours, and assayed for luciferase activity. The values are expressed relative to the control (reporter only) and are means ± SE of n = 4 wells. ∗Represents a significant difference (P < 0.01, two-tailed t test). C, plasmid dose response for wtBRCA1 stimulation of basal NQO1-ARE-Luc activity. The total transfected DNA content was kept constant by the addition of empty pcDNA3 vector. D and E. BRCA1-siRNA inhibits basal (D) and NRF2-stimulated (E) NQO1-ARE-Luc activity. The cells were pretreated with no siRNA (transfection reagent only), control-siRNA, or BRCA1-siRNA for 72 hours, and the transcriptional assays were performed as described above. F, structural determinants for stimulation of NQO1-ARE-Luc activity. MCF-7 cells were cotransfected with NQO1-ARE-Luc and a set of expression vectors encoding mutant or truncated BRCA1 proteins, postincubated for 24 hours, and assayed for luciferase activity. The luciferase values are expressed relative to control cells transfected only with NQO-ARE-Luc (= 100%). G, BRCA1 protein expression levels in different cell types and in response to experimental manipulation. Proliferating cell cultures were harvested and analyzed for BRCA1 and α-actin by Western blotting. Lanes 1 and 2 show BRCA1 protein expression in EBV-immortalized peripheral blood lymphocyte-derived cell lines from female BRCA1 (185delAG) [R794] and BRCA2 (6174delT) [R1041] mutation carriers. Lanes 3 to 12 show BRCA1 protein levels in MCF-7 or DU-145 cells that were untreated (parental), exposed to BRCA1 or control siRNAs (50 nmol/L × 72 hours), or transfected with FLAG-wtBRCA1 or empty pCMV-Tag2B vectors (overnight transfected followed by a 24-hour postincubation).

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Fig. 5.

Inhibition of NRF2 blocks wtBRCA1 stimulation of antioxidant response. A. Dominant negative NRF2 (DN-NRF2) inhibits BRCA1-induced NQO1-ARE-Luc activity. Cotransfection of a DN-NRF2 into MCF-7 cells inhibited basal and wtBRCA1-induced NQO1-ARE-Luc activity (P < 0.001 for comparisons of cells transfected − versus + DN-NRF2). B. DN-NRF2 abrogates wtBRCA1-mediated protection of MCF-7 cells against H2O2. Cells were transfected ± empty pcDNA3 vector, ± wtBRCA1, and ± DN-NRF2 overnight, washed, and postincubated for 24 hours to allow gene expression. The cells were then analyzed for sensitivity to H2O2 using MTT assays, as described above. Control assays in which pcDNA3 vector was omitted (i.e., no vector and DN-NRF2 alone) showed no effect of the pcDNA3 vector and are not shown in the figure for clarity. At 100 to 400 nmol/L, wtBRCA1 protected while DN-NRF2 sensitized cells to H2O2 (P < 0.01). Addition of DN-NRF2 abolished the protection because of wtBRCA1 (P < 0.01).

Fig. 5.

Inhibition of NRF2 blocks wtBRCA1 stimulation of antioxidant response. A. Dominant negative NRF2 (DN-NRF2) inhibits BRCA1-induced NQO1-ARE-Luc activity. Cotransfection of a DN-NRF2 into MCF-7 cells inhibited basal and wtBRCA1-induced NQO1-ARE-Luc activity (P < 0.001 for comparisons of cells transfected − versus + DN-NRF2). B. DN-NRF2 abrogates wtBRCA1-mediated protection of MCF-7 cells against H2O2. Cells were transfected ± empty pcDNA3 vector, ± wtBRCA1, and ± DN-NRF2 overnight, washed, and postincubated for 24 hours to allow gene expression. The cells were then analyzed for sensitivity to H2O2 using MTT assays, as described above. Control assays in which pcDNA3 vector was omitted (i.e., no vector and DN-NRF2 alone) showed no effect of the pcDNA3 vector and are not shown in the figure for clarity. At 100 to 400 nmol/L, wtBRCA1 protected while DN-NRF2 sensitized cells to H2O2 (P < 0.01). Addition of DN-NRF2 abolished the protection because of wtBRCA1 (P < 0.01).

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Grant support: USPHS Grants R01-CA80000, R01-CA82599, and R01-ES09169, Susan G. Komen Breast Cancer Foundation Grant BCTR0201295 (E. Rosen) and United States Army Idea Award DAMD17-02-1-0525 (I. Bae).

The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Note: Supplementary data for this article can be found at Cancer Research Online (http://cancerres.aacrjournals.org).

Requests for reprints: Eliot M. Rosen, Department of Oncology, Lombardi Cancer Center, Georgetown University, 3970 Reservoir Road, NW, Box 571469, Washington, DC 20057-1469. Phone: (202) 687-7695; Fax: (202) 687-7256; E-mail: emr36@georgetown.edu

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Internet address: http://www.aecom.yu.edu/cancer/new/cores/microarray.

Table 1

PCR primers and expected product sizes for semi-quantitative reverse transcription-PCR analyses

Gene nameSymbolPrimer sequences (5′→3′)Genbank accession no.Product size (bp)
Breast cancer susceptibility gene 1 BRCA1 F: ttgcgggaggaaaatgggtagtta U14680 292 
  B: tgtgccaagggtgaatgatgaaag   
Annexin 1 ANX1 F: agtcatccaaggtggtcccgg NM_000700 539 
  B: ggccctggcatctgaatcagcc   
Mesoderm specific transcript homologue MEST F: actatttcctaaaatcacaggacattaagg NM_002402 411 
  B: atcacttaataatcctgctttgactaagac   
Microphthalmia-associated transcription factor MITF F: ctaacctgtacaacaactctcgatctc XM_010977 486 
  B: atcacttaataatcctgctttgactaagac   
Microsomal GST1 MGSTI F: aaaagaccacgagctcagga AY368173 346 
  B: 5 aaagacctgacccaaaac′   
Cardiac ankyrin repeat protein CARP F: gtgttgtgaagatgtacctaatgaagtt XM_051726 297 
  B: taatcagccctctcttaaaaactcttac   
Coch-5B2 COCH1 F: aaagcagatgtcctctgcccaggggg XM_007471 300 
  B: tttcctgtattggaattaccccctctg   
Brain-derived neutrophic factor BDNF F: gattcataaggatagacacttcttgtg XM_006027 287 
  B: aaggaatgtaatgcagactttttaagtt   
G0-S transition 2 G0S2 F: gctgttttttatttggacttaacttcagag M72885 531 
  B: ccttttgatgttaaaatgctaaatctcacg   
Tumor necrosis factor α TNFA F: tacagatgaatgtatttatttgggagac M10988 198 
  B: atcagcattgtttagacaacttaatcag   
Prostacyclin-stimulating factor  F: gtatctcctctaagtaaggaagatgctg S75725 299 
  B: tgtgatctttattttgtatttctctgtg   
Expressed sequence tags, weakly similar to TAL-6  F: ttcttctggtactggagaataataacaac R16604 249 
  B: aatcccataagcctagaatctgtaaggaaac   
Ceruloplasmin CP F: tatagttctgatgtctttgacattttcc XM_011006 293 
  B: atgcttccagtcttcttttaatgtttat   
Tumor necrosis factor-inducible protein TSG6 F: atggatggctaagggcagagttgg NM_007115 386 
  B: gctcatctccacagtatcttccc   
Dickkopf homologue 3 DKK3 F: tctaatgaagacggtgatgttgacactg NM_015881 337 
  B: ctttaaaccttaagaactctggatgaat   
Caveolin 1 CAV1 F: gcaagtgtacgacgcgcacacc NM_001753 318 
  B: ctgatgcactgaatctcaat   
NAD(P)H quinone oxidase 1 NQO1 F: ggtcagaagggaattgctca NM_000903 302 
  B: ctccagcctgggtaacagag   
GST ζ 1 GSTZ1 F: gtggggtggagtagggagat AH006398 334 
  B: aggcaagtggctgactgact   
β-Actin ACTB F: tagcggggttcacccacactgtgccccatcta XM_004814 661 
  B: ctagaagcatttgcggtggaccgatggaggg   
Gene nameSymbolPrimer sequences (5′→3′)Genbank accession no.Product size (bp)
Breast cancer susceptibility gene 1 BRCA1 F: ttgcgggaggaaaatgggtagtta U14680 292 
  B: tgtgccaagggtgaatgatgaaag   
Annexin 1 ANX1 F: agtcatccaaggtggtcccgg NM_000700 539 
  B: ggccctggcatctgaatcagcc   
Mesoderm specific transcript homologue MEST F: actatttcctaaaatcacaggacattaagg NM_002402 411 
  B: atcacttaataatcctgctttgactaagac   
Microphthalmia-associated transcription factor MITF F: ctaacctgtacaacaactctcgatctc XM_010977 486 
  B: atcacttaataatcctgctttgactaagac   
Microsomal GST1 MGSTI F: aaaagaccacgagctcagga AY368173 346 
  B: 5 aaagacctgacccaaaac′   
Cardiac ankyrin repeat protein CARP F: gtgttgtgaagatgtacctaatgaagtt XM_051726 297 
  B: taatcagccctctcttaaaaactcttac   
Coch-5B2 COCH1 F: aaagcagatgtcctctgcccaggggg XM_007471 300 
  B: tttcctgtattggaattaccccctctg   
Brain-derived neutrophic factor BDNF F: gattcataaggatagacacttcttgtg XM_006027 287 
  B: aaggaatgtaatgcagactttttaagtt   
G0-S transition 2 G0S2 F: gctgttttttatttggacttaacttcagag M72885 531 
  B: ccttttgatgttaaaatgctaaatctcacg   
Tumor necrosis factor α TNFA F: tacagatgaatgtatttatttgggagac M10988 198 
  B: atcagcattgtttagacaacttaatcag   
Prostacyclin-stimulating factor  F: gtatctcctctaagtaaggaagatgctg S75725 299 
  B: tgtgatctttattttgtatttctctgtg   
Expressed sequence tags, weakly similar to TAL-6  F: ttcttctggtactggagaataataacaac R16604 249 
  B: aatcccataagcctagaatctgtaaggaaac   
Ceruloplasmin CP F: tatagttctgatgtctttgacattttcc XM_011006 293 
  B: atgcttccagtcttcttttaatgtttat   
Tumor necrosis factor-inducible protein TSG6 F: atggatggctaagggcagagttgg NM_007115 386 
  B: gctcatctccacagtatcttccc   
Dickkopf homologue 3 DKK3 F: tctaatgaagacggtgatgttgacactg NM_015881 337 
  B: ctttaaaccttaagaactctggatgaat   
Caveolin 1 CAV1 F: gcaagtgtacgacgcgcacacc NM_001753 318 
  B: ctgatgcactgaatctcaat   
NAD(P)H quinone oxidase 1 NQO1 F: ggtcagaagggaattgctca NM_000903 302 
  B: ctccagcctgggtaacagag   
GST ζ 1 GSTZ1 F: gtggggtggagtagggagat AH006398 334 
  B: aggcaagtggctgactgact   
β-Actin ACTB F: tagcggggttcacccacactgtgccccatcta XM_004814 661 
  B: ctagaagcatttgcggtggaccgatggaggg   
Table 2

PCR reaction conditions

GenePCR cycle parametersNo. of cycles
BRCA1 94°C (30 s); 56°C (30 s); 72°C (30 s) 23 
ANX1 94°C (1 min); 55°C (1 min); 72°C (1 min) 30 
MEST 94°C (30 s); 53°C (30 s); 72°C (30 s) 35 
MITF 94°C (30 s); 53°C (30 s); 72°C (30 s) 35 
MGST1 94°C (30 s); 50°C (30 s); 72°C (30 s) 30 
CARP 94°C (30 s); 55°C (30 s); 72°C (30 s) 35 
COCH1 94°C (30 s); 55°C (30 s); 72°C (30 s) 38 
BDNF 94°C (30 s); 55°C (30 s); 72°C (30 s) 35 
G0S2 94°C (60 s); 55°C (60 s); 72°C (60 s) 35 
TNFA 94°C (30 s); 53°C (30 s); 72°C (30 s) 35 
Prostacyclin-stimulating factor 94°C (30 s); 55°C (30 s); 72°C (30 s) 35 
Expressed sequence tags, weakly similar to TAL-6 94°C (30 s); 50°C (30 s); 72°C (30 s) 35 
CP 94°C (30 s); 55°C (30 s); 72°C (30 s) 35 
TSG6 94°C (30 s); 53°C (30 s); 72°C (30 s) 35 
DKK3 94°C (30 s); 55°C (30 s); 72°C (30 s) 38 
CAV1 94°C (30 s); 55°C (30 s); 72°C (30 s) 32 
NQO1 94°C (30 s); 55°C (30 s); 72°C (30 s) 35 
GSTZ1 94°C (1 min); 53°C (1 min); 72°C (1 min) 42 
ACTB 94°C (30 s); 56°C (30 s); 72°C (30 s) 23 
GenePCR cycle parametersNo. of cycles
BRCA1 94°C (30 s); 56°C (30 s); 72°C (30 s) 23 
ANX1 94°C (1 min); 55°C (1 min); 72°C (1 min) 30 
MEST 94°C (30 s); 53°C (30 s); 72°C (30 s) 35 
MITF 94°C (30 s); 53°C (30 s); 72°C (30 s) 35 
MGST1 94°C (30 s); 50°C (30 s); 72°C (30 s) 30 
CARP 94°C (30 s); 55°C (30 s); 72°C (30 s) 35 
COCH1 94°C (30 s); 55°C (30 s); 72°C (30 s) 38 
BDNF 94°C (30 s); 55°C (30 s); 72°C (30 s) 35 
G0S2 94°C (60 s); 55°C (60 s); 72°C (60 s) 35 
TNFA 94°C (30 s); 53°C (30 s); 72°C (30 s) 35 
Prostacyclin-stimulating factor 94°C (30 s); 55°C (30 s); 72°C (30 s) 35 
Expressed sequence tags, weakly similar to TAL-6 94°C (30 s); 50°C (30 s); 72°C (30 s) 35 
CP 94°C (30 s); 55°C (30 s); 72°C (30 s) 35 
TSG6 94°C (30 s); 53°C (30 s); 72°C (30 s) 35 
DKK3 94°C (30 s); 55°C (30 s); 72°C (30 s) 38 
CAV1 94°C (30 s); 55°C (30 s); 72°C (30 s) 32 
NQO1 94°C (30 s); 55°C (30 s); 72°C (30 s) 35 
GSTZ1 94°C (1 min); 53°C (1 min); 72°C (1 min) 42 
ACTB 94°C (30 s); 56°C (30 s); 72°C (30 s) 23 
Table 3

Genes for which expression is increased in DU-145 wtBRCA1 [versus control (Neo)] cell clones

