Open Access

Knockdown of miR-21 in human breast cancer cell lines inhibits proliferation, in vitro migration and in vivotumor growth

  • Li Xu Yan1, 2,
  • Qi Nian Wu1, 2,
  • Yan Zhang1, 2,
  • Yang Yang Li1, 2,
  • Ding Zhun Liao1, 2,
  • Jing Hui Hou1, 2,
  • Jia Fu1, 2,
  • Mu Sheng Zeng1, 3,
  • Jing Ping Yun1, 2,
  • Qiu Liang Wu1, 2,
  • Yi Xin Zeng1, 3 and
  • Jian Yong Shao1, 2, 3Email author
Contributed equally
Breast Cancer Research201113:R2

https://doi.org/10.1186/bcr2803

Received: 7 March 2010

Accepted: 10 January 2011

Published: 10 January 2011

Abstract

Introduction

MicroRNAs (miRNAs) are a class of small non-coding RNAs (20 to 24 nucleotides) that post-transcriptionally modulate gene expression. A key oncomir in carcinogenesis is miR-21, which is consistently up-regulated in a wide range of cancers. However, few functional studies are available for miR-21, and few targets have been identified. In this study, we explored the role of miR-21 in human breast cancer cells and tissues, and searched for miR-21 targets.

Methods

We used in vitro and in vivo assays to explore the role of miR-21 in the malignant progression of human breast cancer, using miR-21 knockdown. Using LNA silencing combined to microarray technology and target prediction, we screened for potential targets of miR-21 and validated direct targets by using luciferase reporter assay and Western blot. Two candidate target genes (EIF4A2 and ANKRD46) were selected for analysis of correlation with clinicopathological characteristics and prognosis using immunohistochemistry on cancer tissue microrrays.

Results

Anti-miR-21 inhibited growth and migration of MCF-7 and MDA-MB-231 cells in vitro, and tumor growth in nude mice. Knockdown of miR-21 significantly increased the expression of ANKRD46 at both mRNA and protein levels. Luciferase assays using a reporter carrying a putative target site in the 3' untranslated region of ANKRD46 revealed that miR-21 directly targeted ANKRD46. miR-21 and EIF4A2 protein were inversely expressed in breast cancers (rs = -0.283, P = 0.005, Spearman's correlation analysis).

Conclusions

Knockdown of miR-21 in MCF-7 and MDA-MB-231 cells inhibits in vitro and in vivo growth as well as in vitro migration. ANKRD46 is newly identified as a direct target of miR-21 in BC. These results suggest that inhibitory strategies against miR-21 using peptide nucleic acids (PNAs)-antimiR-21 may provide potential therapeutic applications in breast cancer treatment.

Introduction

Breast cancer (BC) is by far the most frequent cancer of women (23% of all cancers), with an estimated 1.15 million new cases worldwide in 2002 [1]. It is still the leading cause of cancer mortality in women [1]. Despite research and resources dedicated to elucidating the molecular mechanisms of BC, the precise mechanisms of its initiation and progression remain unclear.

MicroRNAs (miRNAs) are small non-coding RNAs (20 to 24 nucleotides) that post-transcriptionally modulate gene expression by negatively regulating the stability or translational efficiency of their target mRNAs [2]. After the discovery of miRNAs, and findings indicating that they play a role in cancer, the concept of "oncomirs" was proposed [3]. In particular, miR-21 [miRBase: MIMAT0000076] has emerged as a key oncomir, since it is the most consistently up-regulated miRNA in a wide range of cancers [47].

Functional studies showed that knockdown of miR-21 in MCF7 cells led to reduced proliferation and tumor growth [8, 9]. Knockdown of miR-21 in MDA-MB-231 cells significantly reduced invasion and lung metastasis [10]. These data clearly implicate miR-21 as a key molecule in carcinogenesis, but functional studies that demonstrate cause and effect relationships between miR-21 and target genes are lacking. Given that miRNAs usually target multiple genes post-transcriptionally, miR-21 is likely to exert its effects by regulating many genes involved in BC.

The inhibition of miRNAs using antisense oligonucleotides (ASOs) is a unique and effective technique for investigating miRNA functions and targets. Peptide nucleic acids (PNAs) are artificial oligonucleotides constructed on a peptide-like backbone. PNAs have a stronger affinity and greater specificity for DNA or RNA than natural nucleic acids, and are resistant to nucleases [11]. PNA-based ASOs can be used without transfection reagents, and are highly effective and sequence-specific. They provide long-lasting inhibition of miRNAs, and show no cytotoxicity up to 1 μM [11]. Therefore, we used a PNA miR-21 inhibitor for in vivo investigation.

In this study, we explored the role of miR-21 in the malignant progression of human BC by assaying in vitro and in vivo function after miR-21 knockdown. We also searched for miR-21 targets using gene prediction-based and systematic screening approaches. Two potential target genes eukaryotic translation initiation factor 4A2 (EIF4A2) [NCBI: NM001967] and ankyrin repeat domain 46 (ANKRD46) [NCBI: NM198401] were selected for correlation analysis between protein levels and clinicopathological characteristics as well as prognosis using immunohistochemistry (IHC) on cancer tissue microrrays (TMAs).

