miR-1290 and its potential targets are associated with characteristics of estrogen receptor α-positive breast cancer

in Endocrine-Related Cancer

Recent analyses have identified heterogeneity in estrogen receptor α (ERα)-positive breast cancer. Subtypes called luminal A and luminal B have been identified, and the tumor characteristics, such as response to endocrine therapy and prognosis, are different in these subtypes. However, little is known about how the biological characteristics of ER-positive breast cancer are determined. In this study, expression profiles of microRNAs (miRNAs) and mRNAs in ER-positive breast cancer tissue were compared between ERhigh Ki67low tumors and ERlow Ki67high tumors by miRNA and mRNA microarrays. Unsupervised hierarchical clustering analyses revealed distinct expression patterns of miRNAs and mRNAs in these groups. We identified a downregulation of miR-1290 in ERhigh Ki67low tumors. Among 11 miRNAs that were upregulated in ERhigh Ki67low tumors, quantitative RT-PCR detection analysis using 64 samples of frozen breast cancer tissue identified six miRNAs (let-7a, miR-15a, miR-26a, miR-34a, miR-193b, and miR-342-3p). We picked up 11 genes that were potential target genes of the selected miRNAs and that were differentially expressed in ERhigh Ki67low tumors and ERlow Ki67high tumors. Protein expression patterns of the selected target genes were analyzed in 256 ER-positive breast cancer samples by immunohistochemistry: miR-1290 and its putative targets, BCL2, FOXA1, MAPT, and NAT1, were identified. Transfection experiments revealed that introduction of miR-1290 into ER-positive breast cancer cells decreased expression of NAT1 and FOXA1. Our results suggest that miR-1290 and its potential targets might be associated with characteristics of ER-positive breast cancer.

Abstract

Recent analyses have identified heterogeneity in estrogen receptor α (ERα)-positive breast cancer. Subtypes called luminal A and luminal B have been identified, and the tumor characteristics, such as response to endocrine therapy and prognosis, are different in these subtypes. However, little is known about how the biological characteristics of ER-positive breast cancer are determined. In this study, expression profiles of microRNAs (miRNAs) and mRNAs in ER-positive breast cancer tissue were compared between ERhigh Ki67low tumors and ERlow Ki67high tumors by miRNA and mRNA microarrays. Unsupervised hierarchical clustering analyses revealed distinct expression patterns of miRNAs and mRNAs in these groups. We identified a downregulation of miR-1290 in ERhigh Ki67low tumors. Among 11 miRNAs that were upregulated in ERhigh Ki67low tumors, quantitative RT-PCR detection analysis using 64 samples of frozen breast cancer tissue identified six miRNAs (let-7a, miR-15a, miR-26a, miR-34a, miR-193b, and miR-342-3p). We picked up 11 genes that were potential target genes of the selected miRNAs and that were differentially expressed in ERhigh Ki67low tumors and ERlow Ki67high tumors. Protein expression patterns of the selected target genes were analyzed in 256 ER-positive breast cancer samples by immunohistochemistry: miR-1290 and its putative targets, BCL2, FOXA1, MAPT, and NAT1, were identified. Transfection experiments revealed that introduction of miR-1290 into ER-positive breast cancer cells decreased expression of NAT1 and FOXA1. Our results suggest that miR-1290 and its potential targets might be associated with characteristics of ER-positive breast cancer.

Introduction

There are large-scale molecular differences between estrogen receptor α (ERα)-positive and ER-negative breast cancers (Sorlie et al. 2003). ER is essential for estrogen-dependent growth, and its level of expression is a crucial determinant of response to endocrine therapy and prognosis in ER-positive breast cancer (Harvey et al. 1999, Yamashita et al. 2006, Dowsett et al. 2008). Recent analyses have identified heterogeneity in ER-positive breast cancer. Subtypes, named luminal A and luminal B, have been defined according to expression levels of Ki67, and the characteristics of these two subtypes are different (Goldhirsch et al. 2011). There is no doubt that higher concentrations of ER in the tumor cells are associated with a greater likelihood of a favorable response to endocrine therapy. However, little is known about how the expression of ER in breast cancer cells is regulated and how the biological characteristics of ER-positive breast cancer are determined. We recently analyzed expressions of microRNAs (miRNAs) that directly target ER in breast cancer. We found that miR-206 and miR-18a were downregulated in ER-positive breast cancer compared with ER-negative tumors and that low miR-18b expression was significantly associated with improved survival in HER2-negative breast cancer, although miR-18b expression was not correlated with ER protein expression (Kondo et al. 2008, Yoshimoto et al. 2011).

miRNAs are small (∼21 nucleotides) noncoding RNAs that negatively regulate target genes by predominantly binding to the 3′-untranslated region (3′-UTR) of target mRNA, resulting in either mRNA degradation or translational repression (Krol et al. 2010). Recent studies have shown that miRNA mutations or dysregulated expression were associated with various human cancers and indicated that miRNAs can function as tumor suppressor genes and oncogenes (Esquela-Kerscher & Slack 2006). Expression profiling also revealed that miRNAs are differently expressed among molecular subtypes of breast cancer (Iorio et al. 2005). Significant associations were found between miRNA expression profiles and clinicopathological factors such as ER status and tumor grade (Blenkiron et al. 2007). Furthermore, recent studies have demonstrated that loss- or gain-of-function of specific miRNAs contributes to breast epithelial cellular transformation, tumorigenesis, and epithelial–mesenchymal transition and metastasis (Zhang & Ma 2012).