Accession no.Gene nameSymbolRatioRatio
Mean ± SE (Range)Affymetrix oligonucleotide array (N = 1)
Transcription/Nuclear proteins     
 AA969184 Cytokine inducible nuclear protein (= cardiac ankyrin repeat protein) CARP 10.1 ± 4.6 (3)  
 H45711 Zinc finger transcription factor hEZF EZF 3.4 ± 1.2 (2)  
 AA115076 Human msg1-related gene 1 (mrg1) mRNA MRG1 2.9 ± 0.3 (2)  
 T72202 Transcription factor IL-4 Stat (also known as Stat6) STAT6 2.7 ± 0.2 (3)  
 AA425238 Proto-oncogene AML1 {alternative products} CBFA2 2.6 ± 0.3 (3) 6.1 
 AA911236 v-Myb avian myeloblastosis viral oncogene homologue-like 1 (= AMYB) MYBL1 2.6 ± 0.2 (3) 13 
 N66177 Microphthalmia-associated transcription factor MITF 2.6 ± 0.3 (2) 2.8 
 H96235 v-Ets avian erythroblastosis virus E26 oncogene homologue 2 ETS2 2.4 ± 0.1 (2) 12 
Stress response: oxidative stress and xenobiotic detoxification     
 AA495936 GST, microsomal 1 MGST1 10.2 ± 4.4 (3)  
 AA670438 Ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) UCHL1 8.2 ± 4.0 (2) 18 
 AA455538 NAD(P)H:menadione oxidoreductase (also called NQO1) NMOR1 3.8 ± 0.9 (3) 4.6 
 AA680300 Member of PAS protein 2 (MOP2, also called HIF2α) MOP2 3.4 ± 0.5 (3)  
 W73474 GST, microsomal 2 MGST2 3.3 ± 1.3 (2) 5.2 
 N93686 Aldehyde dehydrogenase 7 ALDH7 3.2 ± 0.4 (2)  
 AA625806 Ninjurin1 (nerve injury-induced protein 1) NINJ1 2.7 ± 0.3 (4)  
 AA677655 Klotho protein KL 2.6 ± 0.5 (2)  
 H99813 GST θ1 GSTT1 2.5 ± 0.2 (3) 2.3 
 AA664180 Glutathione peroxidase 3 (plasma) GPX3 2.4 ± 0.5 (2) 5.3 
 AA453859 Alcohol dehydrogenase 5 (χ subunit, class III) ADH5 2.3 ± 0.4 (3)  
 AA446301 Paraoxonase (PON2 protein) PON2 2.3 ± 0.4 (3)  
 AA428859 Glutathione transferase ζ 1 (GSTZ1) GSTZ1 2.1 ± 0.1 (2)  
 H99699 Aconitase 2, mitochondrial ACO2 2.0 ± 0.1 (2)  
 H21041 Activating transcription factor 3 ATF3 1.9 ± 0.3 (2)  
Replication/Cell cycle/DNA repair and metabolism     
 R60343 5′; nucleotidase (CD73, placental purine ecto-5′-nucleotidase) NT5E 6.2 ± 2.9 (3)  
 AA429895 Human multidrug resistance-associated protein homologue (MRP3) MRP3 2.6 ± 0.1 (2)  
 AA931758 Putative lymphocyte G0-G1 switch gene (G0S2) G0S2A 2.6 ± 0.4 (4)  
 N72115 Cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4) CDKN2C 2.6 ± 0.5 (2) 2.3 
 H85464 Deleted in split hand/split foot syndrome 1 (DSS1) DSS1 2.5 ± 0.3 (2) 2.2 
 AA430382 Nucleoside phosphorylase NP 1.9 ± 0.0 (2)  
Signal transduction     
 AA598601 Insulin-like growth factor binding protein 3 IGFBP3 5.3 ± 1.3 (2) 2.1 
 T72877 Interleukin 1 receptor antagonist IL1RN 4.0 ± 1.6 (3)  
 AA460286 G protein γ-10 subunit (guanine nucleotide-binding protein GBGA)  2.4 ± 0.3 (3)  
 H26426 Protein tyrosine phosphatase, receptor type, mu polypeptide PTPRM 2.4 ± 0.4 (2) 2.9 
 AA460841 Insulin receptor substrate-1 [human, skeletal muscle, mRNA, 5828 nt] IRS1 2.3 ± 0.3 (3) 6.1 
 AA443302 Rho-related GTP binding protein RhoE RHOE 2.1 ± 0.2 (2) 4.9 
 AA411640 Ras-related GTP-binding protein A (ragA protein) RAGA 2.1 ± 0.3 (2)  
 T57556 Putative protein kinase C inhibitor PKCI-1 (protein kinase C-interacting 1) PRKCNH1 1.9 ± 0.0 (2)  
 AA910443 Nephroblastoma-overexpressed gene NOV 1.7 ± 0.2 (2) 2.3 
Biosynthesis and metabolism     
 H87471 Human l-kynurenine hydrolase (kynureninase) KYNU 4.0 ± 1.5 (2) 5.3 
 AA401111 Glucose phosphate isomerase GPI 4.4 ± 0.6 (4)  
 AA424937 Glucose-6-phosphate dehydrogenase G6PD 3.1 ± 0.6 (2) 2.1 
 AA599158 Multifunctional aminoacyl-tRNA synthetase SYHUQT 2.9 ± 0.3 (2)  
 AA894557 Creatine kinase B CKB 2.9 ± 0.9 (2) 3.4 
 H44956 Fumarylacetoacetate hydrolase FAH 2.9 ± 0.2 (4)  
 AA011215 Spermidine/spermine N1-acetyltransferase SAT 2.8 ± 0.4 (3)  
 T71782 Branched chain Acyl-CoA oxidase BRCOX 2.7 ± 0.1 (2) 7.3 
 AA669689 Malate oxidoreductase (NADH-dependent malic enzyme)  2.5 ± 0.3 (4) 3.7 
 AA485653 Mannosyl (α-1,6) glycoprotein-β-1,2-N-acetylglucosaminyltransferase II MGAT2 2.4 ± 0.0 (4) 2.7 
 W07099 N-acetylglucosaminidase, α- (Sanfilippo disease IIIB) NAGLU 2.3 ± 0.1 (2)  
 AA444009 Acid α-glucosidase GAA 2.3 ± 0.5 (2)  
Growth factor/Cytokine and receptors     
 H15718 XL receptor tyrosine kinase AXL 5.1 ± 3.1 (2) 99 
 T55558 Colony-stimulating factor 1 (M-CSF) CSF1 3.2 ± 0.6 (3) 3.4 
 AA262988 Brain-derived neurotrophic factor BDNF 3.0 ± 0.1 (2) 23 
 R19956 Vascular endothelial growth factor VEGF 2.6 ± 0.6 (3)  
 N31467 Coxsackie virus and adenovirus receptor CXADR 2.6 ± 0.3 (2) 2.3 
 AA504461 Low-density lipoprotein receptor precursor LDLR 2.6 ± 0.0 (2) 2.3 
 T56316 Nerve growth factor β NGFB 2.2 ± 0.2 (2) 17 
 AA053285 Interleukin 15 receptor α chain IL15RA 2.2 ± 0.2 (3) 2.6 
 AA453831 Hepatoma-derived growth factor HDGF 2.1 ± 0.0 (2)  
 T47813 Macrophage-stimulating 1 (hepatocyte growth factor-like) MST1 1.9 ± 0.2 (2)  
Cytoskeleton/Cell adhesion/Cell and organelle structure     
 H15662 Cytoplasmic linker 2 CYLN2 4.2 ± 1.3 (2)  
 H15662 Cytoplasmic linker 2 isoform 2 (Williams Beuren syndrome) [KIAA0291]  4.1 ± 1.1 (2)  
 R78725 Vitamin A responsive; cytoskeleton related JWA 3.3 ± 0.8 (2) 2.8 
 AA490684 Non-lens β γ-crystallin like [absent in melanoma 1 (AIM1)] AIM1 3.1 ± 0.3 (2) 36 
 R06417 Junction plakoglobin JUP 2.6 ± 0.6 (3)  
 R13558 Activated leucocyte cell adhesion molecule ALCAM 2.6 ± 0.5 (2) 31 
 H50993 Actinin, α 4 ACTN4 2.1 ± 0.2 (2) 2.1 
Extracellular matrix     
 T77595 Hexabrachion (tenascin C, cytotactin) HXB 6.8 ± 4.4 (2) 10 
 AA677534 H. sapiens mRNA for laminin  4.8 ± 2.0 (3)  
 AA001432 Laminin, α 3 [nicein (150 kDa), kalinin (165 kDa), BM600 (150 kDa), epilegrin] LAMA3 2.7 ± 0.5 (3) 39 
 AA427561 Heparan sulfate proteoglycan (HSPG2) HSPG2 2.6 ± 0.2 (3)  
Accession no.Gene nameSymbolRatioRatio
Mean ± SE (Range)Affymetrix oligonucleotide array (N = 1)
Transcription/Nuclear proteins     
 AA969184 Cytokine inducible nuclear protein (= cardiac ankyrin repeat protein) CARP 10.1 ± 4.6 (3)  
 H45711 Zinc finger transcription factor hEZF EZF 3.4 ± 1.2 (2)  
 AA115076 Human msg1-related gene 1 (mrg1) mRNA MRG1 2.9 ± 0.3 (2)  
 T72202 Transcription factor IL-4 Stat (also known as Stat6) STAT6 2.7 ± 0.2 (3)  
 AA425238 Proto-oncogene AML1 {alternative products} CBFA2 2.6 ± 0.3 (3) 6.1 
 AA911236 v-Myb avian myeloblastosis viral oncogene homologue-like 1 (= AMYB) MYBL1 2.6 ± 0.2 (3) 13 
 N66177 Microphthalmia-associated transcription factor MITF 2.6 ± 0.3 (2) 2.8 
 H96235 v-Ets avian erythroblastosis virus E26 oncogene homologue 2 ETS2 2.4 ± 0.1 (2) 12 
Stress response: oxidative stress and xenobiotic detoxification     
 AA495936 GST, microsomal 1 MGST1 10.2 ± 4.4 (3)  
 AA670438 Ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) UCHL1 8.2 ± 4.0 (2) 18 
 AA455538 NAD(P)H:menadione oxidoreductase (also called NQO1) NMOR1 3.8 ± 0.9 (3) 4.6 
 AA680300 Member of PAS protein 2 (MOP2, also called HIF2α) MOP2 3.4 ± 0.5 (3)  
 W73474 GST, microsomal 2 MGST2 3.3 ± 1.3 (2) 5.2 
 N93686 Aldehyde dehydrogenase 7 ALDH7 3.2 ± 0.4 (2)  
 AA625806 Ninjurin1 (nerve injury-induced protein 1) NINJ1 2.7 ± 0.3 (4)  
 AA677655 Klotho protein KL 2.6 ± 0.5 (2)  
 H99813 GST θ1 GSTT1 2.5 ± 0.2 (3) 2.3 
 AA664180 Glutathione peroxidase 3 (plasma) GPX3 2.4 ± 0.5 (2) 5.3 
 AA453859 Alcohol dehydrogenase 5 (χ subunit, class III) ADH5 2.3 ± 0.4 (3)  
 AA446301 Paraoxonase (PON2 protein) PON2 2.3 ± 0.4 (3)  
 AA428859 Glutathione transferase ζ 1 (GSTZ1) GSTZ1 2.1 ± 0.1 (2)  
 H99699 Aconitase 2, mitochondrial ACO2 2.0 ± 0.1 (2)  
 H21041 Activating transcription factor 3 ATF3 1.9 ± 0.3 (2)  
Replication/Cell cycle/DNA repair and metabolism     
 R60343 5′; nucleotidase (CD73, placental purine ecto-5′-nucleotidase) NT5E 6.2 ± 2.9 (3)  
 AA429895 Human multidrug resistance-associated protein homologue (MRP3) MRP3 2.6 ± 0.1 (2)  
 AA931758 Putative lymphocyte G0-G1 switch gene (G0S2) G0S2A 2.6 ± 0.4 (4)  
 N72115 Cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4) CDKN2C 2.6 ± 0.5 (2) 2.3 
 H85464 Deleted in split hand/split foot syndrome 1 (DSS1) DSS1 2.5 ± 0.3 (2) 2.2 
 AA430382 Nucleoside phosphorylase NP 1.9 ± 0.0 (2)  
Signal transduction     
 AA598601 Insulin-like growth factor binding protein 3 IGFBP3 5.3 ± 1.3 (2) 2.1 
 T72877 Interleukin 1 receptor antagonist IL1RN 4.0 ± 1.6 (3)  
 AA460286 G protein γ-10 subunit (guanine nucleotide-binding protein GBGA)  2.4 ± 0.3 (3)  
 H26426 Protein tyrosine phosphatase, receptor type, mu polypeptide PTPRM 2.4 ± 0.4 (2) 2.9 
 AA460841 Insulin receptor substrate-1 [human, skeletal muscle, mRNA, 5828 nt] IRS1 2.3 ± 0.3 (3) 6.1 
 AA443302 Rho-related GTP binding protein RhoE RHOE 2.1 ± 0.2 (2) 4.9 
 AA411640 Ras-related GTP-binding protein A (ragA protein) RAGA 2.1 ± 0.3 (2)  
 T57556 Putative protein kinase C inhibitor PKCI-1 (protein kinase C-interacting 1) PRKCNH1 1.9 ± 0.0 (2)  
 AA910443 Nephroblastoma-overexpressed gene NOV 1.7 ± 0.2 (2) 2.3 
Biosynthesis and metabolism     
 H87471 Human l-kynurenine hydrolase (kynureninase) KYNU 4.0 ± 1.5 (2) 5.3 
 AA401111 Glucose phosphate isomerase GPI 4.4 ± 0.6 (4)  
 AA424937 Glucose-6-phosphate dehydrogenase G6PD 3.1 ± 0.6 (2) 2.1 
 AA599158 Multifunctional aminoacyl-tRNA synthetase SYHUQT 2.9 ± 0.3 (2)  
 AA894557 Creatine kinase B CKB 2.9 ± 0.9 (2) 3.4 
 H44956 Fumarylacetoacetate hydrolase FAH 2.9 ± 0.2 (4)  
 AA011215 Spermidine/spermine N1-acetyltransferase SAT 2.8 ± 0.4 (3)  
 T71782 Branched chain Acyl-CoA oxidase BRCOX 2.7 ± 0.1 (2) 7.3 
 AA669689 Malate oxidoreductase (NADH-dependent malic enzyme)  2.5 ± 0.3 (4) 3.7 
 AA485653 Mannosyl (α-1,6) glycoprotein-β-1,2-N-acetylglucosaminyltransferase II MGAT2 2.4 ± 0.0 (4) 2.7 
 W07099 N-acetylglucosaminidase, α- (Sanfilippo disease IIIB) NAGLU 2.3 ± 0.1 (2)  
 AA444009 Acid α-glucosidase GAA 2.3 ± 0.5 (2)  
Growth factor/Cytokine and receptors     
 H15718 XL receptor tyrosine kinase AXL 5.1 ± 3.1 (2) 99 
 T55558 Colony-stimulating factor 1 (M-CSF) CSF1 3.2 ± 0.6 (3) 3.4 
 AA262988 Brain-derived neurotrophic factor BDNF 3.0 ± 0.1 (2) 23 
 R19956 Vascular endothelial growth factor VEGF 2.6 ± 0.6 (3)  
 N31467 Coxsackie virus and adenovirus receptor CXADR 2.6 ± 0.3 (2) 2.3 
 AA504461 Low-density lipoprotein receptor precursor LDLR 2.6 ± 0.0 (2) 2.3 
 T56316 Nerve growth factor β NGFB 2.2 ± 0.2 (2) 17 
 AA053285 Interleukin 15 receptor α chain IL15RA 2.2 ± 0.2 (3) 2.6 
 AA453831 Hepatoma-derived growth factor HDGF 2.1 ± 0.0 (2)  
 T47813 Macrophage-stimulating 1 (hepatocyte growth factor-like) MST1 1.9 ± 0.2 (2)  
Cytoskeleton/Cell adhesion/Cell and organelle structure     
 H15662 Cytoplasmic linker 2 CYLN2 4.2 ± 1.3 (2)  
 H15662 Cytoplasmic linker 2 isoform 2 (Williams Beuren syndrome) [KIAA0291]  4.1 ± 1.1 (2)  
 R78725 Vitamin A responsive; cytoskeleton related JWA 3.3 ± 0.8 (2) 2.8 
 AA490684 Non-lens β γ-crystallin like [absent in melanoma 1 (AIM1)] AIM1 3.1 ± 0.3 (2) 36 
 R06417 Junction plakoglobin JUP 2.6 ± 0.6 (3)  
 R13558 Activated leucocyte cell adhesion molecule ALCAM 2.6 ± 0.5 (2) 31 
 H50993 Actinin, α 4 ACTN4 2.1 ± 0.2 (2) 2.1 
Extracellular matrix     
 T77595 Hexabrachion (tenascin C, cytotactin) HXB 6.8 ± 4.4 (2) 10 
 AA677534 H. sapiens mRNA for laminin  4.8 ± 2.0 (3)  
 AA001432 Laminin, α 3 [nicein (150 kDa), kalinin (165 kDa), BM600 (150 kDa), epilegrin] LAMA3 2.7 ± 0.5 (3) 39 
 AA427561 Heparan sulfate proteoglycan (HSPG2) HSPG2 2.6 ± 0.2 (3)  
Table 3A