Materials and methods

Tissue specimens and TMAs construction

In situ hybridization analysis was performed on fresh samples from BC or fibroadenoma (FA) tissues with paired normal adjacent tissues (NATs, > 2 cm from tumor tissues) obtained from Sun Yat-sen University Cancer Center (SYSUCC) (Guangzhou, China) between January and March 2009. For IHC staining of miR-21 predicted target genes, formalin-fixed paraffin-embedded tissues were obtained from 99 randomly selected BC patients without neoadjuvant therapy at SYSUCC from January 2000 to November 2004, from whom informed consent and agreement, and clinicopathological information was available. A pathologist reviewed slides from all blocks, selecting representative areas of invasive tumor tissue to be cored. Selected cores were analyzed in duplicate using a MiniCore Tissue Arrayer (Alphelys, Passage Paul Langevin, Plaisir, France) with a 1-mm needle. The diagnosis and histological grade of each case were independently confirmed by two pathologists based on World Health Organization classification [12]. The clinical stage was classified according to the American Joint Committee on Cancer (AJCC) tumor-lymph node-metastasis (TNM) classification system [13]. The study was approved by the Research Ethics Committee of SYSUCC (Reference number: YP-2009168). The clinicopathological characteristics and follow-up data of the patients are summarized in Table 1.
Table 1

Clinicopathological characteristics and follow-up data for 99 patients with BC

Characteristics

Number of patients/Number analyzed (%)

Median age (range)

48 (30 to 74) (years)

Histological type*

 

   Ductal

93/99 (94%)

   Lobular

1/99 (1%)

   Other

5/99 (5%)

Histological grade*

 

   I

22/99 (22%)

   II

58/99 (58%)

   III

19/99 (20%)

Lymph node status at time of primary diagnosis

   Metastasis

57/99 (58%)

   No metastasis

42/99 (42%)

AJCC clinical stage**

 

   I

8/99 (8%)

   II

68/99 (69%)

   III

23/99 (23%)

Overall survival (median, range)

74 (6 to 112) (months)

   Alive without evidence of cancer

45/99 (68%)

   Alive with cancer

14/99 (14%)

   Died of cancer

40/99 (40%)

   Died of other disease

0/99 (0%)

* According to the WHO classification of BC. ** According to the AJCC staging system; AJCC, American Joint Committee on Cancer; BC, breast cancer; WHO, World Health Organization.

Locked nucleic acid (LNA)-based in situhybridization for miRNA

To study the spatial and temporal expression of miRNAs with high sensitivity and resolution, the miRNA chromogenic in situ hybridization (CISH) and fluorescein in situ hybridization (FISH) protocol [14] were optimized (Additional file 1).

Transfection of LNA-antimiR-21 into BC cells

MCF-7 and MDA-MB-231 cells were maintained in Dulbecco's modified Eagle's medium, supplemented with 100 U/ml penicillin, 100 μg/ml streptomycin and 10% fetal bovine serum (GIBCO-Invitrogen, Carlsbad, CA, USA). For transfection, the LNA-antimiR-21 or LNA-control (Exiqon A/S, Skelstedet, Vedbaek, Denmark) were delivered at a final concentration of 50 nM using Lipofectamine 2000 reagent (Invitrogen).

3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and colony formation assay

Growing cells (2 × 103 cells per well) were seeded into 96-well plates. At 24 h after LNA-transfection, cells were stained with 20 μl sterile MTT dye (5 mg/ml; Sigma-Aldrich Corp, St. Louis, MO, USA), followed by 4 h at 37°C. After supernatant removal, 150 μl of dimethyl sulphoxide (Sigma) was added and thoroughly mixed for 15 minutes. Absorbence was measured with a microplate reader (SpectraMax M5; Molecular Devices Corp., Silicon Valley, CA, USA) at 490 nm. For colony formation assays, cells were seeded in six-well plates (0.5 × 103 cells per well) and cultured for two weeks. Colonies were fixed with methanol for 10 minutes and stained with 1% crystal violet (Sigma) for 1 minute. Each cell group was measured in triplicate.

Wound healing assay

Cells cultured in the presence of 50 nM LNA-antimiR-21 or LNA-control for 24 h were allowed to reach confluence before dragging a 1-mL sterile pipette tip (Axygen Scientific, Inc., Union City, CA, USA) through the monolayer. Cells were washed to remove cellular debris and allowed to migrate for 24 h or 48 h. Images were taken at time 0 h, 24 h and 48 h post-wounding using a digital camera system (Leica DFC 480; Leica Microsystems, Bannockburn, IL, USA). The motility of the cells was determined as repaired area percentage [15]. Each cell group was measured in triplicate.

Validation of tumor growth-promoting activity of miR-21in an animal model

Five- to six-week-old female BALB/c-nude mice (Slaccas Shanghai Laboratory Animal Co., Ltd., Shanghai, China) were used for experimental tumorigenicity assays. To facilitate estrogen-dependent xenograft establishment, each mouse received 17-estradiol (20 mg/kg; Sigma) intraperitoneally once a week. One week after treatment, equivalent amounts of MCF-7 cells, treated with PNA-antimiR-21 or PNA-control (100 nM for 48 h; Panagene, Inc., Yuseong-gu, Daejeon, Korea) without transfection reagents according to the manufacturer's protocol, were injected subcutaneously (107 cells/tumor) into the left axilla of nude mice [16]. Mice were weighed, and tumor width (W) and length (L) were measured every day. Tumor volume was estimated according to the standard formula: V = ∏/6 × L × W2, as described previously [17]. Animals were killed nine days after initial growth of the MCF-7 xenografts was detectable, and tumors were extracted. In all experiments, the ethics guidelines for investigations in conscious animals were followed, with approval from the local Ethics Committee for Animal Research.