In this study, expression profiles of miRNAs and mRNAs in ER-positive breast cancer tissue were compared between ERhigh Ki67low tumors and ERlow Ki67high tumors by miRNA and mRNA microarrays. Unsupervised hierarchical clustering analyses revealed distinct expression patterns of miRNAs and mRNAs in these two groups. We demonstrated that miR-1290 was downregulated and that six miRNAs were upregulated in ERhigh Ki67low tumors. Protein expression patterns of the predicted target genes and the genes that were identified by mRNA expression profiling were analyzed in ER-positive breast cancer samples by immunohistochemistry (IHC). We identified miR-1290 and its potential target genes, forkhead box A1 (FOXA1) and N-acetyltransferase-1 (NAT1), being associated with characteristics of ER-positive breast cancer.

Materials and methods

Patients and breast cancer tissue

Breast tumor specimens from female patients with invasive breast carcinoma who were treated at Nagoya City University Hospital between 1995 and 2010 were included in the study (Table 1). The study protocol was approved by the institutional review board and conformed to the guidelines of the 1996 Declaration of Helsinki. Written informed consent for the use of surgically resected tumor tissues was provided by all patients before treatments. The samples were chosen from a continuous series of invasive carcinoma. All patients except those with stage IV disease underwent surgical treatment (mastectomy or lumpectomy). Tumor samples of patients with stage IV disease were taken by core needle biopsy. Patients received adequate endocrine or chemotherapy for adjuvant or metastatic diseases.

Table 1

Clinicopathological characteristics of patients and breast tumors with ER-positive, HER2-negative breast cancer

Samples for miRNA and mRNA microarray analysesSamples for miRNA quantitative RT-PCR analysisSamples for immunohistochemistry
ERhigh Ki67lowERlow Ki67highTotalTotal
No. of patients4464256
Age (years)
 Mean±s.d.71.8±20.957.5±12.160.0±12.058.0±13.0
 Range44–9142–6932–8828–91
Tumor size (cm)
 Mean±s.d.1.5±0.41.6±0.7
 ≤2.020 (31%)148 (57.9%)
 2.1–5.038 (59%)102 (39.8%)
 >5.06 (10%)6 (2.3%)
No. of positive lymph nodes
 04 (100%)4 (100%)34 (53%)135 (52.7%)
 1–30 (0%)0 (0%)16 (25%)72 (28.1%)
 4–90 (0%)0 (0%)6 (10%)11 (4.3%)
 ≥100 (0%)0 (0%)4 (6%)7 (2.7%)
 Unknown0 (0%)0 (0%)4 (6%)31 (12.2%)
Tumor grade
 14 (100%)0 (0%)16 (25%)95 (37.1%)
 20 (0%)0 (0%)36 (56%)69 (27.0%)
 30 (0%)4 (100%)12 (19%)92 (35.9%)
ER (Allred score)
 Mean±s.d.7.8±0.53.5±0.6
 0–2 (negative)0 (0%)0 (0%)
 3–8 (positive)64 (100%)256 (100%)
PgR (Allred score)
 Mean±s.d.7.8±0.52.5±0.6
 0–2 (negative)10 (16%)34 (13.3%)
 3–8 (positive)54 (84%)222 (86.7%)
HER2 status
 Negative4 (100%)4 (100%)64 (100%)256 (100%)
 Positive0 (0%)0 (0%)0 (0%)0 (0%)
Ki67 (labeling index, %)
 Mean±s.d.6.1±2.750.8±11.8
Adjuvant therapy
 None827
 Endocrine therapy32127
 Chemotherapy34
 Combined2198

Microarray profiling of miRNA and mRNA expression

Total RNA was extracted from eight frozen samples of breast cancer tissue (Table 1). Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark). Labeled RNAs were hybridized onto 3D-Gene Human miRNA Oligo chips containing 1011 antisense probes printed in duplicate spots (Toray, Kamakura, Japan). The annotation and oligonucleotide sequences of the probes were conformed to the miRBase miRNA data base (http://microrna.sanger.ac.uk/sequences/). After stringent washes, fluorescent signals were scanned with the ScanArray Express Scanner (PerkinElmer, Waltham, MA, USA) and analyzed using GenePix Pro version 5.0 (Molecular Devices, Sunnyvale, CA, USA). These raw data of each spot were normalized by substitution with the mean intensity of the background signal determined by all blank spots' signal intensities at 95% confidence intervals. Measurements of both duplicate spots with signal intensities >2 s.d. of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments after normalization by their median values adjusted equivalently. miRNAs differentially expressed among the ERhigh Ki67low tumors and ERlow Ki67high tumors were statistically identified using the Student's t-test and unsupervised hierarchical clustering analyses. Hierarchical clustering was performed with average linkage and Pearson's correlation. Differential expression was assessed by a nonparametric Wilcoxon's rank sum test for comparison between two groups. A heat-map was constructed by hierarchical clustering analysis using Cluster 2.0 Software (Tokyo, Japan) and the results were displayed with the TreeView program (http://rana.lbl.gov/eisen/). miRNA expression data are available from the National Center for Biotechnology Gene Expression Omnibus (GEO) at accession number (GEO:GSE38280).

mRNA expression profiles were examined using the same frozen breast cancer tissue samples as those used in miRNA analyses. Extracted total RNA was labeled with Cy5 using the Amino Allyl MessageAMP II aRNA Amplification kit (Applied Biosystems). Labeled RNAs were hybridized onto 3D-Gene Human mRNA Oligo chips 25k (Toray) was used (25 370 distinct genes). Hybridization signals were scanned and detected by the same method as that used in miRNA analyses. The gene expression data are available from GEO at accession number (GEO:GSE38280).

