Background
Nearly, 70% of breast cancer patients develop tumors expressing the estrogen receptor (ERα) and are candidates for endocrine therapy. The selective ERα modulator tamoxifen, is the most commonly prescribed endocrine therapy, but 30-40% of patients fail adjuvant tamoxifen therapy and nearly all patients with metastatic disease develop tamoxifen resistance [
1]. Unfortunately,
de novo and acquired tumor resistance to tamoxifen therapy remains a poorly understood and serious clinical problem.
Multiple causal events have been associated with anti-estrogen resistance including loss of ERα expression [
2], selection of ERα mutants [
3,
4], and cross-talk between the type I receptor tyrosine kinase family resulting in ligand-independent activation of the ERα [
5]. Several clinical studies implicate the HER2 receptor tyrosine kinase as a significant risk for tamoxifen failure. Approximately half of the ERα positive tumors also express HER2 and over 70% of these patients may exhibit
de novo tamoxifen resistance [
6,
7]. A large percentage of HER2/ERα positive tumors acquire estrogen-independence and therefore continue to grow when patients are estrogen depleted [
6].
MicroRNAs (miRNAs) are short (~22 bp), single-stranded, non-coding RNAs that suppress gene expression by binding the 3' UTR of target gene mRNAs. They are thought to regulate up to one-third of the human genome by targeting mRNAs for cleavage or translational repression and miRNAs have recently been identified as key players in cellular processes including self-renewal, differentiation, growth and apoptosis, all of which are deregulated in carcinogenesis. Several miRNAs have been shown to be differentially regulated in breast cancer [
8], and individual miRNAs that contribute to tumorigenicity, invasion and metastasis have been identified [
9]. Recently, breast cancer prognostic markers such as ERα and HER2 have been shown to be regulated by miR-221/222 and miR-125, respectively [
10,
11]. Importantly, miR-221/222 and the BCL-2 targeting miR-15a/16 have been shown to contribute to tamoxifen resistance [
11‐
13], implicating multiple miRNAs as important modulators of tamoxifen response. As multiple mechanisms contribute to the acquisition of tamoxifen resistance, it is likely that additional miRNA regulators of endocrine response remain to be identified.
Recently we demonstrated that the oncogenic splice isoform of HER2, HER2Δ16, is associated with metastatic breast cancer and resistance to both trastuzumab [
14] and endocrine therapy [
12,
15]. Here we show that deregulation of miR-342 contributes to tamoxifen resistance in multiple models of tamoxifen resistance including the HER2Δ16 overexpression model. Specifically, we demonstrate that miR-342 is downregulated in tamoxifen resistant breast tumor cell lines and tamoxifen refractory human breast tumors. We propose that miR-342 may emerge as an important marker for tamoxifen response as well as a potential therapeutic.
Methods
Cell Lines
Human mammary carcinoma cell line MCF-7 was purchased from the American Type Culture Collection (Manassas, VA) and maintained in MEM supplemented with 10% fetal bovine serum (FBS). The tamoxifen sensitive MCF-7/HER2, MCF-7/pcDNA, and the tamoxifen-resistant MCF-7/HER2Δ16 cell lines have been described elsewhere [
12,
14,
15]. The tamoxifen resistant MCF-7 variants TAMR1 and LCC2 have been described previously [
16,
17]. To generate the miR-342 expressing MCF-7/HER2Δ16 cell line a 342 bp sequence containing the pre-miR-342 sequence (GRCh37:14:100575892:100576190:1) flanked by 100 bp upstream and downstream was prepared as a minigene (Integrated DNA Technologies) and subcloned into pCMV-puro-silencer (Ambion). The same vector expressing a short scrambled sequence (pCMV-puro-NC) was used as a control. Either pCMV-miR-342 or pCMV-puro-NC were transfected into MCF-7/HER2Δ16 cells using Fugene6 (Roche) and stable clones were isolated.
miRNA Expression Profiling
Total RNA was isolated using miRVANA RNA Isolation System (Ambion) and integrity of samples was confirmed using a Bioanalyzer (Agilent). For miRNA profiling, biological duplicates of cells cultured for 48 h in CS-FBS and then treated with either 100 pM 17-β-estradiol alone or in combination with 1.0 μM 4-hydroxytamoxifen (TAM) were analyzed. Microarray assay was performed and analyzed using a service provider (LC Sciences) using LC-Science microRNA arrays miRHuman_11.0 which detects miRNA transcripts listed in Sanger miRBase Release 11.0.