mRNA array and data mining

MCF-7 and MDA-MB-231 cells were transfected either with LNA-antimiR-21 or with LNA-control at a final concentration of 50 nM. Total RNAs were isolated from MCF-7 cells 48 h post transfection and from MDA-MB-231 cells 36 h post transfection, respectively, using Trizol Reagent (Invitrogen). The mRNA expression profile was performed using human genome oligo array service V1.0 (Catalog Number 400010; CapitalBio, Beijing, China) as described [18]. Each sample was analyzed once, and the CapitalBio data preprocess, normalization and filtering were as previously described [18]. Ratios were defined as marginal signal intensity when there was a substantial amount of variation in the signal intensity within the pixels from 800 to 1,500. All the microarray data have been deposited to the Gene Expression Omnibus (GEO) [19] and are accessible through GEO Series accession number [GEO: GSE20627].

Relative quantitative reverse transcription-polymerase chain reaction (qRT-PCR)

For validation of mRNA array and quantitative analysis of miR-21 as well as potential target genes, qRT-PCR was used as previously described [20]. The primers for qRT-PCR are in Additional file 2. The relative expression was calculated using the equation relative quantification (RQ) = 2-ΔΔCT [21].

Computational prediction of miR-21target genes

Predicted miR-21 targets were identified using the algorithms of TargetScan 5.1 [22], miRBase Targets V5 [23], miRNAMap 2.0 [24], PicTar [25] and miRanda 3.0 [26].

Luciferase reporter assay

The 3' untranslated region (3' UTR) of mRNA sequence of ANKRD46 containing predicted miR-21 binding site was amplified by PCR. PCR primers were listed in Additional file 2. After amplification, PCR products were cloned into the pMIR-REPORT (Applied Biosystems, Foster City, CA, USA), resulting in the pMIR-REPORT-3'ANKRD46. Mutation of ANKRD46 was introduced in the predicted miR-21 binding site by a QuikChange site-directed mutagenesis kit (Stratagene, Foster City, CA, USA). Wild-type EIF4A2 and mutant EIF4A2 were cloned into pMD19-T Simple Vector by TaKaRa Biotechnology CO., LTD. (Dalian, Liaoning, China) and then were individually subcloned downstream of the luciferase coding sequence in the pMIR-REPORT (Applied Biosystems). All constructs were verified by DNA sequencing.

For reporter assays, wide-type or mutant reporter constructs (15 ng) were cotransfected into 293T cells in twelve-well plates with miR-21 or miR-control (50 nM; GenePharma, Shanghai, China) and Renilla plasmid (5 ng) using lipofectamine 2000 (Invitrogen). Firefly and Renilla luciferase activities were measured by using a Dual Luciferase Assay (Promega, Madison, WI, USA) 24 h after transfection. Firefly luciferase values were normalized to Renilla, and the ratio of firefly/renilla was presented.

Immunoblot analysis

Cells were harvested and lysed in radioimmune precipitation buffer (Upstate, Lake Placid, NY, USA) at the indicted time post-transfection. Antibodies used for immunoblot analysis were against ANKRD46 (1:500 dilution; sc-87548, Santa Cruz Biotechnology, Inc., Santa Cruz, CA, USA), EIF4A2 (1:1000 dilution; ab31218, Abcam, Cambridge, UK) and GAPDH (1:3,000 dilution; sc-32233, Santa Cruz Biotechnology), as a loading control. All bands were detected using a SuperSignal West Pico Chemiluminescent Substrate (Pierce, Rockford, IL, USA).

Immunohistochemical staining

IHC and scoring of the estrogen receptor (ER), progesterone receptor (PR) and CerbB2 were performed as previously described [20]. Slides were incubated with primary antibodies against ANKRD46 (1:150 dilution; sc-87548, Santa Cruz Biotechnology); or EIF4A2 (1:700 dilution; ab31218, Abcam). All slides were processed simultaneously in identical conditions per the manufacturer's instructions. Three observers independently determined consensus scoring of EIF4A2 and ANKRD46 immunostaining using a semi-quantitative estimation according to the percentage of positive cells and the intensity of staining as described previously [27]. With these data, the composite score was obtained by adding the values of the staining intensity and relative abundance [28]. Samples with scores lower than the median score were grouped as low protein expression [29].

Statistical analysis

Spearman's rank correlation test was used for correlation analysis between predicted target gene protein levels and endogenous miR-21 levels measured previously by qRT-PCR [20]. Pearson's Chi-Square tests were used to compare target gene expression levels to clinicopathological characteristics. Survival curves were estimated by the Kaplan-Meier method and log-rank test. All analysis used SPSS 16.0 for Windows (SPSS Inc, Chicago, IL, USA). All tests were two-tailed, and the significance level was set at P < 0.05.