Quantitative RT-PCR detection of miRNAs

Total RNA was extracted from ∼500 mg frozen breast cancer tissue using TRIzol reagent (Life Technologies, Inc.) as described previously (Kondo et al. 2008). cDNA was reverse transcribed from total RNA samples using specific miRNA primers from the TaqMan MicroRNA Assays and reagents from the TaqMan MicroRNA RT Kit (Applied Biosystems). The resulting cDNA was amplified by PCR using TaqMan MicroRNA Assay primers with the TaqMan Universal PCR Master Mix and analyzed with a 7300 ABI PRISM Sequence Detector System according to the manufacturer's instructions (Applied Biosystems). The relative levels of miRNA expression were calculated from the relevant signals by normalization with the signal for U6B miRNA expression. The assay names for each miRNA were as follows: hsa-let-7a for let-7a, hsa-miR-10a for miR-10a, hsa-miR-10b for miR-10b, hsa-miR-15a for 15a, hsa-miR-18a for miR-18a, hsa-miR-26a for miR-26a, hsa-miR-29c for miR-29c, hsa-miR-34a for miR-34a, hsa-miR-129 for miR-129, hsa-miR-146a for miR-146a, hsa-miR-193b for miR-193b, hsa-miR-342-3p for miR-342-3p, hsa-miR-1290 for miR-1290, and RNU6B for U6B miRNA (Applied Biosystems).

Immunohistochemistry

Tissue microarrays were constructed using paraffin-embedded, formalin-fixed tissue from 256 ER-positive breast cancer samples, including 64 samples from patients whose frozen samples were used in miRNA expression analysis. Tissue array sections were immunostained with 15 commercially available antibodies using the Bond-Max Autostainer (Leica Microsystems, Newcastle, UK) and the associated Bond Refine Polymer Detection Kit (Yamashita et al. 2006). Details of primary antibodies and scoring manners are described in Supplementary Table 1, see section on supplementary data given at the end of this article. HER2-positive tumors were excluded from this study.

Cell culture and transfections

MCF-7 cells (American Type Culture Collection (ATCC), Manassas, VA, USA) were grown in RPMI 1640 medium containing 10% fetal bovine serum (FBS), 2 mmol/l l-glutamine and penicillin–streptomycin (50 IU/ml and 50 mg/ml respectively), and 0.1% human insulin at 37 °C with 5% CO2. T47D cells (ATCC) were grown in RPMI 1640 medium containing 10% FBS and 2 mmol/l l-glutamine and penicillin–streptomycin (50 IU/ml and 50 mg/ml respectively) at 37 °C with 5% CO2. Transfections of pre-miR-1290 precursor (hsa-miR-1290; Ambion, Inc., Austin, TX, USA) were performed with Cell Line Nucleofector kits (Amaxa Biosystems, Cologne, Germany) using a Nucleofector device (Amaxa Biosystems) according to the manufacturer's instructions (Kondo et al. 2008). A nonspecific control miRNA (Pre-miR miRNA Inhibitors-Negative Control #1; Ambion, Inc.) was used as a negative control.

Quantitative RT-PCR detection of miR-1290 and mRNAs

Total RNA was extracted from 2×106 cells with miRNeasy Mini Kit (Qiagen) using a QIAcube (Qiagen) according to the manufacturer's instructions. cDNA was reverse transcribed using specific miRNA primers and the relative levels of miR-1290 expression were measured as described earlier. Total RNA (1 μg) was also subjected to RT with random primers in a 20 μl reaction volume using High-Capacity cDNA RT Kit (Applied Biosystems). mRNA expression was measured by quantitative RT-PCR with the TaqMan Universal PCR Master Mix using a 7500 ABI PRISM Sequence Detector System according to the manufacturer's instructions (Applied Biosystems; Kondo et al. 2008). The relative levels of mRNA expression were calculated from the relevant signals by normalization with the signal for β-actin mRNA expression. The assay numbers for BCL2, FOXA1, microtubule-associated protein tau (MAPT), NAT1, and β-actin were as follows: Hs00608023_m1 for BCL2, Hs00270129_m1 for FOXA1, Hs00902314_m1 for MAPT, Hs00265080_m1 for NAT1, and 4333762T for β-actin (Applied Biosystems).

Western blotting

Cells were pelleted by centrifugation and solubilized in lysis buffer containing protease inhibitor and phosphatase inhibitor cocktails (Thermo Scientific, Yokohama, Japan). Equal amounts of total protein (30 μg) from whole cell lysates were prepared and electrophoresed on 12% (w/v) SDS–polyacrylamide gels (NuPAGE Bis–Tris Gel, Invitrogen) transferred to polyvinylidene difluoride membranes (Invitrogen) and immunoblotted using specific antibodies (Supplementary Table 1; Yamashita et al. 2003). Anti-mouse or anti-rabbit IgG, HRP-linked Whole Antibodies (GE Healthcare Japan, Tokyo, Japan) were used as secondary antibodies at 1:10 000 dilution. Antibody binding was visualized with ECL Western Blotting Detection System (GE Healthcare Japan) using Light-Capture AE-6981 (ATTO, Tokyo, Japan) according to the manufacturer's instructions. Image J Software from the National Institutes of Health (Bethesda, MD, USA) was used to quantify band intensities.