Northern Blot Analysis
Total RNA was isolated using miRVANA RNA isolation Kit (Ambion) and 10 μg of RNA was separated by electrophoresis on a 15% TBE/urea gel. RNA was transferred to a Hybond NX membrane (Amersham/Pharmacia), UV-crosslinked, and incubated in pre-hybridization solution (6X SSC, 5X Denhart's solution, 0.2% SDS) for 1 h at 30°C. Membranes were then hybridized (42°C for 16 h) with P32-labeled DNA probes corresponding to the complementary sequences of the mature miR-342-3p. The blots were exposed for 48 to 72 hr and developed using Molecular Dynamics Phosphoimaging.
Quantification of miR-342
Expression of miR-342 was quantitated by qRT-PCR from total RNA exactly as described elsewhere [
12].
Analysis of EVL mRNA by Quantitative Reverse Transcription PCR
Expression of EVL was quantitated by qRT-PCR from total RNA exactly as described elsewhere [
12] using the oligonucleotide primers 5'-TGCTGCTCCATCACTTGTCT and 5'-CTCCAATGCAATGCTGTTTG.
Breast Tumor Samples
The patient population used for this study has been described in detail elsewhere [
18]. Formalin fixed paraffin-embedded human primary breast tumors were obtained from the Department of Pathology at the University of Colorado. Tumor samples were collected from 1978 to 1993 and patients underwent tamoxifen therapy. Additional immunohistochemical, clinical, and pathological details of this cohort have been described elsewhere [
18‐
21].
In situ hybridization of miR-342
In situ hybridization (ISH) of 6 μm sections from archived FFPE primary breast tumor specimens was performed using standard techniques and double-DIG Locked Nucleic Acid-modified DNA probe complementary to mature hsa-miR-342-3p or scrambled control (Exiqon) according to the manufacturer's instructions. Each section was scored by comparing staining intensity of stably expressing miR-342 MCF-7/HER2Δ16 cells given a score of 3 and the MCF-7/HER2Δ16 cells with a score of 0 to the staining of tumor cells present in each section. Two independent observers were blind to sample identification and independently scored each slide. Each sample was given a final score based upon consensus.
3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium Bromide Assay
Cell proliferation was measured as a function of metabolism by 3-(4,5-dimethylthiazol-2-yl])-2,5-diphenyltetrazolium bromide (MTT; Sigma, St. Louis, MO) assay exactly as described elsewhere [
22] with detailed modifications [
12]. Each sample was prepared in triplicate and the data represent the mean and SE of at least three independent experiments. Data was normalized to control-mock treated cells. Statistically significant differences between data sets were determined using paired Student's t test.
Apoptosis Assay
Cell death as a result of apoptosis was quantitated by measuring mono- and oligonucleosomes release using the Cell Death Detection ELISA PLUS Kit (Roche) following the manufacturer's instructions.
Inhibition of miR-342
Each cell line plated at 3000 cells per well in a 96-well tissue culture plate was cultured for 24 hrs in CS-MEM and then transfected with 50 nM of miRIDIAN miRNA inhibitor non-specific control 1 or miRIDIAN miRNA inhibitor hsa-miR-342-3p (Dharmacon) using Hyperfect Reagent (Qiagen) according to the manufacturer's instructions. At one day post-transfection cells were treated with 100 pM 17-β-estradiol alone or in combination with 1.0 μM 4-hydroxytamoxifen and a MTT growth assay was performed at five days post-transfection or cell death as a result of apoptosis was quantitated by measuring mono- and oligonucleosomes release using the Cell Death Detection ELISA PLUS Kit (Roche) following the manufacturer's instructions. Each sample was prepared in triplicate and the data represent the mean and SE of at least three independent experiments. Statistically significant differences between data sets were determined using paired Student's t test.