Results

miR-21is overexpressed in BC tissues and cell lines

Expression of miR-21 was detected in the cytoplasm in cancerous and luminal epithelial cells, and occasionally in fibroblasts. In BC patients, an increase in miR-21 staining intensity was observed in BC and FA tissues compared with corresponding NATs (Figure 1a). Parallel detection by FISH is shown in Additional file 3. Consistent with the CISH results, quantitative analysis indicated that miR-21 expression was significantly increased by 4.44- to 2.02-fold in BC tissues compared with NATs (P = 0.019, n = 4), and increased in FA tissues by 3.03- to 1.89-fold (P = 0.008, n = 4, Figure 1b). FISH and qRT-PCR were used to measure miR-21 levels in five BC cell lines (MCF-7, MDA-MB-231, MDA-MB-453, MDA-MB-435, and SK-BR-3) and one non-tumorigenic epithelial cell line (MCF-10A). Consistent with previous findings [8, 10, 30], miR-21 overexpressed in MCF-7, MDA-MB-231 and MDA-MB-453 cell lines from 6.48- to 4.04-fold compared with MCF-10A cell line (P < 0.01, Figure 1d).
Figure 1

Altered expression of miR-21 in different breast tumor types and breast cell lines. (a) CISH detection using miR-21 LNA detection probe (blue) or scramble-miR as negative control were performed on consecutive 8 μM cryo-sections obtained from BC/FA tissues and corresponding NATs. DNA was counterstained with methyl green (green, × 400 magnification). (b) Total RNA was used to quantify miR-21 expression by relative qRT-PCR, normalizing on U6 RNA levels. The graph shows a log2-scale RQ calculated by normalizing the miR-21 expression values in the tumors on those in the NATs. Data indicate the mean (+SD) of four independent samples. * P < 0.05. (c) FISH detection of miR-21 in five BC cell lines (MCF-7, MDA-MB-231, MDA-MB-453, MDA-MB-435, SK-BR-3) and one non-tumorigenic epithelial cell line (MCF-10A). Positive in situ hybridization signals are visualized in green, while blue depicts DAPI nuclear stain (× 1,000 magnification). (d) qRT-PCR analysis show that MCF-7, MDA-MB-231 and MDA-MB-453 cells express higher levels of miR-21 compared with MCF-10A cells. Data are mean (+SD) of three replicates. ** P < 0.01; BC, breast cancer; FA, fibroadenoma; NATs, normal adjacent tissues.

LNA-antimiR-21 inhibits BC cell growth, proliferation and migration in vitro

MCF-7 and MDA-MB-231 cell lines were selected to investigate miR-21 functions and targets by using sequence-specific functional inhibition of miR-21, because both cell lines express higher levels of miR-21 compared with MCF-10A cells. Optimal doses and time points for transfection of LNA reagents were determined by evaluating miR-21 levels using qRT-PCR (Additional file 4). Knockdown of miR-21 reduced miR-21 levels by 98% in MCF-7 cells, and 77% in MDA-MB-231 cells (P < 0.01) (Figure 2a). LNA-antimiR-21 led to a decrease in MCF-7 cell growth (Figure 2b) and proliferation (29%, P = 0.003, Figure 2c). Similar inhibition of cell growth and proliferation effects (51%, P = 0.011, Figure 2c) was also observed in MDA/LNA-antimiR-21 cells (data not shown). In vitro wound healing assays showed that wound repair in MCF/LNA-antimiR-21 and MDA/LNA-antimiR-21 was delayed compared with MCF/LNA-control and MDA/LNA-control cells (data not shown). Knockdown of miR-21 suppressed MCF-7 cell migration by up to 69% (P = 0.013), and MDA-MB-231 migration by 51% (P = 0.001), compared with the LNA-control at 24 h after wound scratch (Figure 2d). These data demonstrate the tumorigenic properties of miR-21 in regulating cell growth, proliferation and migration.
Figure 2

LNA-antimiR-21 suppressed BC cell growth, proliferation and migration in vitro. (a) miR-21 expression levels (normalized to U6 RNA) were significantly depressed by 98% (P < 0.01) in MCF-7/LNA-antimiR-21 and 77% (P < 0.01) in MDA/LNA-antimiR-21 cells, relative to the LNA-control. The graph shows RQ calculated by normalizing the miR-21 expression values in LNA-antimiR-21 treated cells on those in the LNA-control treated cells. (b) MTT assay showed that MCF-7/antimiR-21 and MDA-MB-231/antimiR-21 cells grew slower than cells transfected with the LNA-control. (c) Representative wells showing total numbers of colonies formed by LNA-antimiR-treated cells standardized against control cells (set to 100%). (d) Representative image of in vitro wound healing assay of MCF-7 and MDA-MB-231 at 0, 24 and 48 h after wound scratch. Data are mean + SD, n = 3. * P < 0.05, ** P < 0.01.

PNA-antimiR-21 inhibits tumor growth in vivo

To address the potential effects of PNA-antimiR-21 in vivo on the growth of BC cells, equal numbers (3 × 107) of MCF-7 cells treated with PNA-antimiR-21 or the PNA-control were subcutaneously injected into female nude mice (eight animals per treatment). As seen in Figure 3b and 3c, detectable tumor masses (0.011 ± 0.013 g, mean ± standard deviation, SD) were seen in only 5/8 (62.5%) of mice in the MCF/PNA-antimiR-21 group, while much larger tumors (0.036 ± 0.038 g, mean ± SD) were detected in all mice in the MCF/PNA-control group (P = 0.065, Mann-Whitney test). Both tumor weight and number showed that MCF/PNA-control cells formed larger tumors more rapidly (Figure 3a, c) than MCF/PNA-antimiR-21 cells in nude mice. PNA-antimiR-21 reduced miR-21 expression by 5.72 log2-scale in MCF-7 cells 48 h post-treatment compared with that in the control (P < 0.01). miR-21 expression in xenograft tumors of PNA-antimiR-21 group was 0.96 log2-scale higher than that of the control group (P < 0.05; Figure 3e). Notably, MCF/PNA-antimiR-21 tumor cells were decreased in mitotic and pathological mitotic stages compared with MCF/PNA-control cells, indicating a decreased in cell proliferative activity and apoptosis (Figure 3d).
Figure 3