Statistical analysis

Spearman's rank correlation test was used to study relationships between expression levels of miRNAs and clinicopathological factors, expression levels of proteins and clinicopathological factors, expression levels of miRNAs and proteins, and expression levels of miRNAs and mRNAs. P<0.05 is considered significant in Spearman's rank correlation test.

Results

Differentially expressed miRNAs in ERhigh Ki67low tumors and ERlow Ki67high tumors in breast cancer tissue

Expression profiles of miRNAs and mRNAs in ER-positive breast cancer tissue were compared between ERhigh Ki67low tumors and ERlow Ki67high tumors by miRNA and mRNA microarrays using eight frozen samples of breast cancer tissue (four tumors in each group; Table 1). Unsupervised hierarchical clustering analyses revealed 67 miRNAs in 1011 miRNAs and 657 mRNAs in 25 370 mRNAs that were differentially expressed in ERhigh Ki67low tumors and ERlow Ki67high tumors (P<0.01; Supplementary Figure 1, see section on supplementary data given at the end of this article and Supplementary Table 2, see section on supplementary data given at the end of this article, and P<0.01; Supplementary Figure 2, see section on supplementary data given at the end of this article and Supplementary Tables 3 and 4, see section on supplementary data given at the end of this article respectively). We selected 12 miRNAs (let-7a, miR-10a, miR-10b, miR-15a, miR-26a, miR-29c, miR-34a, miR-129, miR-146a, miR-193b, miR-342-3p, and miR-1290) that were differentially expressed in these two groups. Among differentially expressed 67 miRNAs, the above 12 miRNAs, especially let-7a, miR-10a, miR-10b, miR-15a, miR-26a, miR-29c, miR-34a, miR-146a, and miR-342-3p, have been reported to be related to breast cancer development and carcinogenesis (Mattie et al. 2006, Blenkiron et al. 2007, O'Day & Lal 2010). miR-193b has been reported to be related to ERα (Yoshimoto et al. 2011). Moreover, we referred to the reported mRNA microarray analyses to classify luminal A and luminal B subtypes in order to select key genes (Sorlie et al. 2003, Parker et al. 2009), including FOXA1, NAT1, MAPT, XBP1, and BCL2, which have target sequences in the 3′-UTR regions of 67 differentially expressed miRNAs according to in silico analysis using TargetScan, PicTar, and MiRanda, and selected miR-146a and miR-1290, which were downregulated in ERhigh Ki67low tumors. Quantitative RT-PCR detection analysis using 64 frozen breast cancer tissue samples (Table 2 and Supplementary Table 5, see section on supplementary data given at the end of this article) identified six miRNAs (let-7a, miR-15a, miR-26a, miR-34a, miR-193b, and miR-342-3p) that were upregulated in ERhigh tumors (P=0.0002, P=0.0006, P=0.0082, P<0.0001, P=0.0142, and P=0.0002 respectively; Table 3). miR-1290 was also included in further analyses because it was the only miRNA among the selected miRNAs that was downregulated in ERhigh Ki67low tumors and its expression levels were strongly correlated with tumor grade (P<0.0001; Table 3).

Table 2

Expression levels of 12 selected miRNAs and the control miRNA (U6B) in 64 ER-positive breast cancer tissues by quantitative RT-PCR analysis

Mean±s.e.m.
let-7a22.079±0.173
miR-10a26.585±0.278
miR-10b27.636±0.247
miR-15a27.100±0.285
miR-26a22.711±0.201
miR-29c24.295±0.390
miR-34a26.339±0.240
mR-12934.759±0.185
miR-146a26.160±0.221
miR-193b21.112±0.219
miR-342-3p24.456±0.322
miR-129027.612±0.445
U6B27.091±0.154
Table 3

Correlation between expression levels of miRNAs and clinicopathological factors (n=64)

ERPgRTumor gradeKi67Tumor sizeNo. of positive lymph nodes
let-7a+0.533a+0.349−0.033−0.115−0.068+0.123
0.0002*,b0.0087*0.25360.37170.58540.7959
miR-10a+0.286+0.219+0.005−0.113−0.326+0.132
0.11140.11130.40120.37570.0098*0.7399
miR-10b+0.268+0.130+0.074−0.114−0.185+0.171
0.16460.38940.84110.3750.14390.5025
miR-15a+0.499+0.081+0.215+0.055−0.129+0.062
0.0006*0.63960.30360.67290.30840.7917
miR-26a+0.414+0.165+0.065−0.056−0.003+0.060
0.0082*0.25850.79530.66740.97120.8038
miR-29c+0.206−0.030+0.115+0.018−0.084+0.121
0.38390.66710.87820.89170.51170.7546
miR-34a+0.785+0.164+0.061+0.034−0.168+0.039
<0.0001*0.25580.75350.79410.18510.6458
mR-129+0.334+0.043+0.334−0.056−0.006+0.049
0.05280.87220.0384*0.67110.97460.677
miR-146a+0.101−0.149+0.425+0.007−0.052−0.009
0.90320.18190.0073*0.95860.69660.5031
miR-193b+0.387+0.203+0.223+0.078+0.046+0.214
0.0142*0.14830.26660.54930.72980.2889
miR-342-3p+0.539+0.131+0.131−0.039−0.016+0.107
0.0002*0.39750.80240.76570.89320.9081
miR-1290+0.014−0.211+0.585+0.228+0.029+0.280
0.39870.0581<0.0001*0.07480.82670.1109

*P<0.05 is considered significant.