Transient Expression of miR-342
Pre-miR miRNA Precursor Molecules (Ambion) for hsa-miR-342-3p were transfected into cell lines at the indicated concentrations using Hyperfect (Qiagen).
3' UTR Reporter Assay
MCF-7 cells were plated at 5000 cells per well in a 48 well plate and transfected with 20 nM of hsa-miR-342-3p (Ambion) or pre-miR negative control (Ambion) using Hyperfect. The next day cells were transfected with 1.0 μg of with pMir target firefly luciferase reporter plasmid containing 3' UTR sequences from BMP7 or GEMIN4 (Origene) and 1.0 μg of renilla luciferase expression plasmid pRL-SV40 with Fugene 6. At 48 hrs post-transfection cells were analyzed using the Dual Luciferase Assay Kit (Promega) according to the manufacturer's instructions. Each sample was prepared in duplicate and the entire experiment was repeated three times.
Microarray Gene Expression Analysis
Total RNA from biological triplicates of MCF-7/HER2Δ16-miR-342 and MCF-7/HER2Δ16-puro-NC was labeled and hybridized to Affymetrix GeneChip Human Exon 1.0 ST Array and data was analyzed using GeneSpring GX 9.0 (Agilent) software at the University of Colorado Denver DNA Microarray Core Facility. Molecular pathway and connectively maps of the dataset was performed using Ingenuity Pathway Analysis software.
Discussion
Endocrine resistance remains an important problem in the breast cancer clinic. Currently there are only a few useful tumor markers to guide management decisions for women with ERα(+) breast tumors. Here we investigated the potential role of miRNAs in the regulation of tamoxifen response with the goal of identifying miRNAs that can be used to predict patient outcome during tamoxifen therapy. We found several miRNAs whose expression was altered in tamoxifen resistant breast tumor cells. We further demonstrate that miR-342-3p (miR-342), an ERα associated miRNA [
23], was dramatically suppressed in multiple tamoxifen resistant breast tumor cell lines and in primary breast tumors of patients who failed tamoxifen therapy. Importantly, reintroduction of miR-342 sensitized refractory breast tumor cells to tamoxifen therapy suggesting that miR-342 is an important regulator of tamoxifen response.
Multiple studies have demonstrated that miRNAs are involved in estradiol-dependent breast tumor cell proliferation [
31,
32]. Accordingly, estradiol regulates expression of many miRNAs [
31,
32] and an ERα associated miRNA signature has been identified in human breast tumors [
23]. In contrast, miRNAs appear to counteract estrogen-dependent cell proliferation and their expression is upregulated by anti-estrogen treatment of breast tumor cells [
32]. In this study, we profiled miRNA expression in tamoxifen-sensitive and resistant breast tumor cell lines and we identified several miRNAs differentially regulated in tamoxifen-resistant MCF-7 cells expressing the HER2Δ16 oncogenic isoform of HER2 [
14]. In corroboration with recent findings that deregulation of miRNAs contributes to the acquisition of anti-estrogen resistance [
11‐
13], we show that miR-342, which is suppressed in tamoxifen resistant cells, is associated with increased tamoxifen sensitivity of breast tumor cells. Enhanced expression of miR-342 in tamoxifen sensitive breast tumor cells has been reported previously, however, the functional significance of deregulated miR-342 was not investigated by this group [
13]. MiR-1308 and miR-1180 were also deregulated by greater than 2-fold in tamoxifen treated MCF-7/HER2Δ16 cells. Studies are in progress to decipher the contribution of these miRNAs to HER2Δ16 mediated endocrine resistance.