Continued

Accession no.Gene nameSymbolRatioRatio
Mean ± SE (Range)Affymetrix oligonucleotide array (N = 1)
Apoptosis/Cell death     
 AA454646 Lymphotoxin-β receptor precursor LTB 9.9 ± 4.3 (2)  
 AA452556 TRAMP protein (translocating chain-associating membrane protein) TRAMP 2.6 ± 0.2 (4)  
 AA025275 DAP-kinase (death associated protein kinase) HSDAPK 2.5 ± 0.1 (2)  
Inflammation/Immune and antiviral response/Histocompatibility     
 H63077 Annexin I (lipocortin I) ANX1 9.3 ± 2.7 (2) 145 
 AA458965 Natural killer cells protein 4 precursor  3.0 ± 1.0 (2)  
 AA406020 IFN-induced 17 kDa protein (ubiquitin cross-reactive protein) UCRP 2.4 ± 0.4 (4)  
 AA488367 Host cell factor homologue LCP 2.4 ± 0.3 (2)  
 AA491191 IFN-γ induced protein IFI 16 (myeloid differ. transcriptional activator) IFI16 1.7 ± 0.2 (2)  
Differentiation/Development/Tissue-specific expression or function     
 AA598610 Mesoderm-specific transcript (mouse) homologue MEST 4.9 ± 0.4 (3) 6.1 
 R43605 Homeobox protein Cux-2 (Cut-liKe 2) [KIAA0293] CUTL2 4.7 ± 0.5 (2)  
 R60995 Homo sapiens Coch-5B2 (Cochlin precursor) COCH1 3.8 ± 1.1 (3)  
 AA432066 Sarcoglycan, epsilon (dystrophin complex protein, muscular dystrophy) SGCE 3.0 ± 0.7 (2) 7.1 
 H99813 Keratin 19 KRT19 2.5 ± 0.4 (4) 8.3 
 T97762 IFN-related developmental regulator 1 IFRD1 2.7 ± 0.3 (2) 3.7 
 AA700054 Adipophilin (adipose differentiation-related protein) ADRP 2.4 ± 0.2 (2)  
 R26960 Peripheral myelin protein 22 PMP22 2.0 ± 0.2 (2)  
 AA884015 Tubby-related protein 2 (TULP2) TULP2 2.0 ± 0.1 (2)  
 AA676598 Nerve growth factor-inducible PC4 homologue IFRD2 1.9 ± 0.2 (3) 2.9 
Transmembrane/Membrane/Integrins     
 AA488073 Mucin 1, transmembrane MUC1 3.3 ± 1.2 (3)  
 AA424695 Integrin α-3 subunit ITGA3 2.2 ± 0.3 (4) 2.3 
 AA425451 Integrin, α E (CD103, mucosal lymphocyte antigen 1; α-polypeptide) ITGAE 1.9 ± 0.0 (2) 2.1 
 AA464601 Tetraspanin Tspan-5 (TSPAN-5) gene TM4SF9 1.9 ± 0.0 (2)  
Channels/Pore structure/Transport     
 N62620 Two P-domain K+ channel, subfamily K, member 1 TWIK1 3.5 ± 1.2 (2) 8.8 
 AA292226 Creatine transporter mRNA SLC6A8 2.7 ± 0.1 (3)  
 AA598814 ATPase, Na+/K+ transporting, β 1 polypeptide ATP1B1 2.0 ± 0.1 (2)  
RNA or protein processing/Protein modification and proteolysis     
 H99816 Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2 PLOD2 5.7 ± 2.0 (3) 2.5 
 AA628430 Sm-like protein CaSm (U6 SnRNA-associated LSm1 protein)  2.6 ± 0.1 (4)  
 H59231 Human metalloprotease/disintegrin/cysteine-rich protein (MDC9) MDC9 2.6 ± 0.3 (4)  
 T70122 Ribonuclease L (2′,5′-oligoisoadenylate synthetase-dependent) inhibitor RNASELI 2.5 ± 0.4 (3)  
 AA047338 Proteasome ι chain (prosomal p27K protein, PROS-27) PSA6 2.5 ± 0.1 (2)  
 AA047039 eIF-1A, Y isoform (eukaryotic translation initiation factor 1A, Y isoform) EIF1AY 2.4 ± 0.3 (4) 1260 
 AA934762 26S proteasome subunit p44.5 (26S proteasome regulatory subunit 9) PSDB 2.3 ± 0.3 (4)  
Miscellaneous or function unknown     
 T74192 Plasma protein S (α) (blood coagulation protein) PROS1 3.3 ± 0.6 (3)  
 AA670382 H. sapiens mRNA for 3′; UTR of unknown protein  3.6 ± 0.0 (2)  
 AA875953 KIAA0404 protein (unknown function)  2.6 ± 0.2 (2)  
Accession no.Gene nameSymbolRatioRatio
Mean ± SE (Range)Affymetrix oligonucleotide array (N = 1)
Apoptosis/Cell death     
 AA454646 Lymphotoxin-β receptor precursor LTB 9.9 ± 4.3 (2)  
 AA452556 TRAMP protein (translocating chain-associating membrane protein) TRAMP 2.6 ± 0.2 (4)  
 AA025275 DAP-kinase (death associated protein kinase) HSDAPK 2.5 ± 0.1 (2)  
Inflammation/Immune and antiviral response/Histocompatibility     
 H63077 Annexin I (lipocortin I) ANX1 9.3 ± 2.7 (2) 145 
 AA458965 Natural killer cells protein 4 precursor  3.0 ± 1.0 (2)  
 AA406020 IFN-induced 17 kDa protein (ubiquitin cross-reactive protein) UCRP 2.4 ± 0.4 (4)  
 AA488367 Host cell factor homologue LCP 2.4 ± 0.3 (2)  
 AA491191 IFN-γ induced protein IFI 16 (myeloid differ. transcriptional activator) IFI16 1.7 ± 0.2 (2)  
Differentiation/Development/Tissue-specific expression or function     
 AA598610 Mesoderm-specific transcript (mouse) homologue MEST 4.9 ± 0.4 (3) 6.1 
 R43605 Homeobox protein Cux-2 (Cut-liKe 2) [KIAA0293] CUTL2 4.7 ± 0.5 (2)  
 R60995 Homo sapiens Coch-5B2 (Cochlin precursor) COCH1 3.8 ± 1.1 (3)  
 AA432066 Sarcoglycan, epsilon (dystrophin complex protein, muscular dystrophy) SGCE 3.0 ± 0.7 (2) 7.1 
 H99813 Keratin 19 KRT19 2.5 ± 0.4 (4) 8.3 
 T97762 IFN-related developmental regulator 1 IFRD1 2.7 ± 0.3 (2) 3.7 
 AA700054 Adipophilin (adipose differentiation-related protein) ADRP 2.4 ± 0.2 (2)  
 R26960 Peripheral myelin protein 22 PMP22 2.0 ± 0.2 (2)  
 AA884015 Tubby-related protein 2 (TULP2) TULP2 2.0 ± 0.1 (2)  
 AA676598 Nerve growth factor-inducible PC4 homologue IFRD2 1.9 ± 0.2 (3) 2.9 
Transmembrane/Membrane/Integrins     
 AA488073 Mucin 1, transmembrane MUC1 3.3 ± 1.2 (3)  
 AA424695 Integrin α-3 subunit ITGA3 2.2 ± 0.3 (4) 2.3 
 AA425451 Integrin, α E (CD103, mucosal lymphocyte antigen 1; α-polypeptide) ITGAE 1.9 ± 0.0 (2) 2.1 
 AA464601 Tetraspanin Tspan-5 (TSPAN-5) gene TM4SF9 1.9 ± 0.0 (2)  
Channels/Pore structure/Transport     
 N62620 Two P-domain K+ channel, subfamily K, member 1 TWIK1 3.5 ± 1.2 (2) 8.8 
 AA292226 Creatine transporter mRNA SLC6A8 2.7 ± 0.1 (3)  
 AA598814 ATPase, Na+/K+ transporting, β 1 polypeptide ATP1B1 2.0 ± 0.1 (2)  
RNA or protein processing/Protein modification and proteolysis     
 H99816 Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2 PLOD2 5.7 ± 2.0 (3) 2.5 
 AA628430 Sm-like protein CaSm (U6 SnRNA-associated LSm1 protein)  2.6 ± 0.1 (4)  
 H59231 Human metalloprotease/disintegrin/cysteine-rich protein (MDC9) MDC9 2.6 ± 0.3 (4)  
 T70122 Ribonuclease L (2′,5′-oligoisoadenylate synthetase-dependent) inhibitor RNASELI 2.5 ± 0.4 (3)  
 AA047338 Proteasome ι chain (prosomal p27K protein, PROS-27) PSA6 2.5 ± 0.1 (2)  
 AA047039 eIF-1A, Y isoform (eukaryotic translation initiation factor 1A, Y isoform) EIF1AY 2.4 ± 0.3 (4) 1260 
 AA934762 26S proteasome subunit p44.5 (26S proteasome regulatory subunit 9) PSDB 2.3 ± 0.3 (4)  
Miscellaneous or function unknown     
 T74192 Plasma protein S (α) (blood coagulation protein) PROS1 3.3 ± 0.6 (3)  
 AA670382 H. sapiens mRNA for 3′; UTR of unknown protein  3.6 ± 0.0 (2)  
 AA875953 KIAA0404 protein (unknown function)  2.6 ± 0.2 (2)  
Table 4

Genes whose expression is decreased in DU-145 wtBRCA1 [versus control (Neo)] cell clones