Spearman's correlation coefficient.

P, Spearman's rank correlation test.

The potential target genes for seven selected miRNAs (let-7a, miR-15a, miR-26a, miR-34a, miR-193b, miR-342-3p, and miR-1290) were predicted according to in silico analysis using TargetScan, PicTar, and MiRanda. In addition, 657 mRNAs that were differentially expressed in ERhigh Ki67low tumors and ERlow Ki67high tumors in microarray analysis were considered to select putative target genes. Finally, we picked up 11 proteins (ANKRD30, BCL2, cyclin D1, FOXA1, GATA3, LIN28, MAPT, NAT1, RB1, P53 (TP53), and XBP1) that were products of potential target genes for seven selected miRNAs and that were considered to be differentially expressed in ERhigh Ki67low tumors and ERlow Ki67high tumors (Table 4). ANKRD30 was the most differentially expressed gene between ERhigh Ki67low tumors and ERlow Ki67high tumors. BCL2, cyclin D1, LIN28, and RB1 are potential targets of the selected miRNAs as shown in Table 4. FOXA1, GATA3, NAT1, and XBP1 were strongly downregulated in ERlow Ki67high tumors, putative targets of the selected miRNAs, and reported as to be related with ER-positive breast cancer. MAPT is also reported to be related with ER-positive breast cancer and a potential target of miR-1290. P53 was selected as a target of let-7a.

Table 4

Correlation between expression levels of potential target proteins and clinicopathological factors (n=256)

ERPgRTumor gradeKi67Tumor sizeNo. of positive lymph nodesmiRNAs
ANKRD30+0.260a+0.250+0.002+0.142−0.145+0.176miR-193b
0.2265b0.0246*0.0012*0.5865<0.0001*0.2769
BCL2+0.467+0.320+0.102+0.132+0.078+0.278let-7a, miR-10a, miR-15a, miR-26a, miR-29c, miR-34a, miR-1290
<0.0001*0.0059*0.0109*0.45850.09680.8608
CCND1+0.177+0.083−0.190+0.078−0.085+0.046miR-15a, miR-34a, miR-193b
0.53640.62160.0101*0.54150.49810.6898
FOXA1+0.407+0.234−0.235−0.082−0.210+0.009miR-129, miR-1290
<0.0001*0.0005*<0.0001*0.19390.0009*0.103
GATA3+0.448+0.286−0.224−0.004−0.242−0.005miR-10a, miR-10b, miR-34a
<0.0001*<0.0001*<0.0001*0.94410.0001*0.0655
LIN28+0.289+0.173−0.081+0.138−0.238+0.068let-7a, miR-26a, miR-34a, miR-129, miR-342-3p
0.0008*0.017*0.0099*0.0446*<0.0001*0.3681
MAPT+0.3560.494−0.254−0.144−0.149+0.030miR-34a, miR-1290
<0.0001*<0.0001*<0.0001*0.0419*0.0093*0.1314
NAT1+0.316+0.394−0.274−0.122−0.180+0.105miR-1290
0.0005*<0.0001*<0.0001*0.0095*0.0004*0.4956
RB1+0.248+0.261+0.327+0.290+0.263+0.374let-7a, miR-26a, miR-34a, miR-129, miR-1290
0.07510.83690.46510.24240.69560.6748
TP53−0.016−0.010+0.211+0.197−0.133+0.074let-7a
0.07430.68150.0108*0.002*0.0336*0.5783
XBP1+0.183−0.042−0.236+0.079−0.278−0.040miR-34a
0.56530.53180.0018*0.59060.0203*0.2069

*P<0.05 is considered significant.

Spearman's correlation coefficient.

P, Spearman's rank correlation test.

Expression of the potential target genes in ER-positive, HER2-negative breast cancer

We examined protein expression of 11 selected target genes in ER-positive, HER2-negative breast cancer by IHC (Supplementary Table 6, see section on supplementary data given at the end of this article). Expression levels of BCL2, FOXA1, GATA3, LIN28, MAPT, and NAT1 were positively correlated with expression levels of ER (P<0.0001, P<0.0001, P<0.0001, P=0.0008, P<0.0001, and P=0.0005 respectively; Table 4). Expression levels of ANKRD30, BCL2, FOXA1, GATA3, LIN28, MAPT, and NAT1 were positively correlated with expression levels of progesterone receptor (PgR; P=0.0246, P=0.0059, P=0.0005, P<0.0001, P=0.017, P<0.0001, and P<0.0001 respectively). Expression levels of ANKRD30, BCL2, and TP53 were positively correlated with tumor grade (P=0.0012, P=0.0109, and P=0.0108 respectively), whereas expression levels of CCND1, FOXA1, GATA3, LIN28, MAPT, NAT1, and XBP1 were negatively correlated with tumor grade (P=0.0101, P<0.0001, P<0.0001, P=0.0099, P<0.0001, P<0.0001, and P=0.0018 respectively). Expression levels of LIN28 and TP53 were positively correlated with expression levels of Ki67 (P=0.0446 and P=0.002 respectively), while expression levels of MAPT and NAT1 were negatively correlated with expression levels of Ki67 (P=0.0419 and P=0.0095 respectively). Expression levels of ANKRD30, FOXA1, GATA3, LIN28, MAPT, NAT1, TP53, and XBP1 were negatively correlated with tumor size (P<0.0001, P=0.0009, P=0.0001, P<0.0001, P=0.0093, P=0.0004, P=0.0336, and P=0.0203 respectively). There was no association between expression of 11 selected proteins and lymph node status (Table 4).