Effect of miR-21-knockdown on MCF-7 cells growth in nude mice: in vivo functional studies. MCF-7 cells (107 cells/tumor), treated with PNA-antimiR-21 or PNA-control (100 nM for 48 h) without transfection reagents, were injected subcutaneously into the left axilla of nude mice. (a) Growth curves for MCF/PNA-antimiR-21 (n = 5) vs. MCF/PNA-control (n = 8) cells in an in vivo proliferation assay. All P-values > 0.05. (b) Tumors were weighed after animals were killed at 17 days post-tumor-cell injection. Decreasing trend for both number and size of tumors from MCF/PNA-antimiR-21 compared with MCF/PNA-control group, although differences were not significant (P = 0.065, Mann-Whitney test). (c) Mice and tumors extracted from MCF/PNA-antimiR-21 and MCF/PNA-control groups. (d) Representative photomicrographs of CISH for miR-21 on xenograft tumor sections obtained from mice bearing MCF/PNA-antimiR-21 or MCF/PNA-control groups (× 400). (e) qRT-PCR analysis of miR-21 expression in MCF-7 cells 48 h post PNA-treatment and in xenograft tumors after mice sacrifice. Data in (a), (b) and (e) indicate the mean + SD. * P < 0.05, ** P < 0.01. PNA, peptide nucleic acid.

Identification of potential miR-21targets

It is known that animal miRNAs regulate gene expression by inhibiting translation and/or by inducing degradation of target. In our study, most modulated genes in the mRNA differential expression profiles changed by less than two-fold. Since mRNA levels regulated by less than two-fold may still be miRNA targets, we defined differentially expressed genes as no less than 1.3-fold change [31]. Comparative analysis of LNA-antimiR-21 and LNA-control mRNA profiles showed differential regulation of 394 genes in MCF/LNA-antimiR-21, of which 228 (58%) were up-regulated and 166 (42%) were down-regulated. 321 genes were differentially expressed in MDA/LNA-antimiR-21 cells, of which 190 (59%) were up-regulated, and 131 (41%) down-regulated (Figure 4a). The intersection of MCF/LNA-antimiR-21 and MDA/LNA-antimiR-21 consisted of 27 genes (18 up- and 9 down-regulated; Figure 4b and Table 2).
Figure 4

mRNA profiling of miR-21-knockdown BC cell lines. MCF-7 and MDA-MB-231 cells were transfected with 50 nM LNA-antimiR-21 or LNA-control. Total RNAs were isolated from MCF-7 cells 48 h post transfection and from MDA-MB-231 cells 36 h post transfection, respectively, and were hybridized to the human genome oligo array V1.0 (CapitalBio, China). (a) The scatter plot shows the LNA-antimiR-21 expression values normalized to LNA-control values, applying a cut-off of 1.3. Each dot represents one probe set. (b) Unsupervised hierarchical cluster analysis of intersection of mRNAs differentially expressed in MCF-7 and MDA-MB-231 cells upon LNA-antimiR-21 treatment. Rows, mRNAs; columns, biological samples. For each mRNA, red is expression higher than average expression across all samples, green is expression lower than average. (c) Validation of microarray results by qRT-PCR, normalizing on GAPDH RNA levels. MCF/A, MCF/LNA-antimiR-21; MCF/C, MCF/LNA-control; MDA/A, MDA/LNA-antimiR-21, MDA/C, MDA/LNA-control.

Table 2

Regulated mRNAs in BC cells after miR-2 1 knockdown determined by oligo array

    

Fold change

 

Gene Name

NCBI accession number

Genbank accession number

Description

MCF-7

MDA-MB-231

Prediction program

ANKRD46

NM_198401

U79297, BC035087

ankyrin repeat domain 46

1.78

2.57 #

miRBase Targets V5

ACTN4

NM_004924

BC005033

Alpha-actin 4 (F-actin cross linking protein)

1.75

1.55

 

NR0B1

NM_000475

S74720

Nuclear receptor 0B1 (Nuclear receptor DAX-1)

1.60

1.32

 

HIRA

NM_003325

BC039835, X89887

HIRA protein

1.48

1.32

 

COL18A1

NM_030582, NM_130444, NM_130445

AF018081

Collagen alpha 1(XVIII) chain precursor

1.43

1.35

 

SAMD11

NM_152486

BC024295, AK054643

sterile alpha motif domain containing 11

1.42

1.34

 

EIF4A2

NM_001967

AL117412

Eukaryotic initiation factor 4A-II

1.42

1.41

miRNAMap

SFRS16

NM_007056

AF042800, AK094681

Splicing factor, arginine/serine-rich 16

1.40

1.34

 

NP_079316

-

BC004930

zinc finger protein 614

1.37

1.36

 

IL18BP

NM_173043, NM_005699, NM_173042

AF110801

Interleukin-18 binding protein precursor

1.36

1.34

 

GBF1

NM_004193

AK025330, AF068755

Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1

1.35

1.51

 

GNPDA1

NM_005471

AJ002231

Glucosamine-6-phosphate isomerase

1.34

1.32

 

SPUF_HUMAN

NM_013349

-

SPUF protein precursor

1.34

1.31

 