Accession no.Gene nameSymbolRatio
Mean ± SE (range)Affymetrix array (N = 1)
Transcription/Nuclear proteins     
 AA857131 HIV Tat-SF1 (Tat-specific factor 1) HTATSF1 0.29 ± 0.00 (2)  
 W00975 p300/CBP-associated factor (P/CAF) PCAF 0.33 ± 0.09 (2)  
 H27379 Transcription elongation factor S-II (also called transcription elongation factor A) TCEA2 0.39 ± 0.00 (2)  
 AA504265 PINCH protein (LIM and senescent cell antigen like domains 1) LIMS1 0.41 ± 0.05 (2)  
Stress response: oxidative stress and xenobiotic detoxification     
 H86554 Ceruloplasmin (ferroxidase) [multicopper oxidase, Fe & Cu homeostasis] CP 0.18 ± 0.09 (3) 0.030 
 R33755 GST π-1 GSTP1 0.39 ± 0.00 (2) 0.27 
Replication/Cell cycle/DNA repair and metabolism     
 AA042990 Semaphorin E (protein associated with drug resistance) SEMA3C 0.26 ± 0.13 (3)  
 R19031 Photolyase homologue [similar to Drosophila (6-4) photolyase] PH 0.35 ± 0.10 (3)  
 R10662 DNA mismatch repair protein MLH1 MLH1 0.37 ± 0.05 (2)  
 N54344 KIAA0074 (also called condensin subunit 2, Barren homologue protein 1) BRRN1 0.38 ± 0.09 (2)  
 AA598887 KIAA0178 (SMC1 structural maintenance of chromosomes 1-like 1) SMC1L1 0.42 ± 0.01 (2)  
 AA683578 Adenosine deaminase ADA 0.42 ± 0.06 (2) 0.28 
 H94617 Replication factor C (activator 1) 3 (38 kDa) RFC3 0.47 ± 0.00 (2)  
 AA045192 Retinoblastoma 1 (including osteosarcoma) RB1 0.49 ± 0.01 (2)  
Signal transduction     
 S75725 Prostacyclin-stimulating factor (also known as IGFBP7) IGFBP7 0.21 ± 0.04 (2)  
 AA055835 Caveolin, caveolae protein, 22 kDa CAV1 0.31 ± 0.04 (3)  
 AA284634 Janus kinase 1 (a protein tyrosine kinase) JAK1 0.32 ± 0.09 (3) 0.26 
 AA425947 RIG (regulated in glioma) [putative tumor suppressor, Ras-related gene] RIG 0.32 ± 0.08 (3) 0.29 
 NM_015881 Dickkopf homologue 3 (regulator of Wnt signaling) DKK3 0.37 ± 0.12 (2)  
 AA418999 Smad5 (a MAD-like protein, putative tumor suppressor) SMAD5 0.40 ± 0.04 (2)  
 AA101793 Lipid-activated, protein kinase PRK2 PRK2 0.43 ± 0.06 (3)  
Biosynthesis and metabolism     
 AA599187 Phosphoglycerate kinase 1 (hypoxia-inducible glycolytic enzyme) PGK1 0.32 ± 0.12 (2) 0.35 
 AA018372 Liver glutamate dehydrogenase GLUD1 0.36 ± 0.12 (2)  
 AA489611 Lactate dehydrogenase A LDHA 0.40 ± 0.02 (2)  
 H07926 Mitochondrial 3-oxoacyl-CoA thiolase (acetyl-Coenzyme A acyltransferase 2) ACAA2 0.44 ± 0.02 (3)  
Growth factor/Cytokine and receptors     
 AA425028 Human cytokine receptor EB13 (induced by EBV infection) EBI3 0.35 ± 0.05 (2) 0.018 
 AA424629 Latent transforming growth factor β binding protein 2 LTBP2 0.38 ± 0.11 (2) 0.32 
 R72075 Human heregulin-β gene HRGA 0.39 ± 0.01 (2)  
 T64134 Monocyte chemoattractant protein MCP-4 (= small inducible cytokine A13) CCL13 0.40 ± 0.05 (2)  
 R39227 Cytokine IK (also called IK factor, RER protein, red protein) IK 0.40 ± 0.06 (2)  
 H98636 CD40L receptor precursor (CD40 antigen, member of TNF receptor family) CD40 0.41 ± 0.03 (2)  
Cytoskeleton/Cell adhesion/Cell and organelle structure     
 AA196000 Actinin α-3 ACTN3 0.31 ± 0.08 (3)  
 AA669758 Nucleophosmin (nucleolar phosphoprotein B23, numatrin) NPM1 0.38 ± 0.01 (2)  
 AA452566 Peroxisomal membrane protein 3 (35 D, Zellweger syndrome) PXMP3 0.46 ± 0.00 (2) 0.47 
Extracellular matrix     
 W93163 TNF-inducible protein TSG-6 precursor (a hyaluron binding protein) TNFAIP6 0.24 ± 0.10 (3) 0.038 
 AA134871 Fibulin 1 FBLN1 0.32 ± 0.07 (2) 0.19 
 AA418811 Fibrillin 1 (Marfan syndrome) FBN1 0.44 ± 0.04 (2) 0.092 
Apoptosis/Cell death     
 AA699697 Tumor necrosis factor TNF 0.18 ± 0.01 (2) 0.043 
 N69204 Chromosome segregation gene homologue CAS (apoptosis susceptibility) CSE1L 0.29 ± 0.03 (2)  
 AA455413 Ceramide glucosyltransferase (glucosylceramide synthase, GCS) UGCG 0.40 ± 0.03 (3)  
Inflammation/Immune and antiviral response/Histocompatibility     
 AA625981 FK506-binding protein 1 (12 kDa) [an immunophilin] FKBP1 0.40 ± 0.08 (4) 0.066 
 AA625981 FK506-binding protein 1A (12 kDa) [an immunophilin] FKBP1A 0.41 ± 0.08 (2) 0.35 
 AA419108 Annexin IV (placental anticoagulant protein II) ANX4 0.40 ± 0.02 (2) 0.36 
Differentiation/Development/Tissue-specific expression or function     
 AA400739 SRY (sex-determining region Y)-box 9 (campomelic dysplasia, sex-reversal) SOX9 0.23 ± 0.03 (2) 0.090 
 H20758 ZyginI (synaptogamin-interacting protein) [axonal growth and fasciculation]  0.25 ± 0.06 (2)  
 AA911661 Homeo box B2 HOXB2 0.29 ± 0.01 (2) 0.045 
 W58092 Tropomyosin α chain (skeletal muscle) TPM1 0.31 ± 0.07 (3) 0.17 
 N79708 Fragile X mental retardation protein 1 homologue FXR1 FXR1 0.34 ± 0.12 (2) 0.49 
 AA598517 Keratin 8 KRT8 0.38 ± 0.07 (3)  
Transmembrane/Membrane/Integrins     
 N46419 Synaptogyrin 3 (integral membrane protein, function unclear) SYNGR3 0.48 ± 0.02 (3) 0.10 
 H78244 Intestinal and liver tetraspan membrane protein (il-TMP) TM4SF4 0.40 ± 0.06 (2)  
RNA or protein processing/Protein modification and proteolysis     
 AA476294 Nucleolin (nuclear phosphoprotein) [synthesis & maturation of ribosomes] NCL 0.27 ± 0.09 (2)  
 AA143201 Matrix metalloproteinase 1 (interstitial collagenase) MMP1 0.35 ± 0.07 (2) 0.36 
Function unknown     
 R16604 ESTs, weakly similar to TAL-6  0.14 ± 0.09 (2)  
 AA455476 Homo sapiens cDNA: FLJ22921 fis, clone KAT06711 (unnamed protein product)  0.38 ± 0.06 (2)  
 AA431438 H. sapiens cDNA FLJ10500 fis, clone NT2RP2000369  0.38 ± 0.06 (2)  
 R67042 KIAA0265 (Kelch motif containing protein of unknown function)  0.40 ± 0.00 (2) 0.49 
Accession no.Gene nameSymbolRatio
Mean ± SE (range)Affymetrix array (N = 1)
Transcription/Nuclear proteins     
 AA857131 HIV Tat-SF1 (Tat-specific factor 1) HTATSF1 0.29 ± 0.00 (2)  
 W00975 p300/CBP-associated factor (P/CAF) PCAF 0.33 ± 0.09 (2)  
 H27379 Transcription elongation factor S-II (also called transcription elongation factor A) TCEA2 0.39 ± 0.00 (2)  
 AA504265 PINCH protein (LIM and senescent cell antigen like domains 1) LIMS1 0.41 ± 0.05 (2)  
Stress response: oxidative stress and xenobiotic detoxification     
 H86554 Ceruloplasmin (ferroxidase) [multicopper oxidase, Fe & Cu homeostasis] CP 0.18 ± 0.09 (3) 0.030 
 R33755 GST π-1 GSTP1 0.39 ± 0.00 (2) 0.27 
Replication/Cell cycle/DNA repair and metabolism     
 AA042990 Semaphorin E (protein associated with drug resistance) SEMA3C 0.26 ± 0.13 (3)  
 R19031 Photolyase homologue [similar to Drosophila (6-4) photolyase] PH 0.35 ± 0.10 (3)  
 R10662 DNA mismatch repair protein MLH1 MLH1 0.37 ± 0.05 (2)  
 N54344 KIAA0074 (also called condensin subunit 2, Barren homologue protein 1) BRRN1 0.38 ± 0.09 (2)  
 AA598887 KIAA0178 (SMC1 structural maintenance of chromosomes 1-like 1) SMC1L1 0.42 ± 0.01 (2)  
 AA683578 Adenosine deaminase ADA 0.42 ± 0.06 (2) 0.28 
 H94617 Replication factor C (activator 1) 3 (38 kDa) RFC3 0.47 ± 0.00 (2)  
 AA045192 Retinoblastoma 1 (including osteosarcoma) RB1 0.49 ± 0.01 (2)  
Signal transduction     
 S75725 Prostacyclin-stimulating factor (also known as IGFBP7) IGFBP7 0.21 ± 0.04 (2)  
 AA055835 Caveolin, caveolae protein, 22 kDa CAV1 0.31 ± 0.04 (3)  
 AA284634 Janus kinase 1 (a protein tyrosine kinase) JAK1 0.32 ± 0.09 (3) 0.26 
 AA425947 RIG (regulated in glioma) [putative tumor suppressor, Ras-related gene] RIG 0.32 ± 0.08 (3) 0.29 
 NM_015881 Dickkopf homologue 3 (regulator of Wnt signaling) DKK3 0.37 ± 0.12 (2)  
 AA418999 Smad5 (a MAD-like protein, putative tumor suppressor) SMAD5 0.40 ± 0.04 (2)  
 AA101793 Lipid-activated, protein kinase PRK2 PRK2 0.43 ± 0.06 (3)  
Biosynthesis and metabolism     
 AA599187 Phosphoglycerate kinase 1 (hypoxia-inducible glycolytic enzyme) PGK1 0.32 ± 0.12 (2) 0.35 
 AA018372 Liver glutamate dehydrogenase GLUD1 0.36 ± 0.12 (2)  
 AA489611 Lactate dehydrogenase A LDHA 0.40 ± 0.02 (2)  
 H07926 Mitochondrial 3-oxoacyl-CoA thiolase (acetyl-Coenzyme A acyltransferase 2) ACAA2 0.44 ± 0.02 (3)  
Growth factor/Cytokine and receptors     
 AA425028 Human cytokine receptor EB13 (induced by EBV infection) EBI3 0.35 ± 0.05 (2) 0.018 
 AA424629 Latent transforming growth factor β binding protein 2 LTBP2 0.38 ± 0.11 (2) 0.32 
 R72075 Human heregulin-β gene HRGA 0.39 ± 0.01 (2)  
 T64134 Monocyte chemoattractant protein MCP-4 (= small inducible cytokine A13) CCL13 0.40 ± 0.05 (2)  
 R39227 Cytokine IK (also called IK factor, RER protein, red protein) IK 0.40 ± 0.06 (2)  
 H98636 CD40L receptor precursor (CD40 antigen, member of TNF receptor family) CD40 0.41 ± 0.03 (2)  
Cytoskeleton/Cell adhesion/Cell and organelle structure     
 AA196000 Actinin α-3 ACTN3 0.31 ± 0.08 (3)  
 AA669758 Nucleophosmin (nucleolar phosphoprotein B23, numatrin) NPM1 0.38 ± 0.01 (2)  
 AA452566 Peroxisomal membrane protein 3 (35 D, Zellweger syndrome) PXMP3 0.46 ± 0.00 (2) 0.47 
Extracellular matrix     
 W93163 TNF-inducible protein TSG-6 precursor (a hyaluron binding protein) TNFAIP6 0.24 ± 0.10 (3) 0.038 
 AA134871 Fibulin 1 FBLN1 0.32 ± 0.07 (2) 0.19 
 AA418811 Fibrillin 1 (Marfan syndrome) FBN1 0.44 ± 0.04 (2) 0.092 
Apoptosis/Cell death     
 AA699697 Tumor necrosis factor TNF 0.18 ± 0.01 (2) 0.043 
 N69204 Chromosome segregation gene homologue CAS (apoptosis susceptibility) CSE1L 0.29 ± 0.03 (2)  
 AA455413 Ceramide glucosyltransferase (glucosylceramide synthase, GCS) UGCG 0.40 ± 0.03 (3)  
Inflammation/Immune and antiviral response/Histocompatibility     
 AA625981 FK506-binding protein 1 (12 kDa) [an immunophilin] FKBP1 0.40 ± 0.08 (4) 0.066 
 AA625981 FK506-binding protein 1A (12 kDa) [an immunophilin] FKBP1A 0.41 ± 0.08 (2) 0.35 
 AA419108 Annexin IV (placental anticoagulant protein II) ANX4 0.40 ± 0.02 (2) 0.36 
Differentiation/Development/Tissue-specific expression or function     
 AA400739 SRY (sex-determining region Y)-box 9 (campomelic dysplasia, sex-reversal) SOX9 0.23 ± 0.03 (2) 0.090 
 H20758 ZyginI (synaptogamin-interacting protein) [axonal growth and fasciculation]  0.25 ± 0.06 (2)  
 AA911661 Homeo box B2 HOXB2 0.29 ± 0.01 (2) 0.045 
 W58092 Tropomyosin α chain (skeletal muscle) TPM1 0.31 ± 0.07 (3) 0.17 
 N79708 Fragile X mental retardation protein 1 homologue FXR1 FXR1 0.34 ± 0.12 (2) 0.49 
 AA598517 Keratin 8 KRT8 0.38 ± 0.07 (3)  
Transmembrane/Membrane/Integrins     
 N46419 Synaptogyrin 3 (integral membrane protein, function unclear) SYNGR3 0.48 ± 0.02 (3) 0.10 
 H78244 Intestinal and liver tetraspan membrane protein (il-TMP) TM4SF4 0.40 ± 0.06 (2)  
RNA or protein processing/Protein modification and proteolysis     
 AA476294 Nucleolin (nuclear phosphoprotein) [synthesis & maturation of ribosomes] NCL 0.27 ± 0.09 (2)  
 AA143201 Matrix metalloproteinase 1 (interstitial collagenase) MMP1 0.35 ± 0.07 (2) 0.36 
Function unknown     
 R16604 ESTs, weakly similar to TAL-6  0.14 ± 0.09 (2)  
 AA455476 Homo sapiens cDNA: FLJ22921 fis, clone KAT06711 (unnamed protein product)  0.38 ± 0.06 (2)  
 AA431438 H. sapiens cDNA FLJ10500 fis, clone NT2RP2000369  0.38 ± 0.06 (2)  
 R67042 KIAA0265 (Kelch motif containing protein of unknown function)  0.40 ± 0.00 (2) 0.49 
Table 5

Effect of exogenous wtBRCA1 on gene expression in MCF-7 breast cancer cells (selected)