We then compared expression levels of seven selected miRNAs (let-7a, miR-15a, miR-26a, miR-34a, miR-193b, miR-342-3p, and miR-1290) and their potential target genes (ANKRD30, BCL2, cyclin D1, FOXA1, GATA3, LIN28, MAPT, NAT1, RB1, P53, and XBP1) using 64 samples of breast cancer tissue, simultaneously analyzing miRNA expression by quantitative RT-PCR and protein expression by IHC. Interestingly, expression levels of miR-1290 were inversely correlated with expression levels of BCL2, FOXA1, MAPT, and NAT1, all of which are predictive targets of miR-1290 according to in silico analysis (P=0.020, P=0.044, P=0.040, and P=0.0098 respectively; Fig. 1A, B, C and D), suggesting that miR-1290 might downregulate these four genes in ER-positive breast cancer. Moreover, let-7a expression was inversely correlated with P53 expression (P=0.038; Fig. 1E). No association was found between other miRNA expressions and their putative target gene expressions.

Figure 1
Figure 1

miR-1290 expression is inversely correlated with expressions of BCL2, FOXA1, MAPT, and NAT1. Scatter plots show inverse correlations between miR-1290 and BCL2 (A), FOXA1 (B), MAPT (C), and NAT1 (D) protein expression in breast cancer tissue (P=0.020, P=0.044, P=0.040, and P=0.0098 respectively). (E) let-7 expression is inversely correlated with P53 protein expression in breast cancer tissue (P=0.038).

Citation: Endocrine-Related Cancer 20, 1; 10.1530/ERC-12-0207

miR-1290 downregulates FOXA1 and NAT1 in ER-positive breast cancer cells

We extended our analysis to clarify whether miR-1290 downregulates BCL2, FOXA1, MAPT, and NAT1 in ER-positive breast cancer cells. Pre-miR-1290 precursor was introduced into T47D and MCF-7 cells. Cells were transfected with either control miRNA (300 nmol/l) or pre-miR-1290 precursor at various concentrations (10–300 nmol/l) and incubated for 24 h in T47D cells and for 36 h in MCF-7 cells. Expression levels of miR-1290 and mRNA expression levels of BCL2, FOXA1, MAPT, and NAT1 were quantitatively measured using parallel samples. Transfection with pre-miR-1290 produced a dose-dependent increase in miR-1290 expression levels (Fig. 2A, left), whereas expression levels of miR-1290 were inversely correlated with expression levels of FOXA1 (P=0.0003; Fig. 2A, top right) and NAT1 (P<0.0001; Fig. 2A, bottom right) mRNAs, but not with BCL2 or MAPT mRNA, in T47D cells (Fig. 2A). Moreover, expression levels of miR-1290 were inversely correlated with expression levels of NAT1 mRNA (P=0.037; Fig. 2B, bottom right), but not with BCL2, FOXA1, or MAPT mRNA, in MCF-7 cells (Fig. 2B).

Figure 2
Figure 2

Gene expressions of miR-1290 putative targets in T47D and MCF-7 cells transfected with miR-1290. (A) T47D cells were transfected with either control miRNA (300 nmol/l) or pre-miR-1290 precursor at 10–300 nmol/l and incubated for 24 h. Expression levels of miR-1290 and mRNA levels of BCL2, FOXA1, MAPT, and NAT1 were measured by quantitative RT-PCR. Scatter plots show inverse correlation between miR-1290 expression and FOXA1 and NAT1 mRNA expression (P=0.0003 and P<0.0001 respectively). (B) MCF-7 cells were transfected with either control miRNA (300 nmol/l) or pre-miR-1290 precursor at 10–300 nmol/l and incubated for 36 h. Expression levels of miR-1290 and mRNA levels of BCL2, FOXA1, MAPT, and NAT1 were measured by quantitative RT-PCR. Scatter plots show inverse correlation between miR-1290 expression and NAT1 mRNA expression (P=0.037). (C) T47D cells were transfected with either control miRNA (300 nmol/l) or pre-miR-1290 precursor at 30–1000 nmol/l and incubated for 48 h. Protein expression of BCL2, FOXA1, MAPT, and NAT1 was assayed by western blot analysis. The number below the band represents the mean value from densitometry reading, relative to the negative control, which was set at 1.00. Representative results from one of the three experiments are shown. (D) MCF-7 cells were transfected with either control miRNA (300 nmol/l) or pre-miR-1290 precursor at 30–1000 nmol/l and incubated for 48 h. Protein expression of BCL2, FOXA1, MAPT, and NAT1 was assayed by western blot analysis. The number below the band represents the mean value from densitometry reading, relative to the negative control, which was set at 1.00. Representative results from one of the three experiments are shown.

Citation: Endocrine-Related Cancer 20, 1; 10.1530/ERC-12-0207

The effects of miR-1290 on protein expression of BCL2, FOXA1, MAPT, and NAT1 were examined in T47D and MCF-7 cells by western blot analysis. When T47D cells were transfected with either control miRNA (300 nmol/l) or pre-miR-1290 precursor at various concentrations (30–1000 nmol/l) and incubated for 48 h, miR-1290 induced a dose-dependent decrease in protein expression of NAT1, reducing it ∼60%, but not BCL2, FOXA1, or MAPT (Fig. 2C). Effects of miR-1290 on protein expression of BCL2, FOXA1, MAPT, and NAT1 were not clear in MCF-7 cells (Fig. 2D). From these analyses, we conclude that miR-1290 might downregulate FOXA1 and NAT1 in ER-positive breast cancer cells.