PLXNA1

NM_032242

AK127254

plexin A1; plexin 1

1.32

1.57

 

STMN3

NM_015894

AK094112

Stathmin 3 (SCG10-like protein)

1.32

1.47

 

NP_056236

NM_015421

AK093383, AL080088

DKFZP564K2062 protein

1.31

1.33

 

-

-

AK056473

-

1.31

1.30

 

AP2B1

NM_001282

M34175

adaptor-related protein complex 2, beta 1 subunit

1.31

1.45

 

HIST1H2AC

-

CR608156

Histone H2A.l (H2A/l)

-1.47

-1.67

 

PRKCI

NM_002740

L33881, BC042405, BC022016

Protein kinase C, iota type

-1.43

-1.32

 

SLC25A3

NM_002635, NM_213611, NM_213612, NM_005888

BX647062, AK057575

Phosphate carrier protein, mitochondrial precursor (PTP)

-1.39

-1.39

 

CCNE1

NM_057182, NM_001238

M74093, BC035498

G1/S-specific cyclin E1

-1.37

-1.39

 

DCAMKL1

NM_004734

AB002367

Serine/threonine-protein kinase DCAMKL1

-1.34

-1.46

 

GNG12

NM_018841

AL832431

Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-12 subunit

-1.32

-1.40

Miranda

Q8TAY7

NM_024869

BC025658

hypothetical protein FLJ14050

-1.32

-1.31

 

NP_653284

NM_144683

BC015582

hypothetical protein MGC23280

-1.31

-1.35

 

NP_055182

NM_014367

-

growth and transformation-dependent protein

-1.30

-1.34

 

Fold-regulation of mRNAs affected by miR-21 knockdown compared with control-transfected cells (MCF-7 and MDA-MB-231) at indicated time points. Fold-changes for all mRNAs are derived from a single microarray experiment, with two relevant genes confirmed by qRT-PCR (Figure 4B). Shown are mRNAs changing by at least 1.3-fold in both cell lines. Genes in bold were selected for candidate gene analyses by qRT-PCR.; # marginal signal intensity; NCBI, National Center for Biotechnology Information; GB, GenBank.

To further screen potential direct targets, we compared the 27 candidate mRNAs with miR-21 targets predicted by TargetScan 5.1, miRBase Targets V.5, miRNAMap 2.0, PicTar and miRanda 3.0. Of the 27 mRNAs, 3 were recognized by the algorithms (Table 2). Because miR-21 targets are expected to up-regulated for the LNA-antimiR-21 samples, ANKRD46 and EIF4A2, the two up-regulated genes upon miR-21 knockdown in the two cell lines and predicted by target prediction programs, were selected for further investigation.

miR-21 directly targets ANKRD46in BC cells

The microarrays were validated by qRT-PCR assay. Consistent with the microarray results, qRT-PCR showed increased ANKRD46 and EIF4A2 mRNA levels in MCF-7 and MDA-MB-231 cell lines upon miR-21 inhibition, although the increase of EIF4A2 in MDA/LNA-antimiR-21 cells was relatively modest (Figure 4c). To determine whether miR-21 affects the expression of the potential endogenous target genes, we transfected MCF-7 and MDA-MB-231 cells with LNA-antimiR-21 or LNA-control. Western bolt showed that LNA-antimiR-21 led to up-regulation of endogenous ANKRD46 in both MCF-7 (P = 0.005) and MDA-MB-231 cells (P = 0.004), but no significant up-regulation of EIF4A2 protein (Figure 5c).
Figure 5

ANKRD46 is a direct target of miR-21 in BC cell lines. (a) Predicted alignment of miR-21 with the target site derived from ANKRD46 and EIF4A2 3' UTR, determined with the software miRBase Targets V5 and miRNAMap, respectively. Note the seed matches at the 5' end of miR-21 (grey boxes) and the mutated nucleotides (underlined). (b) Luciferase assays show that miR-21 directly repress ANKRD46 mRNAs through 3' UTR interactions. Part of the 3' UTRs of wild-type ANKRD46 (478-bp length) and EIF4A2 (194-bp length), or the mutations were cloned into pMIR-REPORT vector (Applied Biosystems), downstream of luciferase. These vectors were then cotransfected with synthetic miR-21 (pre-miR-21) or miR-control in 293T cells, and luciferase activity was quantified. The graph shows the percentage of remaining luciferase activity calculated by normalizing the miR-21 expression values on the miR-control values. (c) Western blot to assay ANKRD46 and EIF4A2 after miR-21 knockdown, with GAPDH as equal loading control, followed by densitometric analysis. Cells were treated and harvested as described in Figure 4b. Data in (b) and (c) are mean + SD (n = 3). * P < 0.05. WT, wild-type; Mut, mutant.

