Abstract
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.
INTRODUCTION
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.
MATERIALS AND METHODS
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.
RESULTS
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).
DISCUSSION
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.
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.
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.
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).
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).
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).
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).
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).
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).
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).
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).
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: [email protected]
Internet address: http://www.aecom.yu.edu/cancer/new/cores/microarray.
PCR primers and expected product sizes for semi-quantitative reverse transcription-PCR analyses
Gene name . | Symbol . | Primer 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 name . | Symbol . | Primer 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 |
PCR reaction conditions
Gene . | PCR cycle parameters . | No. 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 |
Gene . | PCR cycle parameters . | No. 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 |
Genes for which expression is increased in DU-145 wtBRCA1 [versus control (Neo)] cell clones
Accession no. . | Gene name . | Symbol . | Ratio . | Ratio . | ||||
---|---|---|---|---|---|---|---|---|
. | . | . | 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 name . | Symbol . | Ratio . | Ratio . | ||||
---|---|---|---|---|---|---|---|---|
. | . | . | 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) |
Continued
Accession no. . | Gene name . | Symbol . | Ratio . | Ratio . | ||||
---|---|---|---|---|---|---|---|---|
. | . | . | 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 name . | Symbol . | Ratio . | Ratio . | ||||
---|---|---|---|---|---|---|---|---|
. | . | . | 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) |
Genes whose expression is decreased in DU-145 wtBRCA1 [versus control (Neo)] cell clones
Accession no. . | Gene name . | Symbol . | Ratio . | . | ||||
---|---|---|---|---|---|---|---|---|
. | . | . | 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 name . | Symbol . | Ratio . | . | ||||
---|---|---|---|---|---|---|---|---|
. | . | . | 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 |
Effect of exogenous wtBRCA1 on gene expression in MCF-7 breast cancer cells (selected)
Accession no. . | Gene name (symbol) . | Ratio (wtBRCA1/control) . | . | . | ||||
---|---|---|---|---|---|---|---|---|
. | . | DU-145 . | MCF-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-145 . | MCF-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) |
Continued
Accession no. . | Gene name (symbol) . | Ratio (wtBRCA1/control) . | . | . | ||||
---|---|---|---|---|---|---|---|---|
. | . | DU-145 . | MCF-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-145 . | MCF-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) |
Selected genes whose expression is decreased in Brca1Δex11Δex (versus Brca1+/+) mouse embryo fibroblasts
Accession no. . | Gene name . | Symbol . | Ratio . | . | ||||
---|---|---|---|---|---|---|---|---|
. | . | . | 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. cerevisiae) | Supt4 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 name . | Symbol . | Ratio . | . | ||||
---|---|---|---|---|---|---|---|---|
. | . | . | 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. cerevisiae) | Supt4 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) |
Continued
Accession no. . | Gene name . | Symbol . | Ratio . | . | ||||
---|---|---|---|---|---|---|---|---|
. | . | . | 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 name . | Symbol . | Ratio . | . | ||||
---|---|---|---|---|---|---|---|---|
. | . | . | 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 |
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) . | MEFs . | DU-145 . | MCF-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) . | MEFs . | DU-145 . | MCF-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 Name . | Published 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 Name . | Published 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 |