Accession no.Gene name (symbol)Ratio (wtBRCA1/control)
DU-145MCF-7 (−E2)MCF-7 (+E2)
Increased by BRCA1     
 Transcription factors/Nuclear proteins     
  H27379 Transcription elongation factor (S-II)   2.1 ± 0.5 (2) 
   Pre-B-cell–enhancing factor (PBEF)   2.0 ± 0.2 (2) 
  AA600217 Activating transcription factor-4 (ATF4)   1.9 ± 0.4 (2) 
  AA685085 High mobility group protein 1 (HMG1) 1.9 ± 0.0 (2)  1.8 ± 0.0 (2) 
  AA418670 JunD proto-oncogene (JUND)   1.8 ± 0.0 (2) 
  T99236 JunB proto-oncogene (JUNB)   1.7 ± 0.1 (2) 
  AA62599 Zf9 (cellular nucleic acid binding protein) [ST12, ZF9, KLF6]   1.7 ± 0.0 (2) 
  AA421977 Dr1-associated transcriptional corepressor (DRAP1)   1.7 ± 0.2 (2) 
  T55801 Transcription factor TFIIA, γ (GTFA2) 2.1 ± 0.3 (4)  1.6 ± 0.0 (2) 
  AA291513 B-cell lymphoma 7B (BCL7) 1.9 ± 0.3 (2)  1.6 ± 0.0 (2) 
 Stress response/Xenobiotic detoxification/Mitochondrial function     
  AA629719 Cytochrome c oxidase VIIc subunit (COX7C)  2.6 ± 0.7  
  T90999 UDP glucuronosyl transferase 1A, microsomal (UGT1A)   2.5 ± 0.7 (2) 
  AA453859 Alcohol dehydrogenase 5 (ADH5) 2.2 ± 0.4 (3) 1.5 (1) 2.3 (1) 
  AA680322 Ubiquinone oxidoreductase MLRQ subunit (NUOMS)   2.2 ± 0.6 (2) 
  W77812 Cis-platinum resistance-associated α protein  2.1 ± 0.1 (2)  
  AA680300 Member of PAS protein 2 (MOP2) 3.4 ± 0.5 (3) 1.9 ± 0.1 (2) 1.6 (1) 
  AA495936 GST, microsomal (MGST1) 10.2 ± 4.4 (3)  1.8 ± 0.1 (3) 
  R73525 Epoxide hydrolase 2, cytoplasmic [EPHX2]   1.8 ± 0.1 (2) 
  AA488081 Selenium donor protein (selenoprotein synthetase) [SelD, SEPHS1]   1.7 ± 0.0 (3) 
  AA443630 Aldehyde dehydrogenase-8 (ALHD8)  1.9 ± 0.2 (2) 1.7 ± 0.1 (2) 
  AA459663 Anti-oxidant protein AOE37-2 (thioredoxin peroxidase) [PRDX4]   1.6 ± 0.1 (2) 
  H68845 Thiol-specific anti-oxidant (thioredoxin peroxidase 1) [TSA, PRP]   1.6 ± 0.0 (2) 
  AA283629 Selenoprotein W (Se1W, SEPW1)   1.6 ± 0.1 (2) 
 Replication/Cell cycle/DNA repair     
  AA489752 Cyclin G2 (CCNG2)   4.0 ± 0.8 (2) 
  R19031 Brain mRNA for photolyase homologue  2.1 ± 0.5 (2)  
  N70463 B-cell translocation gene 1, antiproliferative (BTG1)  2.1 ± 0.4 (2) 1.8 ± 0.2 (3) 
  H54417 Nucleoside diphosphate kinase  2.1 ± 0.4 (2) 1.8 ± 0.1 (2) 
  AA496013 Protein serine/threonine kinase 2 (STK2, also called NEK4)   1.9 ± 0.0 (2) 
  H85464 Deleted in split hand/split foot syndrome 1 (DSS1) 2.5 ± 0.3 (2)  1.8 ± 0.1 (2) 
  AA291715 DNA ligase I, ATP-dependent (LIG1)  1.7 ± 0.1 (2)  
  AA885642 H2B/g (= histone H2B.1) [H2BFG]  1.7 ± 0.1 (2)  
  AA156571 Alanyl tRNA synthase (AARS)  1.7 ± 0.1 (2)  
 Signal transduction     
  AA598601 Insulin-like growth factor binding protein 3 5.3 ± 1.3 (2) 3.8 ± 0.8 (2) 3.6 ± 0.5 (2) 
  H08899 Homologue of yeast IPP isomerase 2.6 ± 0.8 (3)  3.2 ± 0.2 (2) 
  AA460286 G protein γ-10 subunit 2.4 ± 0.3 (3) 1.8 ± 0.1 (2) 2.5 ± 0.3 (2) 
  R24543 Guanine nucleotide regulatory protein (NET1)   2.0 ± 0.2 (2) 
  W73473 Bone morphogenetic protein-7 (BMP7)  2.0 ± 0.4 (2)  
  T72202 IL4-STAT (STAT6) 2.7 ± 0.2 (3) 1.8 ± 0.1 (2) 1.6 ± 0.1 (2) 
  AA521411 Calcium modulating ligand (CAMLG)   1.7 ± 0.0 (2) 
  AA482328 Myristolated ala-rich C-kinase substrate (MACS, MARCKS)   1.7 ± 0.1 (2) 
  T57556 Protein kinase C inhibitor PKCI-1 (PRKCNH1) 1.9 ± 0.0 (2)  1.7 ± 0.1 (3) 
  AA490300 PDGF receptor-associated protein 2.1 ± 0.2 (3)  1.7 ± 0.1 (3) 
  AA910443 Nephrobastoma overexpressed gene (NOV) 1.7 ± 0.2 (2) 1.6 ± 0.1 (2) 1.6 (1) 
  AI017398 Sodium channel 2 (amiloride-sensitive) [BNaC2, ACCN2] 2.1 ± 0.1 (2)  1.5 ± 0.0 (2) 
 Biosynthesis and metabolism     
  AA424937 Glucose-6-phosphate dehydrogenase (G6PD) 3.1 ± 0.6 (2) 1.7 ± 0.1 (2) 2.6 (1) 
  H87471 Human l-kynurenine hydrolase (KYNU) 4.0 ± 1.5 (2)  2.5 ± 0.5 (2) 
  H51574 Arachidonate 5-lipoxygenase (ALOX5)   2.0 ± 0.2 (2) 
  AA444009 Acid-α glucosidase (GAA) 2.3 ± 0.5 (2) 1.9 ± 0.3 (2) 1.6 (1) 
  AA434024 Lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase) [LSS]   1.8 ± 0.1 (3) 
  AA633882 Retinol dehydrogenase 1 (11-cis) [RDH1] 2.7 ± 0.7 (2)  1.7 ± 0.0 (2) 
  AA157955 Methyl sterol oxidase (sterol-C4-methyl oxidase-like) [ERG25]  1.7 ± 0.1 (2)  
 Ligands and receptors     
  H22652 Glial maturation factor β (GMFB)   2.6 ± 0.7 (2) 
  AA452556 Translocation-associated membrane protein 1 (TRAMP) 2.6 ± 0.2 (4)   
  R19956 Vascular endothelial growth factor (VEGF) 2.6 ± 0.6 (3)  2.2 ± 0.5 (2) 
  T77810 RYK receptor-like tyrosine kinase (RYK)   2.0 ± 0.4 (3) 
  AA679177 Follistatin-related protein precursor (follistatin-like 1) [FSTL1]   2.0 ± 0.2 (2) 
  N48698 Hybrid receptor gp250 precursor (SORLA, LRP9) 2.1 ± 0.0 (2)  1.7 ± 0.1 (2) 
  AA233809 Transforming growth factor β2 (TGFB2)  1.6 ± 0.1 (2)  
 Cytoskeleton/Cell adhesion/Cell structure     
  H72027 Gelsolin precursor, plasma (Finnish amyloidosis) [GSN]  2.4 ± 0.7 (2)  
  N77754 Lysosome-associated membrane protein 2 (LAMP2)   2.0 ± 0.1 (2) 
  R06417 Junction plakoglobin (JUP) 2.6 ± 0.6 (3) 1.8 ± 0.1 (2)  
 Extracellular matrix     
  AA029997 Procollagen type IV, α 5 (Alport’s Syndrome) [COL4A5]  2.0 ± 0.4 (2)  
 Apoptosis/Cell death     
  AA063521 E1B 19K/Bcl-2 binding protein Nip3 (BNIP3)  1.6 (1) 2.8 ± 0.1 (2) 
  AA598483 Tax1 binding protein-151 (TXBP151)   2.1 ± 0.1 (2) 
 Inflammation/Immune responses     
  H63077 Annexin I (lipocortin) [ANX1] 9.3 ± 2.7 (2)  2.3 ± 0.6 (2) 
  AA630328 Galectin 3 (GALS3) 1.8 ± 0.2 (2) 2.1 ± 0.3 (2)  
  AA634103 Thymosin β-4 (THYB4) 2.0 ± 0.1 (2) 1.6 ± 0.1 (2) 1.6 ± 0.1 (2) 
Accession no.Gene name (symbol)Ratio (wtBRCA1/control)
DU-145MCF-7 (−E2)MCF-7 (+E2)
Increased by BRCA1     
 Transcription factors/Nuclear proteins     
  H27379 Transcription elongation factor (S-II)   2.1 ± 0.5 (2) 
   Pre-B-cell–enhancing factor (PBEF)   2.0 ± 0.2 (2) 
  AA600217 Activating transcription factor-4 (ATF4)   1.9 ± 0.4 (2) 
  AA685085 High mobility group protein 1 (HMG1) 1.9 ± 0.0 (2)  1.8 ± 0.0 (2) 
  AA418670 JunD proto-oncogene (JUND)   1.8 ± 0.0 (2) 
  T99236 JunB proto-oncogene (JUNB)   1.7 ± 0.1 (2) 
  AA62599 Zf9 (cellular nucleic acid binding protein) [ST12, ZF9, KLF6]   1.7 ± 0.0 (2) 
  AA421977 Dr1-associated transcriptional corepressor (DRAP1)   1.7 ± 0.2 (2) 
  T55801 Transcription factor TFIIA, γ (GTFA2) 2.1 ± 0.3 (4)  1.6 ± 0.0 (2) 
  AA291513 B-cell lymphoma 7B (BCL7) 1.9 ± 0.3 (2)  1.6 ± 0.0 (2) 
 Stress response/Xenobiotic detoxification/Mitochondrial function     
  AA629719 Cytochrome c oxidase VIIc subunit (COX7C)  2.6 ± 0.7  
  T90999 UDP glucuronosyl transferase 1A, microsomal (UGT1A)   2.5 ± 0.7 (2) 
  AA453859 Alcohol dehydrogenase 5 (ADH5) 2.2 ± 0.4 (3) 1.5 (1) 2.3 (1) 
  AA680322 Ubiquinone oxidoreductase MLRQ subunit (NUOMS)   2.2 ± 0.6 (2) 
  W77812 Cis-platinum resistance-associated α protein  2.1 ± 0.1 (2)  
  AA680300 Member of PAS protein 2 (MOP2) 3.4 ± 0.5 (3) 1.9 ± 0.1 (2) 1.6 (1) 
  AA495936 GST, microsomal (MGST1) 10.2 ± 4.4 (3)  1.8 ± 0.1 (3) 
  R73525 Epoxide hydrolase 2, cytoplasmic [EPHX2]   1.8 ± 0.1 (2) 
  AA488081 Selenium donor protein (selenoprotein synthetase) [SelD, SEPHS1]   1.7 ± 0.0 (3) 
  AA443630 Aldehyde dehydrogenase-8 (ALHD8)  1.9 ± 0.2 (2) 1.7 ± 0.1 (2) 
  AA459663 Anti-oxidant protein AOE37-2 (thioredoxin peroxidase) [PRDX4]   1.6 ± 0.1 (2) 
  H68845 Thiol-specific anti-oxidant (thioredoxin peroxidase 1) [TSA, PRP]   1.6 ± 0.0 (2) 
  AA283629 Selenoprotein W (Se1W, SEPW1)   1.6 ± 0.1 (2) 
 Replication/Cell cycle/DNA repair     
  AA489752 Cyclin G2 (CCNG2)   4.0 ± 0.8 (2) 
  R19031 Brain mRNA for photolyase homologue  2.1 ± 0.5 (2)  
  N70463 B-cell translocation gene 1, antiproliferative (BTG1)  2.1 ± 0.4 (2) 1.8 ± 0.2 (3) 
  H54417 Nucleoside diphosphate kinase  2.1 ± 0.4 (2) 1.8 ± 0.1 (2) 
  AA496013 Protein serine/threonine kinase 2 (STK2, also called NEK4)   1.9 ± 0.0 (2) 
  H85464 Deleted in split hand/split foot syndrome 1 (DSS1) 2.5 ± 0.3 (2)  1.8 ± 0.1 (2) 
  AA291715 DNA ligase I, ATP-dependent (LIG1)  1.7 ± 0.1 (2)  
  AA885642 H2B/g (= histone H2B.1) [H2BFG]  1.7 ± 0.1 (2)  
  AA156571 Alanyl tRNA synthase (AARS)  1.7 ± 0.1 (2)  
 Signal transduction     
  AA598601 Insulin-like growth factor binding protein 3 5.3 ± 1.3 (2) 3.8 ± 0.8 (2) 3.6 ± 0.5 (2) 
  H08899 Homologue of yeast IPP isomerase 2.6 ± 0.8 (3)  3.2 ± 0.2 (2) 
  AA460286 G protein γ-10 subunit 2.4 ± 0.3 (3) 1.8 ± 0.1 (2) 2.5 ± 0.3 (2) 
  R24543 Guanine nucleotide regulatory protein (NET1)   2.0 ± 0.2 (2) 
  W73473 Bone morphogenetic protein-7 (BMP7)  2.0 ± 0.4 (2)  
  T72202 IL4-STAT (STAT6) 2.7 ± 0.2 (3) 1.8 ± 0.1 (2) 1.6 ± 0.1 (2) 
  AA521411 Calcium modulating ligand (CAMLG)   1.7 ± 0.0 (2) 
  AA482328 Myristolated ala-rich C-kinase substrate (MACS, MARCKS)   1.7 ± 0.1 (2) 
  T57556 Protein kinase C inhibitor PKCI-1 (PRKCNH1) 1.9 ± 0.0 (2)  1.7 ± 0.1 (3) 
  AA490300 PDGF receptor-associated protein 2.1 ± 0.2 (3)  1.7 ± 0.1 (3) 
  AA910443 Nephrobastoma overexpressed gene (NOV) 1.7 ± 0.2 (2) 1.6 ± 0.1 (2) 1.6 (1) 
  AI017398 Sodium channel 2 (amiloride-sensitive) [BNaC2, ACCN2] 2.1 ± 0.1 (2)  1.5 ± 0.0 (2) 
 Biosynthesis and metabolism     
  AA424937 Glucose-6-phosphate dehydrogenase (G6PD) 3.1 ± 0.6 (2) 1.7 ± 0.1 (2) 2.6 (1) 
  H87471 Human l-kynurenine hydrolase (KYNU) 4.0 ± 1.5 (2)  2.5 ± 0.5 (2) 
  H51574 Arachidonate 5-lipoxygenase (ALOX5)   2.0 ± 0.2 (2) 
  AA444009 Acid-α glucosidase (GAA) 2.3 ± 0.5 (2) 1.9 ± 0.3 (2) 1.6 (1) 
  AA434024 Lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase) [LSS]   1.8 ± 0.1 (3) 
  AA633882 Retinol dehydrogenase 1 (11-cis) [RDH1] 2.7 ± 0.7 (2)  1.7 ± 0.0 (2) 
  AA157955 Methyl sterol oxidase (sterol-C4-methyl oxidase-like) [ERG25]  1.7 ± 0.1 (2)  
 Ligands and receptors     
  H22652 Glial maturation factor β (GMFB)   2.6 ± 0.7 (2) 
  AA452556 Translocation-associated membrane protein 1 (TRAMP) 2.6 ± 0.2 (4)   
  R19956 Vascular endothelial growth factor (VEGF) 2.6 ± 0.6 (3)  2.2 ± 0.5 (2) 
  T77810 RYK receptor-like tyrosine kinase (RYK)   2.0 ± 0.4 (3) 
  AA679177 Follistatin-related protein precursor (follistatin-like 1) [FSTL1]   2.0 ± 0.2 (2) 
  N48698 Hybrid receptor gp250 precursor (SORLA, LRP9) 2.1 ± 0.0 (2)  1.7 ± 0.1 (2) 
  AA233809 Transforming growth factor β2 (TGFB2)  1.6 ± 0.1 (2)  
 Cytoskeleton/Cell adhesion/Cell structure     
  H72027 Gelsolin precursor, plasma (Finnish amyloidosis) [GSN]  2.4 ± 0.7 (2)  
  N77754 Lysosome-associated membrane protein 2 (LAMP2)   2.0 ± 0.1 (2) 
  R06417 Junction plakoglobin (JUP) 2.6 ± 0.6 (3) 1.8 ± 0.1 (2)  
 Extracellular matrix     
  AA029997 Procollagen type IV, α 5 (Alport’s Syndrome) [COL4A5]  2.0 ± 0.4 (2)  
 Apoptosis/Cell death     
  AA063521 E1B 19K/Bcl-2 binding protein Nip3 (BNIP3)  1.6 (1) 2.8 ± 0.1 (2) 
  AA598483 Tax1 binding protein-151 (TXBP151)   2.1 ± 0.1 (2) 
 Inflammation/Immune responses     
  H63077 Annexin I (lipocortin) [ANX1] 9.3 ± 2.7 (2)  2.3 ± 0.6 (2) 
  AA630328 Galectin 3 (GALS3) 1.8 ± 0.2 (2) 2.1 ± 0.3 (2)  
  AA634103 Thymosin β-4 (THYB4) 2.0 ± 0.1 (2) 1.6 ± 0.1 (2) 1.6 ± 0.1 (2) 
Table 5A