We further tested whether miR-21 could directly repress the identified mRNA targets through 3' UTR interactions (Figure 5a). Thus, the full-length 3' UTRs of the human genes ANKRD46 and EIF4A2 were cloned into the downstream of the luciferase gene (pMIR-REPORT), respectively. These vectors were then used to assess whether miR-21 could repress luciferase activity in 293T cells. ANKRD46 3' UTR showed a reduction to 54.8% of total luciferase reporter activity, in presence of miR-21, but EIF4A2 3' UTR did not display significant reduction of luciferase levels, compared with the miR-control (Figure 5b). These results suggest that miR-21 directly targets ANKRD46 in BC cells.

miR-21 and EIF4A2 proteins are inversely expressed in resected patient tumors in vivo

We examined ANKRD46 [NCBI: NP940683] and EIF4A2 [NCBI: NP001958] protein levels by IHC on TMAs constructed by the BC cases described in Materials and Methods. EIF4A2 was found in the cytoplasm, and ANKRD46 was seen in both the cytoplasm and nucleus (Figure 6a). ANKRD46 low expression was found in 47.5% (staining score < 4; median = 4); EIF4A2 low expression was found in 21.2% (staining score < 7; median = 7) of the 99 BC cases. Next, we investigated the negative regulation of endogenous EIF4A2 and ANKRD46 protein by endogenous miR-21 in vivo. In 99 successfully tested cases out of 113, endogenous miR-21 and EIF4A2 protein levels were inversely expressed in resected patient tumors (rs = -0.283, n = 99, P = 0.005, Spearman's correlation analysis). However, no significant association between miR-21 and ANKRD46 (P = 0.181, Spearman's correlation analysis) was observed.
Figure 6

EIF4A2 or ANKRD46 expression and survival in BC patients. (a) Representative TMAs sections stained for ANKRD46 and EIF4A2 from different BC. Examples for staining score 0 (negative), 3, 5 and 7 of marker expression are shown. All images were taken at × 200. (b) Kaplan-Meier survival curve and log-rank test for 99 BC patients showing five-year overall survival. ANKRD46 expression had no significant relationship to patient survival (P = 0.146). High EIF4A2 expression was associated with significantly improved OS (P = 0.044) in women with BC. TMAs, tissue microarrays; OS, overall survival.

Correlation of ANKRD46 and EIF4A2 expression with BC clinicopathological features and prognosis

Using Pearson's Chi-Square test, we found that, in BC tissues, IF4A2 protein correlated with CerbB2 status (P = 0.019), and ANKRD46 protein correlated with ER (P = 0.021) and PR (P = 0.001, Table 3). No significant correlation was observed between EIF4A2, ANKRD46, or other parameters. The five-year overall survival rate of the 99 BC patients was 59.60% (Figure 6b). The five-year survival rate in patients with high EIF4A2 protein level was 64.10% (n = 78), significantly higher than those with a low EIF4A2 protein level (42.86%, n = 21; P = 0.044, log-rank test; Figure 6b). The five-year survival rate in patients with high ANKRD46 protein was 53.85% (n = 52), which was not statistically different from those with low ANKRD46 protein (65.96%, n = 47; P = 0.146, log-rank test; Figure 6b).
Table 3

Correlation between target gene protein levels and clinicopathological parameters of 99 BC cases

Variable

EIF4A2

ANKRD46

 

Low (n = 21)

High (n = 78)

P*

Low (n = 47)

High (n = 52)

P*

Age (years)

      

   < 48

8

39

0.332

23

24

0.782

   ≥ 48

13

39

 

24

28

 

Pathologic grade

      

   I

2

20

0.115

14

10

0.221

   II, III

19

58

 

33

42

 

Clinical stage**

      

   I, II

15

61

0.514

41

37

0.051

   III

6

17

 

6

15

 

Lymph node status

      

   Metastasis

14

43

0.342

23

34

0.098

   No Metastasis

7

35

 

24

18

 

ER status

      

Negative

12

36

0.371

18

32

0.021

Positive

9

42

 

29

20

 

PR status

      

Negative

11

28

0.170

11

29

0.001

Positive

10

50

 

36

23

 

CerbB2 status

      

0,1+

17

41

0.019

29

18

0.832

2+,3+

4

37

 

31

21

 

*Two-sided Pearson Chi-Square Test; ** there were no stage IV patients because all the cases selected were surgical patients without neoadjuvant therapy to avoid the effect of the preoperative radiotherapy and/or chemotherapy on miRNAs; EIF4A2, eukaryotic translation initiation factor 4A2 protein; ANKRD46, ankyrin repeat domain 46 protein; ER, estrogen receptor; PR, progesterone receptor; CerbB2, v-erb-b2 erythroblastic leukaemia viral oncogene homolog 2 receptors.

Discussion

miR-21 is a key molecule in a wide range of cancers, and identifying its functional role in BC has direct clinical implications. We show here that knockdown of miR-21 suppresses cell growth and proliferation of MCF-7 cells in vitro, and suppresses MCF-7 xenograft growth. This result is consistent with the findings of Si et al. [9]. Interestingly, our study suggests that LNA-antimiR-21 also suppresses the growth and proliferation of MDA-MB-231 in vitro, in contrast to a recent report that found no effect of LNA-antimiR-21 on the growth of MDA-MB-231 in vitro or in vivo, although anti-miR-21-treated tumors were slightly smaller than control tumors [10]. One possibility could be differences in transfection efficiency, or miRNA ASO potency. Our results suggest that, as an oncomir, miR-21 also affects cell migration.