Discussion

In this study, we have shown distinct expression patterns of miRNAs and mRNAs in luminal A and luminal B subtypes in ER-positive breast cancer. We demonstrated that miR-1290 and its potential target genes, FOXA1 and NAT1, might be associated with characteristics of ER-positive disease. miR-1290 expression was strongly downregulated in ERhigh Ki67low tumors and was positively correlated with tumor grade. Although the role of miR-1290 has not been analyzed as yet, it was reported that 36 miRNAs, including miR-1290, were circulating at increased levels in patients with renal cell carcinoma and were overexpressed in corresponding renal cell carcinoma tissue (Wulfken et al. 2011). It was also reported that six miRNAs, including miR-1290, were upregulated in drug-sensitive cells following Y-Box protein 1 inhibition, but no differences in miRNA expression could be detected in multidrug-resistant gastric carcinoma cells (Belian et al. 2010).

FOXA1, a forkhead family transcription factor, has been reported to be expressed predominantly in luminal A breast cancer with favorable prognosis (Badve et al. 2007, Mehta et al. 2012). Hurtado et al. recently reported that FOXA1 creates an open conformation at ER-binding sites and that ER can bind and activate target gene expression in the presence of estrogen. Thus, FOXA1 is a key determinant of ER function and endocrine response in breast cancer (Hurtado et al. 2011). They also reported that the differential ER-binding program observed in tumors from patients with poor outcome is due to the FOXA1-mediated reprogramming of ER binding (Ross-Innes et al. 2012). We demonstrated that FOXA1 expression is much higher in ERhigh Ki67low tumors than in ERlow Ki67high tumors and that expression levels of FOXA1 were strongly and positively correlated with expression levels of ER and PgR and negatively associated with tumor grade in ER-positive breast cancer. Moreover, introduction of miR-1290 into estrogen-dependent breast cancer cells reduced FOXA1 expression. Because FOXA1 is a putative target of miR-1290 according to in silico analysis, we suggest that miR-1290 is a key factor for regulating FOXA1, which is associated with characteristics of ER-positive breast cancer.

Arylamine NATs, known as drug- and carcinogen-metabolizing enzymes, transfer an acetyl group from acetyl coenzyme A to arylamines (Sim et al. 2008). Several studies have shown higher mRNA and protein expression of NAT1 in ER-positive breast cancer compared with the expression in ER-negative disease (Perou et al. 2000, Adam et al. 2003, Tozlu et al. 2006, Wakefield et al. 2008). Moreover, it was reported that high expression of NAT1 was correlated with better outcome in ER-positive breast cancer (Bieche et al. 2004, Dolled-Filhart et al. 2006). Our results demonstrated that NAT1 mRNA expression was much higher in ERhigh Ki67low tumors than in ERlow Ki67high tumors by microarray analyses and that NAT1 protein expression by IHC showed positive correlation with expression levels of ER and PgR and negative correlation with expression levels of Ki67, tumor grade, and tumor size. In addition, introduction of miR-1290 into estrogen-dependent breast cancer cells strongly reduced NAT1 expression. Because NAT1, as well as FOXA1, is a putative target of miR-1290 according to in silico analysis, it is possible that miR-1290 also regulates NAT1, which will be associated with characteristics of ER-positive breast cancer.

BCL2 and MAPT are also potential targets of miR-1290 according to in silico analysis. BCL2 is an anti-apoptotic protein that has an anti-proliferative effect influencing cell cycle entry (Zinkel et al. 2006). BCL2 is an ER-induced gene, and its protein expression assessed by IHC has been shown to be a favorable prognostic marker in breast cancer (Callagy et al. 2006, Dawson et al. 2010). Our results also showed that expression levels of BCL2 were strongly and positively correlated with expression levels of ER and PgR in ER-positive breast cancer. It was recently reported that miR-195, miR-24-2, and miR-365-2 act as negative regulators of BCL2 through direct binding to their respective binding sites in the 3′-UTR of human BCL2 gene (Singh & Saini 2012).

MAPT binds to both the outer and the inner surfaces of microtubules, leading to tubulin assembly and microtubule stabilization. As taxanes also bind to the inner surface of microtubules, MAPT might be considered to obstruct the function of these drugs. Most of the studies reported that MAPT expression has prognostic value, with high expression associated with favorable patient outcome. However, at the present time, there are few studies indicating that MAPT is a predictive marker for taxane-based chemotherapy (Baquero et al. 2011, Smoter et al. 2011). We demonstrated that expression levels of MAPT showed positive correlation with expression levels of ER and PgR and negative correlation with expression levels of Ki67, tumor grade, and tumor size in ER-positive breast cancer. Because miR-1290 did not decrease BCL2 or MAPT protein expression in ER-positive breast cancer cells in our analysis, BCL2 and MAPT might be regulated by other mechanisms.

Interaction between miRNAs and putative target proteins that might be associated with characteristics of ER-positive breast cancer is shown in Fig. 3, which was created by Ingenuity systems Pathway Analysis (http://www.ingenuity.com/index.html) and referring to previous reports (Gomez et al. 2007, Badve & Nakshatri 2009, Clarke et al. 2009, O'Day & Lal 2010).