Continued

Accession no.Gene name (symbol)Ratio (wtBRCA1/control)
DU-145MCF-7 (−E2)MCF-7 (+E2)
 Differentiation/Development/Tissue-specific expression     
  AA402207 Eyes absent homologue (EAB1, EYA2)  2.6 ± 0.6 (3) 3.0 ± 1.0 (2) 
  R26960 Peripheral myelin protein 22 (PMP22) 2.0 ± 0.2 (2) 2.1 (1) 2.8 ± 0.8 (2) 
  AA464250 Keratin 19 (KRT19) 2.5 ± 0.4 (4)  1.8 ± 0.2 (2) 
  AA676598 Nerve growth factor-inducible PC4 homologue (IFRD2) 1.9 ± 0.2 (3)  1.8 ± 0.2 (2) 
 Channels/Pore structure/Transport     
  R39446 WHITE protein homologue  2.4 ± 0.8 (2)  
  N62620 Two P-domain K+ channel (TWIK1) 3.5 ± 1.2 (2) 1.5 ± 0.0 (2)  
 RNA or protein processing/Protein modification     
  W73874 Cathepsin L (CTSL)   2.6 ± 0.3 (2) 
  AA490124 Ubiquitin conjugating enzyme E2 (Drosophila bandless) [UBE2N]   2.1 ± 0.3 (2) 
  AA011215 Spermine/spermidine N1-acetyltransferase (SAT) 2.8 ± 0.4 (3) 2.0 ± 0.1 (2)  
  AA459039 Placental bikunin (serine protease inhibitor) [SPINT2, HAI2]   2.0 ± 0.2 (3) 
  AA628430 Sm-like protein CaSm (LSM1) 2.6 ± 0.1 (4)  1.7 ± 0.2 (2) 
 Miscellaneous or function unknown     
  AA418918 Nuclear autoantigen GS2NA (striatin-3) [GS2NA] 3.4 ± 0.7 (3)  2.2 ± 0.2 (2) 
Decreased by BRCA1     
 Transcription factors/Nuclear proteins     
  H32858 X2 box repressor (putative zinc finger transcriptional regulator)  0.43 ± 0.13 (2)  
  N67262 Zinc finger protein 135 (clone PH8-17) [ZNF135]  0.51 ± 0.17  
  N49526 Myb proto-oncogene (MYB)  0.52 ± 0.20  
  AA704809 SIL [TAL1 (SCL) interrupting locus] (hypoxia-sensitive) [SIL] 0.40 ± 0.09 (2) 0.64 ± 0.08 (2)  
 Stress response/Xenobiotic detoxification/Mitochondrial function     
  AA099134 Oxygen-regulated protein, 150 kDa (ORP150)  0.40 ± 0.11 (2) 0.41 ± 0.22 (2) 
  AA133187 Iron-regulated protein (IRP2, IREB2)  0.42 ± 0.25 (2)  
  N55459 Metallothionein hMT-1f (functional) [MT1F]  0.69 ± 0.05 (2) 0.50 ± 0.06 (2) 
  AA621218 Carnitine acetyltransferase (CRAT)   0.58 ± 0.05 (3) 
  N66957 Cytochrome P450 subfamily XXVII (CYP27, CYP27A1)  0.66 ± 0.06  
 Signal transduction     
  AA284634 Janus kinase 1 (JAK1) 0.32 ± 0.09 (3) 0.34 ± 0.13 (3) 0.50 ± 0.22 (2) 
  AA282196 Homo sapiens serine/threonine protein kinase  0.40 ± 0.23 (2) 0.56 ± 0.01 (2) 
  AA101793 Lipid-activated, protein kinase 2 (PRK2) 0.43 ± 0.06 (3) 0.43 ± 0.11 (2)  
  AA418999 Smad5 (a MAD-like protein) [SMAD5] 0.40 ± 0.04 (2) 0.50 ± 0.18 (2)  
 Biosynthesis and metabolism     
  AA070357 Transketolase (Wernicke-Korsakoff syndrome) [TKT]  0.29 ± 0.07 (3)  
  R84263 CAD protein (multifunctional enzyme) (CAD)  0.46 ± 0.23  
  AA018372 Liver glutamate dehydrogenase (GLUD1) 0.36 ± 0.12 (2) 0.53 ± 0.17 (2)  
 Growth factor/Cytokine and receptors     
  AA425028 Human cytokine receptor EBI3 (EBI3) 0.35 ± 0.05 (2)  0.61 ± 0.05 (2) 
  AA019320 Adducin 2 (β) [ADD2, ADDB]  0.65 ± 0.08 (3) 0.41 ± 0.07 (2) 
 Cytoskeleton/Cell Adhesion/Cell structure     
  AA598659 NuMA (nuclear matrix protein) [NUMA, NUMA1]  0.20 ± 0.12  
  W31983 X104 (tight junction protein 2, zona occludens 2) [TJP2, ZO2]  0.32 ± 0.17 (2) 0.59 ± 0.09 (2) 
  W13290 Tight junction protein 1 (TJP1)  0.45 ± 0.14 (3)  
  AA455062 Zyxin (YX)  0.48 ± 0.16 (3)  
  AA669758 Nucleophosmin (B23, numatrin) [NPM1] 0.38 ± 0.01 (2) 0.58 ± 0.14 (2)  
  AA452566 Peroxisomal membrane protein 3 (XMP3) 0.46 ± 0.00 (2) 0.69 ± 0.01 (2)  
 Extracellular matrix     
  AA464630 Thrombospondin 1 (HBS1)  0.50 ± 0.13 (3) 0.41 ± 0.16 (2) 
  H24650 Laminin γ 1 (AMC1)  0.49 ± 0.16 (3) 0.46 ± 0.18 (2) 
  W93163 TNF-inducible protein 6 (TSG-6) [TNFAIP6] 0.24 ± 0.10 (3) 0.70 ± 0.01 (2)  
 Apoptosis/Cell death     
  AA476272 Putative DNA-binding protein A20 (TNFα-induced) [TNFAIP3]  0.56 ± 0.05 (2)  
 Differentiation/Development/Tissue specific     
  AA455145 Semaphorin V (guidance of neuronal growth cones) [SEMA3B]   0.64 ± 0.09 (2) 
 Channels/Pore structure/Transport     
  AA457050 Treacher-Collins syndrome susceptibility-1 (treacle) [TCOF1]  0.50 ± 0.07  
  N46843 Aquaporin 4 (AQP4)  0.66 ± 0.01  
 RNA or protein processing/Protein modification     
  AA284634 Antithrombin III [AT3, SERPINC1]  0.25 ± 0.11 (2)  
 Miscellaneous or function unknown     
  AA056465 54 kDa protein (RNP repeat domain protein) 0.25 ± 0.06 (2) 0.44 ± 0.23 (2)  
Accession no.Gene name (symbol)Ratio (wtBRCA1/control)
DU-145MCF-7 (−E2)MCF-7 (+E2)
 Differentiation/Development/Tissue-specific expression     
  AA402207 Eyes absent homologue (EAB1, EYA2)  2.6 ± 0.6 (3) 3.0 ± 1.0 (2) 
  R26960 Peripheral myelin protein 22 (PMP22) 2.0 ± 0.2 (2) 2.1 (1) 2.8 ± 0.8 (2) 
  AA464250 Keratin 19 (KRT19) 2.5 ± 0.4 (4)  1.8 ± 0.2 (2) 
  AA676598 Nerve growth factor-inducible PC4 homologue (IFRD2) 1.9 ± 0.2 (3)  1.8 ± 0.2 (2) 
 Channels/Pore structure/Transport     
  R39446 WHITE protein homologue  2.4 ± 0.8 (2)  
  N62620 Two P-domain K+ channel (TWIK1) 3.5 ± 1.2 (2) 1.5 ± 0.0 (2)  
 RNA or protein processing/Protein modification     
  W73874 Cathepsin L (CTSL)   2.6 ± 0.3 (2) 
  AA490124 Ubiquitin conjugating enzyme E2 (Drosophila bandless) [UBE2N]   2.1 ± 0.3 (2) 
  AA011215 Spermine/spermidine N1-acetyltransferase (SAT) 2.8 ± 0.4 (3) 2.0 ± 0.1 (2)  
  AA459039 Placental bikunin (serine protease inhibitor) [SPINT2, HAI2]   2.0 ± 0.2 (3) 
  AA628430 Sm-like protein CaSm (LSM1) 2.6 ± 0.1 (4)  1.7 ± 0.2 (2) 
 Miscellaneous or function unknown     
  AA418918 Nuclear autoantigen GS2NA (striatin-3) [GS2NA] 3.4 ± 0.7 (3)  2.2 ± 0.2 (2) 
Decreased by BRCA1     
 Transcription factors/Nuclear proteins     
  H32858 X2 box repressor (putative zinc finger transcriptional regulator)  0.43 ± 0.13 (2)  
  N67262 Zinc finger protein 135 (clone PH8-17) [ZNF135]  0.51 ± 0.17  
  N49526 Myb proto-oncogene (MYB)  0.52 ± 0.20  
  AA704809 SIL [TAL1 (SCL) interrupting locus] (hypoxia-sensitive) [SIL] 0.40 ± 0.09 (2) 0.64 ± 0.08 (2)  
 Stress response/Xenobiotic detoxification/Mitochondrial function     
  AA099134 Oxygen-regulated protein, 150 kDa (ORP150)  0.40 ± 0.11 (2) 0.41 ± 0.22 (2) 
  AA133187 Iron-regulated protein (IRP2, IREB2)  0.42 ± 0.25 (2)  
  N55459 Metallothionein hMT-1f (functional) [MT1F]  0.69 ± 0.05 (2) 0.50 ± 0.06 (2) 
  AA621218 Carnitine acetyltransferase (CRAT)   0.58 ± 0.05 (3) 
  N66957 Cytochrome P450 subfamily XXVII (CYP27, CYP27A1)  0.66 ± 0.06  
 Signal transduction     
  AA284634 Janus kinase 1 (JAK1) 0.32 ± 0.09 (3) 0.34 ± 0.13 (3) 0.50 ± 0.22 (2) 
  AA282196 Homo sapiens serine/threonine protein kinase  0.40 ± 0.23 (2) 0.56 ± 0.01 (2) 
  AA101793 Lipid-activated, protein kinase 2 (PRK2) 0.43 ± 0.06 (3) 0.43 ± 0.11 (2)  
  AA418999 Smad5 (a MAD-like protein) [SMAD5] 0.40 ± 0.04 (2) 0.50 ± 0.18 (2)  
 Biosynthesis and metabolism     
  AA070357 Transketolase (Wernicke-Korsakoff syndrome) [TKT]  0.29 ± 0.07 (3)  
  R84263 CAD protein (multifunctional enzyme) (CAD)  0.46 ± 0.23  
  AA018372 Liver glutamate dehydrogenase (GLUD1) 0.36 ± 0.12 (2) 0.53 ± 0.17 (2)  
 Growth factor/Cytokine and receptors     
  AA425028 Human cytokine receptor EBI3 (EBI3) 0.35 ± 0.05 (2)  0.61 ± 0.05 (2) 
  AA019320 Adducin 2 (β) [ADD2, ADDB]  0.65 ± 0.08 (3) 0.41 ± 0.07 (2) 
 Cytoskeleton/Cell Adhesion/Cell structure     
  AA598659 NuMA (nuclear matrix protein) [NUMA, NUMA1]  0.20 ± 0.12  
  W31983 X104 (tight junction protein 2, zona occludens 2) [TJP2, ZO2]  0.32 ± 0.17 (2) 0.59 ± 0.09 (2) 
  W13290 Tight junction protein 1 (TJP1)  0.45 ± 0.14 (3)  
  AA455062 Zyxin (YX)  0.48 ± 0.16 (3)  
  AA669758 Nucleophosmin (B23, numatrin) [NPM1] 0.38 ± 0.01 (2) 0.58 ± 0.14 (2)  
  AA452566 Peroxisomal membrane protein 3 (XMP3) 0.46 ± 0.00 (2) 0.69 ± 0.01 (2)  
 Extracellular matrix     
  AA464630 Thrombospondin 1 (HBS1)  0.50 ± 0.13 (3) 0.41 ± 0.16 (2) 
  H24650 Laminin γ 1 (AMC1)  0.49 ± 0.16 (3) 0.46 ± 0.18 (2) 
  W93163 TNF-inducible protein 6 (TSG-6) [TNFAIP6] 0.24 ± 0.10 (3) 0.70 ± 0.01 (2)  
 Apoptosis/Cell death     
  AA476272 Putative DNA-binding protein A20 (TNFα-induced) [TNFAIP3]  0.56 ± 0.05 (2)  
 Differentiation/Development/Tissue specific     
  AA455145 Semaphorin V (guidance of neuronal growth cones) [SEMA3B]   0.64 ± 0.09 (2) 
 Channels/Pore structure/Transport     
  AA457050 Treacher-Collins syndrome susceptibility-1 (treacle) [TCOF1]  0.50 ± 0.07  
  N46843 Aquaporin 4 (AQP4)  0.66 ± 0.01  
 RNA or protein processing/Protein modification     
  AA284634 Antithrombin III [AT3, SERPINC1]  0.25 ± 0.11 (2)  
 Miscellaneous or function unknown     
  AA056465 54 kDa protein (RNP repeat domain protein) 0.25 ± 0.06 (2) 0.44 ± 0.23 (2)  
Table 6