MCF-7 cells are hormone-sensitive and difficult to culture in vivo. Therefore, we used 17-estradiol to facilitate MCF-7 cells growth in nude mice, which is a common technique. Recently, estradiol was shown to down-regulate miR-21 expression in MCF-7 cells [32], although another study found estradiol-mediated up-regulation of miR-21 in MCF-7 cells [33]. In our study, the miR-21 knockdown effect was reduced from 5.72 log2-scale reduction before cell injection to 0.96 log2-scale reduction after mice sacrifice. Based on our results, we propose that estradiol reduced differences in miR-21 level between MCF/PNA-antimiR-21 and MCF/PNA-control cells, which would explain, in part, why differences in tumor weight between the two groups were not significance (P = 0.065). Nonetheless, treatment with anti-miR-21 reduced MCF-7 xenograft growth by approximately 68% for up to nine days. In vivo results suggested that the PNA-based miR-21 inhibitor had a subtle yet reproducible inhibitory effect on tumor growth. MCF-7 xenograft tumor sections demonstrated that miR-21 inhibition induced apoptosis of MCF-7 cells, confirming a previous study [9]. We also showed that miRNA inhibition can be achieved without transfection or electroporation of human BC cell lines, highlighting the potential of PNA for future therapeutic applications.

ANKRD46, also known as ankyrin repeat small protein (ANK-S), is a 228-amino acid single-pass membrane protein, of unclear function. For the first time, we identify miR-21 as an important regulator of ANKRD46 mRNA and protein levels in BC cells. Our data showed that miR-21 directly interacted with the ANKRD46 3' UTR and inhibited ANKRD46 expression, though there was no significant association between miR-21 and ANKRD46 in resected patient tumors. This discrepancy may be due to three reasons. First, the artificial luciferase reporter assays do not fully recapitulate miRNA regulation in vivo [34]; second, the expression of ANKRD46 protein in patient tumors reflected specific time-point feature, which maybe different to the in vitro subsequent increase of ANKRD46 protein at the time point of observation (the indicated hours after transfection); third, immunohistochemistry (IHC) is conventional a semi-quantitative method with relatively limited sensitivity. IHC may not be sensitive enough to observe the down-regulation of ANKRD46 by miR-21. Functional study of ANKRD46 is required in the future to determine weather ANKRD46 is a functional target of miR-21 in BC progression as demonstrated in this study.

EIF4A2, an ATP-dependent RNA helicase, is expressed widely in human tissues [35]. In this study, we found that miR-21 and EIF4A2 protein were inversely expressed in resected BC patient tumors. But we did not find miR-21 binding sites in the EIF4A2 3' UTR and found no significant increase of EIF4A2 protein upon miR-21 knockdown in MCF-7 and MDA-MB-231 cells, although EIF4A2 mRNA increased after anti-miR-21 transfection. Taken together, the data reported here suggest that there maybe unknown indirect interactions between miR-21 and EIF4A2 in BC progression. In adult mice, the expression of the two EIF4A isoforms is dependent on cell growth status, with EIF4A1 expressed in all tissues, while EIF4A2 is expressed only in tissues with a low rate of cell proliferation [36], indicating an anti-proliferative effect for EIF4A2. We for the first time revealed that low EIF4A2 expression correlated with low ERBB2 expression and poor survival of BC patients, suggesting its possible functional role in BC and urging further investigation.

Conclusions

We demonstrate that MCF-7 and MDA-MB-231 cells transfected with anti-miR-21 show growth inhibition in vitro and in vivo, as well as cell migration in vitro. In addition, ANKRD46 is newly identified as a direct target of miR-21 in BC. These results suggest that miR-21 inhibitory strategies using PNA-antimiR-21 may have potential for therapeutic applications in BC treatment.

Notes

Abbreviations

3' UTR: 

3' untranslated region

AJCC: 

American Joint Committee on Cancer

ANK-S: 

ankyrin repeat small protein

ASOs: 

antisense oligonucleotides

BC: 

breast cancer

CerbB2: 

v-erb-b2 erythroblastic leukaemia viral oncogene homolog 2 receptors

CISH: 

chromogenic in situ hybridization

DAPI: 

4',6-diamidino-2-phenylindole

EIF4A2: 

eukaryotic initiation factor 4A: isoform 2

ER: 

estrogen receptor

F: 

forward primer

FA: 

fibroadenoma

FISH: 

fluorescein in situ hybridization

FITC: 

fluorescein isothiocyanate

GEO: 

Gene Expression Omnibus

IHC: 

immunohistochemistry

L: 

length

LNA: 

Locked nucleic acid

miRNAs: 

microRNAs

MTT: 

3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide

Mut: 

mutation

NATs: 

normal adjacent tissues

NBT/BCIP: 

nitro blue tetrazolium/5-bromo-4-chloro-3-indolyl phosphate

NCBI: 

National Center for Biotechnology Information

OS: 

overall survival

PNAs: 

peptide nucleic acids

PR: 

progesterone receptor

qRT-PCR: 

quantitative reverse transcription-polymerase chain reaction

R: 

reverse primer

RQ: 

relative quantification

RT: 

reverse transcription primer

SABC-AP: 

alkaline phosphatase-conjugated strept-avidin-biotin complex

SD: 

standard deviation: SYSUCC: Sun Yat-sen University Cancer Center

TMAs: 

tissue microrrays

TNM: 

tumor-lymph node-metastasis

W: 

width

WT: 

wild-type.

Declarations

Acknowledgements

This work was supported in part by the National High Technology Research and Development Program of China (863 Program) (No. 20060102A4002), a research grant from State Key Laboratory of Oncology in Southern China, 985-II Project.

Authors’ Affiliations

(1)
State Key Laboratory of Oncology in Southern China, Sun Yat-Sen University Cancer Center
(2)
Department of Pathology, Sun Yat-Sen University Cancer Center
(3)
Department of Experiment Research, Sun Yat-Sen University Cancer Center

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