It is common for miRNAs located within transcriptional units to be co-expressed with their host gene. Although
in situ methods for the detection of miRNA expression are not in clinical use, the fact that miR-342 expression is tightly correlated to its host gene EVL in multiple tumor cell models [
24,
33] including our breast tumor cell lines, provides a unique opportunity to use EVL mRNA expression as a surrogate marker for miR-342 expression in breast cancer patients. Mining of archived microarray data revealed that EVL expression is significantly associated with ERα(+) breast tumors [
25‐
27] which is consistent with recent studies reporting a strong correlation between ERα and miR-342 expression [
23]. Significantly, ERα(+) breast tumors that fail tamoxifen therapy with rapid recurrence within 3 years have significantly lower EVL expression levels [
34], providing compelling support for the hypothesis that miR-342 suppression promotes tamoxifen resistance. In colorectal cancer cells EVL/miR-342 expression is suppressed through hypermethylation of the
EVL promoter [
24]. We are currently investigating a similar mechanism of miR-342 suppression in tamoxifen resistant breast tumor cells.
A direct gene target of miR-342 remains to be experimentally confirmed and bioinformatics reveals over 1000 potential miR-342 targets. As an approach to the identification of miR-342 targets we examined transcriptome changes in miR-342 overexpressing cells by microarray analysis. We observed significant alteration of 13 genes predicted by bioinformatics to be miR-342 targets. Interestingly, the majority of predicted target genes were up-regulated by miR-342 expression. Although miRNAs commonly suppress target gene mRNA levels, accumulating evidence suggests that miRNAs can target genes for up-regulation by at least two different mechanisms [
35]. Although we could not identify an obvious association between the direct targets of miR-342 and tumor cell response to tamoxifen, Ingenuity Pathway Analysis of the entire set of genes significantly altered by miR-342 revealed a highly significant association of miR-342 regulated genes with cell apoptosis. This result is consistent with our observation that ectopic miR-342 expression sensitized tamoxifen resistant cells to tamoxifen-induced apoptosis. Similarly, miR-342 expression in colorectal cancer cells results in tumor cell apoptosis [
24]. Nevertheless, activity of miR-342 appears to be functionally different in colorectal and breast tumor cells. Our results indicate that miR-342 expression alone is not sufficient to induce cell death, but miR-342 sensitizes cells to apoptosis associated with estrogen-deprivation and tamoxifen exposure. In this context, the miR-342 indirect target thioredoxin-interacting protein (TXNIP) is the most dramatically upregulated gene in response to miR-342 expression and could potentially mediate miR-342 action. Accordingly, TXNIP expression is induced in tumor cells by various stresses including serum starvation [
36], which mimics ERα inactivation in breast tumors, and enhanced TXNIP expression has tumor-suppressor activity [
36,
37]. Similar to our findings that miR-342 sensitizes breast tumor cells to tamoxifen, TXNIP sensitizes breast tumor cells to paclitaxel [
38]. Although these results are compelling, TXNIP is an upregulated indirect target of miR-342 and deciphering the interplay between miR-342 and TXNIP has proved difficult.
Although tamoxifen clearly induces breast tumor cell apoptosis, cytostasis is considered the predominant tumor cell response to tamoxifen therapy. Accordingly, IPA analysis identified miR-342 regulated genes significantly represented in multiple pathways that directly regulate breast tumor cell cycle progression including cyclin B1, p53, and BRCA1. Taken together our results provide a genomic basis to explore the role of miR-342 regulated genes in multiple tamoxifen actions including both apoptosis and cytostasis.
Competing interests
The authors declare that they have no competing interests.
Authors' contributions
DMC performed all miR-342 and apoptosis analyses as well as prepared the manuscript draft. PMD performed all miR-342 and cell growth analyses required for the revised manuscript. NSS and SME performed miR-342 ISH experiments. JKR and ADT evaluated and monitored ISH experiments. FEJ conceived of the study, participated in data analysis at each stage, and finalized preparation of the manuscript. All authors read and approved the final manuscript.