Selected genes whose expression is decreased in Brca1Δex11Δex (versus Brca1+/+) mouse embryo fibroblasts

Accession no.Gene nameSymbolRatio
Mean ± SE (range)Affymetrix Array (N = 1)
Transcription/Nuclear proteins     
 AA208865 Nuclear receptor corepressor 1 Ncor1 0.47 ± 0.08 (2)  
 AA276365 Myocyte enhancer factor 2c Mef2c 0.47 ± 0.07 (2) 0.44 
 AA244944 CCAAT/enhancer binding protein α (C/EBP), related sequence 1 Cebpa-rs1 0.51 ± 0.02 (2)  
 AA212695 Trans-acting transcription factor Sp1 (cell cycle-regulated) Sp1 0.51 ± 0.09 (2)  
 AA036347 Kruppel-like factor 9 Klf9 0.52 ± 0.11 (2)  
 AA125037 Zinc finger protein 148 Zfp148 0.52 ± 0.01 (2)  
 AA138529 Zinc finger protein 62 Zfp62 0.56 ± 0.15 (2)  
 AA501045 Nuclear receptor subfamily 2, group H, member 2 Nr2c2 0.56 ± 0.11 (2) 0.061 
 AA155377 Zinc finger protein X linked Zfx 0.57 ± 0.01 (2)  
 W83524 Transcription factor 12 Tcf12 0.58 ± 0.06 (3)  
 AA097341 Nuclear receptor coactivator 1 Ncoa1 0.59 ± 0.07 (3)  
Stress response: oxidative stress and xenobiotic detoxification     
 AA200734 Ethanol decreased 2 Etohd2 0.47 ± 0.07 (2)  
 AA445861 Activating transcription factor 2 (stress response transcription factor) Atf2 0.50 ± 0.07 (2)  
 AA139271 Glutathione peroxidase 3 Gpx3 0.51 ± 0.05 (3) 0.12 
 W54349 GST, α 1 (Ya) Gsta1 0.51 (1)  
 AA120574 Superoxide dismutase 1, soluble Sod1 0.53 ± 0.07 (2)  
 AA044475 Nuclear factor, erythroid-derived 2, like 2 (also called Nrf2) Nfe2l2 0.53 ± 0.07 (2)  
 AA033466 Myeloperoxidase Mpo 0.53 ± 0.06 (2)  
 AA060716 Early growth response 1 (stress-responsive transcription factor) Egr1 0.54 ± 0.16 (2)  
 AA276440 Selenoprotein P, plasma, 1 Sepp1 0.57 ± 0.02 (3)  
 W82873 Aryl hydrocarbon receptor Ahr 0.59 ± 0.15 (2)  
 AA250120 GST, α 2 (Yc2) Gsta2 0.61 ± 0.10 (2)  
Heat shock-related proteins     
 AA212162 Chaperonin subunit 8 (θ) Cct8 0.48 ± 0.12 (2)  
 AA498713 Heat shock protein, 74 kDa Hsp74 0.58 ± 0.13 (2)  
 W62018 Heat shock cognate protein, 70 Hsc70 0.61 ± 0.03 (2)  
Replication/Cell cycle/DNA repair and metabolism     
 AA17363 Ectonucleotide pyrophosphatase/phosphodiesterase 2 Enpp2 0.38 ± 0.22 (2)  
 AA386895 Tetratricopeptide repeat domain 3 (chromosome segregation) Ttc3 0.43 ± 0.07 (2)  
 AA288567 Suppressor of Ty 4 homologue (S. cerevisiaeSupt4 h 0.44 ± 0.04 (3)  
 AA268478 Serine/threonine kinase 2 (homologous to mitotic egulator NIMA) Stk2 0.45 ± 0.03 (2)  
 AA273291 Chromodomain helicase DNA binding protein 1 Chd1 0.47 ± 0.04 (3)  
 AA498480 Centrosomin A Csma 0.49 ± 0.06 (2)  
 AA542278 Clusterin Clu 0.50 ± 0.04 (3) 0.46 
 AA122530 SNM1 protein (required for repair of DNA double-strand cross-links) SNM1 0.55 ± 0.14 (2)  
 AA285484 G1 to phase transition 1 Gspt1 0.55 ± 0.05 (2)  
 AA475568 5′-3′; exoribonuclease 2 Xrn2 0.57 ± 0.05 (2)  
 AW544661 Serine/threonine kinase 10 (Polo-like kinase) Stk10 0.57 ± 0.18 (2)  
 AA170792 Topoisomerase (DNA) I Top1 0.58 ± 0.08 (2)  
 AA108933 CDC-like kinase (serine/threonine kinase, cell cycle regulatory) Clk 0.58 ± 0.09 (3)  
 AA020165 Uridine phosphorylase Upp 0.59 ± 0.05 (3)  
Signal transduction     
 AA254238 Rho-associated coiled-coil forming kinase 2 Rock2 0.44 ± 0.11 (2)  
 AA286039 Ras-binding protein SUR-8 (also called suppressor of clear, Soc-2) Sur8 0.50 ± 0.02 (2)  
 AA200336 Tumor protein D52 (? Role in calcium-mediated signal transduction) Tpd52 0.51 ± 0.09 (2)  
 AA177814 MAD homologue (Drosophila) [also called Smad1] Madh1 0.52 ± 0.10 (2)  
 AA271494 Myristoylated alanine rich protein kinase Csubstrate Macs 0.54 ± 0.14 (3) 0.33 
 AA124332 Phosphodiesterase 8 Pde8 0.57 ± 0.06 (2)  
 AA413508 SAPK/Erk/kinase 1 Serk1 0.60 ± 0.01 (2)  
 AA396114 NET1 homologue member of Dbl family of Rho A GEFs) Net1 0.60 ± 0.02 (2)  
Biosynthesis and metabolism     
 AA068968 Involved in GPI-anchor biosynthesis Pig-b 0.51 ± 0.08 (2)  
 AA199988 Mannosidase 1, alpha Man1a 0.60 ± 0.08 (2) 0.29 
Growth factor/Cytokine and receptors     
 AA020307 Very low density lipoprotein receptor Vldlr 0.54 ± 0.15 (3)  
 AA008515 Transforming growth factor, β receptor III Tgfbr3 0.56 ± 0.01 (2)  
 W53962 Transforming growth factor, β 2 Tgfb2 0.66 ± 0.05 (3)  
Cytoskeleton/Cell adhesion/Cell and organelle structure     
 W99951 Neurofilament, light polypeptide (68 kDa) Nfl 0.40 ± 0.03 (3)  
 W13290 Tight junction protein 1 Tjp1 0.45 ± 0.00 (2)  
 AA388122 Maternal embryonic message 3 (vacuolar sorting protein 35) Mem3 0.45 ± 0.05 (2)  
 AA009086 Golgi autoantigen, golgin subfamily a, 4 Golga4 0.49 ± 0.03 (2)  
 AA021816 Adducin 3 (γ) [membrane skeletal protein] Add3 0.56 ± 0.08 (3)  
 AA060038 Epsin 2 (involved in clathrin-mediated endocytosis) Epn2 0.58 ± 0.11 (3)  
 AA472871 Lysosomal membrane glycoprotein 2 Lamp2 0.59 ± 0.11 (2) 0.31 
 AA274739 Pinin (desmosome-associated and nuclear mRNA splicing protein) Pnn 0.62 ± 0.07 (3)  
Extracellular matrix     
 AA239404 Nidogen Nid 0.48 ± 0.07 (2)  
 AA059779 Laminin, γ 1 Lamc1 0.60 ± 0.03 (2)  
 AA260280 Procollagen, type III, α1 Col3a1 0.68 ± 0.03 (2) 0.12 
Apoptosis/Cell death     
 AA175651 Caspase 11 Casp11 0.38 ± 0.22 (2)  
 AA098139 Caspase 1 Casp1 0.54 ± 0.09 (3)  
Inflammation/Immune and antiviral response/histocompatibility     
 AA174447 IFN-activated gene 203 Ifi203 0.54 ± 0.02 (3) 0.13 
 AA189587 Natural killer tumor recognition sequence Nktr 0.59 ± 0.02 (3)  
Accession no.Gene nameSymbolRatio
Mean ± SE (range)Affymetrix Array (N = 1)
Transcription/Nuclear proteins     
 AA208865 Nuclear receptor corepressor 1 Ncor1 0.47 ± 0.08 (2)  
 AA276365 Myocyte enhancer factor 2c Mef2c 0.47 ± 0.07 (2) 0.44 
 AA244944 CCAAT/enhancer binding protein α (C/EBP), related sequence 1 Cebpa-rs1 0.51 ± 0.02 (2)  
 AA212695 Trans-acting transcription factor Sp1 (cell cycle-regulated) Sp1 0.51 ± 0.09 (2)  
 AA036347 Kruppel-like factor 9 Klf9 0.52 ± 0.11 (2)  
 AA125037 Zinc finger protein 148 Zfp148 0.52 ± 0.01 (2)  
 AA138529 Zinc finger protein 62 Zfp62 0.56 ± 0.15 (2)  
 AA501045 Nuclear receptor subfamily 2, group H, member 2 Nr2c2 0.56 ± 0.11 (2) 0.061 
 AA155377 Zinc finger protein X linked Zfx 0.57 ± 0.01 (2)  
 W83524 Transcription factor 12 Tcf12 0.58 ± 0.06 (3)  
 AA097341 Nuclear receptor coactivator 1 Ncoa1 0.59 ± 0.07 (3)  
Stress response: oxidative stress and xenobiotic detoxification     
 AA200734 Ethanol decreased 2 Etohd2 0.47 ± 0.07 (2)  
 AA445861 Activating transcription factor 2 (stress response transcription factor) Atf2 0.50 ± 0.07 (2)  
 AA139271 Glutathione peroxidase 3 Gpx3 0.51 ± 0.05 (3) 0.12 
 W54349 GST, α 1 (Ya) Gsta1 0.51 (1)  
 AA120574 Superoxide dismutase 1, soluble Sod1 0.53 ± 0.07 (2)  
 AA044475 Nuclear factor, erythroid-derived 2, like 2 (also called Nrf2) Nfe2l2 0.53 ± 0.07 (2)  
 AA033466 Myeloperoxidase Mpo 0.53 ± 0.06 (2)  
 AA060716 Early growth response 1 (stress-responsive transcription factor) Egr1 0.54 ± 0.16 (2)  
 AA276440 Selenoprotein P, plasma, 1 Sepp1 0.57 ± 0.02 (3)  
 W82873 Aryl hydrocarbon receptor Ahr 0.59 ± 0.15 (2)  
 AA250120 GST, α 2 (Yc2) Gsta2 0.61 ± 0.10 (2)  
Heat shock-related proteins     
 AA212162 Chaperonin subunit 8 (θ) Cct8 0.48 ± 0.12 (2)  
 AA498713 Heat shock protein, 74 kDa Hsp74 0.58 ± 0.13 (2)  
 W62018 Heat shock cognate protein, 70 Hsc70 0.61 ± 0.03 (2)  
Replication/Cell cycle/DNA repair and metabolism     
 AA17363 Ectonucleotide pyrophosphatase/phosphodiesterase 2 Enpp2 0.38 ± 0.22 (2)  
 AA386895 Tetratricopeptide repeat domain 3 (chromosome segregation) Ttc3 0.43 ± 0.07 (2)  
 AA288567 Suppressor of Ty 4 homologue (S. cerevisiaeSupt4 h 0.44 ± 0.04 (3)  
 AA268478 Serine/threonine kinase 2 (homologous to mitotic egulator NIMA) Stk2 0.45 ± 0.03 (2)  
 AA273291 Chromodomain helicase DNA binding protein 1 Chd1 0.47 ± 0.04 (3)  
 AA498480 Centrosomin A Csma 0.49 ± 0.06 (2)  
 AA542278 Clusterin Clu 0.50 ± 0.04 (3) 0.46 
 AA122530 SNM1 protein (required for repair of DNA double-strand cross-links) SNM1 0.55 ± 0.14 (2)  
 AA285484 G1 to phase transition 1 Gspt1 0.55 ± 0.05 (2)  
 AA475568 5′-3′; exoribonuclease 2 Xrn2 0.57 ± 0.05 (2)  
 AW544661 Serine/threonine kinase 10 (Polo-like kinase) Stk10 0.57 ± 0.18 (2)  
 AA170792 Topoisomerase (DNA) I Top1 0.58 ± 0.08 (2)  
 AA108933 CDC-like kinase (serine/threonine kinase, cell cycle regulatory) Clk 0.58 ± 0.09 (3)  
 AA020165 Uridine phosphorylase Upp 0.59 ± 0.05 (3)  
Signal transduction     
 AA254238 Rho-associated coiled-coil forming kinase 2 Rock2 0.44 ± 0.11 (2)  
 AA286039 Ras-binding protein SUR-8 (also called suppressor of clear, Soc-2) Sur8 0.50 ± 0.02 (2)  
 AA200336 Tumor protein D52 (? Role in calcium-mediated signal transduction) Tpd52 0.51 ± 0.09 (2)  
 AA177814 MAD homologue (Drosophila) [also called Smad1] Madh1 0.52 ± 0.10 (2)  
 AA271494 Myristoylated alanine rich protein kinase Csubstrate Macs 0.54 ± 0.14 (3) 0.33 
 AA124332 Phosphodiesterase 8 Pde8 0.57 ± 0.06 (2)  
 AA413508 SAPK/Erk/kinase 1 Serk1 0.60 ± 0.01 (2)  
 AA396114 NET1 homologue member of Dbl family of Rho A GEFs) Net1 0.60 ± 0.02 (2)  
Biosynthesis and metabolism     
 AA068968 Involved in GPI-anchor biosynthesis Pig-b 0.51 ± 0.08 (2)  
 AA199988 Mannosidase 1, alpha Man1a 0.60 ± 0.08 (2) 0.29 
Growth factor/Cytokine and receptors     
 AA020307 Very low density lipoprotein receptor Vldlr 0.54 ± 0.15 (3)  
 AA008515 Transforming growth factor, β receptor III Tgfbr3 0.56 ± 0.01 (2)  
 W53962 Transforming growth factor, β 2 Tgfb2 0.66 ± 0.05 (3)  
Cytoskeleton/Cell adhesion/Cell and organelle structure     
 W99951 Neurofilament, light polypeptide (68 kDa) Nfl 0.40 ± 0.03 (3)  
 W13290 Tight junction protein 1 Tjp1 0.45 ± 0.00 (2)  
 AA388122 Maternal embryonic message 3 (vacuolar sorting protein 35) Mem3 0.45 ± 0.05 (2)  
 AA009086 Golgi autoantigen, golgin subfamily a, 4 Golga4 0.49 ± 0.03 (2)  
 AA021816 Adducin 3 (γ) [membrane skeletal protein] Add3 0.56 ± 0.08 (3)  
 AA060038 Epsin 2 (involved in clathrin-mediated endocytosis) Epn2 0.58 ± 0.11 (3)  
 AA472871 Lysosomal membrane glycoprotein 2 Lamp2 0.59 ± 0.11 (2) 0.31 
 AA274739 Pinin (desmosome-associated and nuclear mRNA splicing protein) Pnn 0.62 ± 0.07 (3)  
Extracellular matrix     
 AA239404 Nidogen Nid 0.48 ± 0.07 (2)  
 AA059779 Laminin, γ 1 Lamc1 0.60 ± 0.03 (2)  
 AA260280 Procollagen, type III, α1 Col3a1 0.68 ± 0.03 (2) 0.12 
Apoptosis/Cell death     
 AA175651 Caspase 11 Casp11 0.38 ± 0.22 (2)  
 AA098139 Caspase 1 Casp1 0.54 ± 0.09 (3)  
Inflammation/Immune and antiviral response/histocompatibility     
 AA174447 IFN-activated gene 203 Ifi203 0.54 ± 0.02 (3) 0.13 
 AA189587 Natural killer tumor recognition sequence Nktr 0.59 ± 0.02 (3)  
Table 6A