Figure 3
Figure 3

Interaction between miRNAs and putative target proteins that might be associated with characteristics of ER-positive breast cancer. Pathway analyses show five miRNAs (let-7a, miR-15a, miR-26a, miR-34a, and miR-1290) and nine target genes (BCL2, CCND1, FOXA1, GATA3, MAPT, NAT1, RB1, TP53, and XBP1) that were picked up in our present analyses. These proteins and their pathways have diverse cellular functions, such as differentiation, detoxification, anti-apoptosis, cell cycle progression, and microtubule stabilization.

Citation: Endocrine-Related Cancer 20, 1; 10.1530/ERC-12-0207

Finally, our results indicated that let-7a was strongly upregulated in ERhigh Ki67low tumors and that expression levels of p53, one of the let-7a targets, was inversely correlated with let-7a expression in ER-positive breast cancer. The let-7 miRNA family is a group of tumor suppressing miRNAs that can inhibit both tumorigenesis and metastasis (Zhang et al. 2010). It was recently reported that let-7 family miRNAs, especially let-7a, let-7b, and let-7i, were downregulated in breast cancer tissue compared with normal tissue and that let-7 miRNAs induced apoptosis in MCF-7 cells (Zhao et al. 2011). Thus, let-7 might have a role in ER-positive breast cancer.

In conclusion, this study indicates for the first time that miR-1290 and its potential targets, NAT1 and FOXA1, are strongly downregulated in ERhigh Ki67low tumors and are associated with characteristics of ER-positive breast cancer. miR-1290 could be a novel therapeutic target in ER-positive breast cancer.

Supplementary data

This is linked to the online version of the paper at http://dx.doi.org/10.1530/ERC-12-0207.

Declaration of interest

The authors declare that there is no conflict of interest that could be perceived as prejudicing the impartiality of the research reported.

Funding

This work was supported in part by grant-in-aid for scientific research from Japan Society for the Promotion of Science.

Author contribution statement

Y Endo designed the study, executed miRNA and mRNA expression profiling, target prediction and target validation, carried out immunostaining and western blotting, and drafted the manuscript. T Toyama, N Yoshimoto, M Iwasa, and T Asano provided tissue samples. S Takahashi assessed the immunostaining and western blotting. Y Fujii participated in its design and coordination. H Yamashita conceived of the study and participated in its design, coordination, and manuscript writing. All authors read and approved the final manuscript.

Acknowledgements

The authors wish to thank Prof. Edith Sim and Dr Hilary Long (University of Oxford, UK) for kindly providing anti-NAT1 antibodies.

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H Yamashita is now at Breast and Endocrine Surgery, Hokkaido University Hospital, Kita 14, Nishi 5, Sapporo 060-8648, Japan

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    miR-1290 expression is inversely correlated with expressions of BCL2, FOXA1, MAPT, and NAT1. Scatter plots show inverse correlations between miR-1290 and BCL2 (A), FOXA1 (B), MAPT (C), and NAT1 (D) protein expression in breast cancer tissue (P=0.020, P=0.044, P=0.040, and P=0.0098 respectively). (E) let-7 expression is inversely correlated with P53 protein expression in breast cancer tissue (P=0.038).

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    Gene expressions of miR-1290 putative targets in T47D and MCF-7 cells transfected with miR-1290. (A) T47D cells were transfected with either control miRNA (300 nmol/l) or pre-miR-1290 precursor at 10–300 nmol/l and incubated for 24 h. Expression levels of miR-1290 and mRNA levels of BCL2, FOXA1, MAPT, and NAT1 were measured by quantitative RT-PCR. Scatter plots show inverse correlation between miR-1290 expression and FOXA1 and NAT1 mRNA expression (P=0.0003 and P<0.0001 respectively). (B) MCF-7 cells were transfected with either control miRNA (300 nmol/l) or pre-miR-1290 precursor at 10–300 nmol/l and incubated for 36 h. Expression levels of miR-1290 and mRNA levels of BCL2, FOXA1, MAPT, and NAT1 were measured by quantitative RT-PCR. Scatter plots show inverse correlation between miR-1290 expression and NAT1 mRNA expression (P=0.037). (C) T47D cells were transfected with either control miRNA (300 nmol/l) or pre-miR-1290 precursor at 30–1000 nmol/l and incubated for 48 h. Protein expression of BCL2, FOXA1, MAPT, and NAT1 was assayed by western blot analysis. The number below the band represents the mean value from densitometry reading, relative to the negative control, which was set at 1.00. Representative results from one of the three experiments are shown. (D) MCF-7 cells were transfected with either control miRNA (300 nmol/l) or pre-miR-1290 precursor at 30–1000 nmol/l and incubated for 48 h. Protein expression of BCL2, FOXA1, MAPT, and NAT1 was assayed by western blot analysis. The number below the band represents the mean value from densitometry reading, relative to the negative control, which was set at 1.00. Representative results from one of the three experiments are shown.

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    Interaction between miRNAs and putative target proteins that might be associated with characteristics of ER-positive breast cancer. Pathway analyses show five miRNAs (let-7a, miR-15a, miR-26a, miR-34a, and miR-1290) and nine target genes (BCL2, CCND1, FOXA1, GATA3, MAPT, NAT1, RB1, TP53, and XBP1) that were picked up in our present analyses. These proteins and their pathways have diverse cellular functions, such as differentiation, detoxification, anti-apoptosis, cell cycle progression, and microtubule stabilization.