Continued

Accession no.Gene nameSymbolRatio
Mean ± SE (range)Affymetrix Array (N = 1)
Differentiation/Development/Tissue-specific expression or function     
 AA200033 Fragile X mental retardation syndrome 1 homologue (RNA binding protein) Fmr1 0.54 ± 0.08 (2)  
 AA174970 Quaking (KH domain, GGA repeat protein; role in myelination) Qk 0.60 ± 0.03 (3)  
 W91526 Homeobox B9 Hoxb9 0.62 ± 0.12 (2) 0.061 
Channels/Pore structure/Transport     
 AA137859 Rabaptin 5 (RAB5 effector protein, vesicular transport) Rab5ep-pending 0.35 ± 0.02 (2)  
 AA063753 ATP-binding cassette 1 (multidrug transport & scavenger receptor) Abc1 0.38 ± 0.05 (3) 0.20 
RNA or Protein processing/Protein modification and proteolysis     
 AA153909 Itchy (E3 ubiquitin protein ligase) Itch 0.50 ± 0.03 (2)  
 AA154542 Tripeptidyl peptidase II (subtilase family serine protease) Tpp2 0.51 ± 0.08 (3)  
 AA466714 YME1-like 1 (yeast) [ATP-dependent metalloprotease, mitochondrial] Yme1l1 0.51 ± 0.07 (2)  
 AA267222 Ubiquitin-conjugating enzyme E3A Ube3a 0.54 ± 0.05 (3)  
Miscellaneous and function unknown     
 AA146494 Kidney androgen regulated protein (function unknown) Kap 0.50 ± 0.07 (3)  
 W11889 Hemochromatosis Hfe 0.64 ± 0.04 (2) 0.19 
Accession no.Gene nameSymbolRatio
Mean ± SE (range)Affymetrix Array (N = 1)
Differentiation/Development/Tissue-specific expression or function     
 AA200033 Fragile X mental retardation syndrome 1 homologue (RNA binding protein) Fmr1 0.54 ± 0.08 (2)  
 AA174970 Quaking (KH domain, GGA repeat protein; role in myelination) Qk 0.60 ± 0.03 (3)  
 W91526 Homeobox B9 Hoxb9 0.62 ± 0.12 (2) 0.061 
Channels/Pore structure/Transport     
 AA137859 Rabaptin 5 (RAB5 effector protein, vesicular transport) Rab5ep-pending 0.35 ± 0.02 (2)  
 AA063753 ATP-binding cassette 1 (multidrug transport & scavenger receptor) Abc1 0.38 ± 0.05 (3) 0.20 
RNA or Protein processing/Protein modification and proteolysis     
 AA153909 Itchy (E3 ubiquitin protein ligase) Itch 0.50 ± 0.03 (2)  
 AA154542 Tripeptidyl peptidase II (subtilase family serine protease) Tpp2 0.51 ± 0.08 (3)  
 AA466714 YME1-like 1 (yeast) [ATP-dependent metalloprotease, mitochondrial] Yme1l1 0.51 ± 0.07 (2)  
 AA267222 Ubiquitin-conjugating enzyme E3A Ube3a 0.54 ± 0.05 (3)  
Miscellaneous and function unknown     
 AA146494 Kidney androgen regulated protein (function unknown) Kap 0.50 ± 0.07 (3)  
 W11889 Hemochromatosis Hfe 0.64 ± 0.04 (2) 0.19 
Table 7

Comparison of Brca1 Δ exon 11 MEFs versus exogenous wtBRCA1 in DU-145/MCF-7 (this study)

A. Concordance of BRCA1-regulated gene expression in different cell types
Accession no.Gene name (symbol)MEFsDU-145MCF-7 (−E2)MCF-7 (+E2)
T74192 Plasma protein S (α) [PROS1] ↓ in Brca1 Δ exon 11 MEFs 3.3 ± 0.6 (3)   
AA664180 Glutathione peroxidase 3 (plasma) [GPX3] ↓ in Brca1 Δ exon 11 MEFs 2.4 ± 0.5 (2)   
AA063521 E1B 19K/Bcl-2 binding protein Nip3 (BNIP3) ↓ in Brca1 Δ exon 11 MEFs  1.6 (1) 2.8 ± 0.1 (2) 
H27379 Transcription elongation factor (S-II) ↓ in Brca1 Δ exon 11 MEFs   2.1 ± 0.5 (2) 
N77754 Lysosome-associated membrane protein 2 (LAMP2) ↓ in Brca1 Δ exon 11 MEFs   2.0 ± 0.1 (2) 
R24543 Guanine nucleotide regulatory protein (NET1) ↓ in Brca1 Δ exon 11 MEFs   2.0 ± 0.2 (2) 
AA496013 Protein serine/threonine kinase (STK2) ↓ in Brca1 Δ exon 11 MEFs   1.9 ± 0.0 (2) 
AA482328 Myristolated ala-rich C-kinase substrate (MACS) ↓ in Brca1 Δ exon 11 MEFs   1.7 ± 0.1 (2) 
AA233809 Transforming growth factor β2 (TGFB2) ↓ in Brca1 Δ exon 11 MEFs  1.6 ± 0.1 (2)  
A. Concordance of BRCA1-regulated gene expression in different cell types
Accession no.Gene name (symbol)MEFsDU-145MCF-7 (−E2)MCF-7 (+E2)
T74192 Plasma protein S (α) [PROS1] ↓ in Brca1 Δ exon 11 MEFs 3.3 ± 0.6 (3)   
AA664180 Glutathione peroxidase 3 (plasma) [GPX3] ↓ in Brca1 Δ exon 11 MEFs 2.4 ± 0.5 (2)   
AA063521 E1B 19K/Bcl-2 binding protein Nip3 (BNIP3) ↓ in Brca1 Δ exon 11 MEFs  1.6 (1) 2.8 ± 0.1 (2) 
H27379 Transcription elongation factor (S-II) ↓ in Brca1 Δ exon 11 MEFs   2.1 ± 0.5 (2) 
N77754 Lysosome-associated membrane protein 2 (LAMP2) ↓ in Brca1 Δ exon 11 MEFs   2.0 ± 0.1 (2) 
R24543 Guanine nucleotide regulatory protein (NET1) ↓ in Brca1 Δ exon 11 MEFs   2.0 ± 0.2 (2) 
AA496013 Protein serine/threonine kinase (STK2) ↓ in Brca1 Δ exon 11 MEFs   1.9 ± 0.0 (2) 
AA482328 Myristolated ala-rich C-kinase substrate (MACS) ↓ in Brca1 Δ exon 11 MEFs   1.7 ± 0.1 (2) 
AA233809 Transforming growth factor β2 (TGFB2) ↓ in Brca1 Δ exon 11 MEFs  1.6 ± 0.1 (2)  
B. Comparison of results from this study versus previously published data
Gene NamePublished data (reference)Our results
Concordant findings   
 Rho-associated coiled-coil forming kinase 2 (Rock2) ↓ in Brca1-deficient embryonic stem cells (39) ↓ in Brca1-deficient MEFs 
 Creatine kinase B (Ckb) ↓ in Brca1-deficient embryonic stem cells (39) ↑ in DU-145 wtBRCA1 clones 
 Quaking (Qk) ↓ in Brca1-deficient embryonic stem cells (39) ↓ in Brca1-deficient MEFs 
 Multifunctional aminoacyl tRNA synthtase (Syhuqt) ↓ in Brca1-deficient embryonic stem cells (39) ↑ in DU-145 wtBRCA1 clones 
 Neurofilament, light polypeptide (68 kDa) [Nfl, NF68] ↓ in Brca1-deficient embryonic stem cells (39) ↓ in Brca1-deficient MEFs 
 26S proteasome regulatory subunit 7 (Psmc2) ↓ in Brca1-deficient embryonic stem cells (39) ↑ in DU-145 wtBRCA1 clones 
 UDP-N-acteylglucosamine transferase (MGAT2) ↑ by wtBRCA1 in 293T cells (37) ↑ in DU-145 wtBRCA1 clones 
 Cyclin G2 [CCNG2] ↑ by wtBRCA1 in 293T cells (37) ↑ by wtBRCA1 in MCF-7 cells 
 Follistatin-like 1 [FSTL1] ↑ by wtBRCA1 in 293T cells (37) ↑ by wtBRCA1 in MCF-7 cells 
 Selenoprotein plasma protein 1 [SEPP1] ↑ by wtBRCA1 in 293T cells (37) ↓ in Brca1-deficient MEFs 
 Zing finger protein 148 (ZNF148) ↑ by wtBRCA1 in 293T cells (37) ↓ in Brca1-deficient MEFs 
 Laminin α-3 (LAMA3) ↑ by wtBRCA1 in 293T cells (37) ↑ in DU-145 wtBRCA1 clones 
 Ectonucleotide phosphodiesterase 2 (ENPP2) ↑ by wtBRCA1 in 293T cells (37) ↓ in Brca1-deficient MEFs 
 Potassium channel KCNK1 (= TWIK1) ↑ by wtBRCA1 in 293T cells (37) ↑ in DU-145 wtBRCA1 clones 
 DNA topoisomerase I (TOP1) ↑ by wtBRCA1 in colon cancer cells (38) ↓ in Brca1-deficient MEFs 
 Superoxide dismutase 1 (Sod1) ↑ by wtBRCA1 in colon cancer cells (38) ↓ in Brca1-deficient MEFs 
 CD59 antigen (CD59) ↓ by wtBRCA1 in colon cancer cells (38) ↓ in wtBRCA1 clones 
Nonconcordant Findings   
 Janus kinase 1 (JAK1) ↑ by wtBRCA1 in 293T cells (37) ↓ in DU-145 wtBRCA1 clones 
 COP9 subunit 3 (COP9S3) ↑ by wtBRCA1 in 293T cells (37) ↓ in DU-145 wtBRCA1 clones 
 Lim and senescent cell antigen-like domain 1 (LIMS1) ↑ by wtBRCA1 in 293T cells (37) ↓ in DU-145 wtBRCA1 clones 
 HIV Tat-interacting protein (HTATIP) ↑ by wtBRCA1 in 293T cells (37) ↓ in DU-145 wtBRCA1 clones 
B. Comparison of results from this study versus previously published data
Gene NamePublished data (reference)Our results
Concordant findings   
 Rho-associated coiled-coil forming kinase 2 (Rock2) ↓ in Brca1-deficient embryonic stem cells (39) ↓ in Brca1-deficient MEFs 
 Creatine kinase B (Ckb) ↓ in Brca1-deficient embryonic stem cells (39) ↑ in DU-145 wtBRCA1 clones 
 Quaking (Qk) ↓ in Brca1-deficient embryonic stem cells (39) ↓ in Brca1-deficient MEFs 
 Multifunctional aminoacyl tRNA synthtase (Syhuqt) ↓ in Brca1-deficient embryonic stem cells (39) ↑ in DU-145 wtBRCA1 clones 
 Neurofilament, light polypeptide (68 kDa) [Nfl, NF68] ↓ in Brca1-deficient embryonic stem cells (39) ↓ in Brca1-deficient MEFs 
 26S proteasome regulatory subunit 7 (Psmc2) ↓ in Brca1-deficient embryonic stem cells (39) ↑ in DU-145 wtBRCA1 clones 
 UDP-N-acteylglucosamine transferase (MGAT2) ↑ by wtBRCA1 in 293T cells (37) ↑ in DU-145 wtBRCA1 clones 
 Cyclin G2 [CCNG2] ↑ by wtBRCA1 in 293T cells (37) ↑ by wtBRCA1 in MCF-7 cells 
 Follistatin-like 1 [FSTL1] ↑ by wtBRCA1 in 293T cells (37) ↑ by wtBRCA1 in MCF-7 cells 
 Selenoprotein plasma protein 1 [SEPP1] ↑ by wtBRCA1 in 293T cells (37) ↓ in Brca1-deficient MEFs 
 Zing finger protein 148 (ZNF148) ↑ by wtBRCA1 in 293T cells (37) ↓ in Brca1-deficient MEFs 
 Laminin α-3 (LAMA3) ↑ by wtBRCA1 in 293T cells (37) ↑ in DU-145 wtBRCA1 clones 
 Ectonucleotide phosphodiesterase 2 (ENPP2) ↑ by wtBRCA1 in 293T cells (37) ↓ in Brca1-deficient MEFs 
 Potassium channel KCNK1 (= TWIK1) ↑ by wtBRCA1 in 293T cells (37) ↑ in DU-145 wtBRCA1 clones 
 DNA topoisomerase I (TOP1) ↑ by wtBRCA1 in colon cancer cells (38) ↓ in Brca1-deficient MEFs 
 Superoxide dismutase 1 (Sod1) ↑ by wtBRCA1 in colon cancer cells (38) ↓ in Brca1-deficient MEFs 
 CD59 antigen (CD59) ↓ by wtBRCA1 in colon cancer cells (38) ↓ in wtBRCA1 clones 
Nonconcordant Findings   
 Janus kinase 1 (JAK1) ↑ by wtBRCA1 in 293T cells (37) ↓ in DU-145 wtBRCA1 clones 
 COP9 subunit 3 (COP9S3) ↑ by wtBRCA1 in 293T cells (37) ↓ in DU-145 wtBRCA1 clones 
 Lim and senescent cell antigen-like domain 1 (LIMS1) ↑ by wtBRCA1 in 293T cells (37) ↓ in DU-145 wtBRCA1 clones 
 HIV Tat-interacting protein (HTATIP) ↑ by wtBRCA1 in 293T cells (37) ↓ in DU-145 wtBRCA1 clones 
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Supplementary data