Long Noncoding RNASBF2-AS1 Promotes Gastric Cancer Progression via Regulating miR-545/EMS1 Axis.

OBJECTIVE: Long noncoding RNA (LncRNA) SBF2-AS1 was reportedly to function as an oncogene in several types of cancers, such as hepatocellular carcinoma, nonsmall cell lung cancer, glioma, and colorectal cancer. However, the biological roles and regulatory mechanisms of SBF2-AS1 in gastric cancer (GC) are unknown.
METHODS: The expression of SBF2-AS1 and miR-545 were examined in GC tissues and cell lines via real-time quantitative PCR. The relationship of SBF2-AS1 with miR-545 was verified via dual-luciferase reporter gene assay and RNA immunoprecipitation. The influences of SBF2-AS1 on cell proliferation, migration, and invasion were determined using cell counting Kit-8 (CCK-8), wound healing, and transwell invasion assays, respectively.
RESULTS: LncRNA SBF2-AS1 expression was upregulated in GC tissues, especially in advanced clinical stage cases. Moreover, increased SBF2-AS1 indicated a poor survival rate. Functionally, the downregulation of SBF2-AS1 by siRNA in GC cells suppressed the proliferation, migration, and invasion. In terms of mechanism, SBF2-AS1 can directly bind to miR-545 and regulate its expression. Moreover, SBF2-AS1 knockdown significantly decreased the expression of EMS1, which was the direct target of miR-545. Importantly, inhibition of miR-545 or overexpression of EMS1 partially reversed SBF2-AS1-depletion-caused suppression on proliferation, migration, and invasion.
CONCLUSION: These findings elucidated a crucial role of SBF2-AS1 as a miR-545 sponge in GC cells, suggesting that SBF2-AS1 might be a potential target for GC.

1. Introduction

Gastric cancer (GC) is the fourth most commonly malignant with a high global morbidity [1]. Although morbidity and mortality of patients diagnosed in the early stage had been decreased by surgical techniques, chemo/radiotherapy, the survival rate of patients with advanced GC remains poor due to tumor metastasis, and drug resistance [2]. Therefore, it is important to elucidate the mechanism of gastric carcinogenesis for finding novel diagnosis and therapy for GC.

Long noncoding RNAs (lncRNA) are a class of sequences over 200 nucleotides in length without protein-coding potential, instead of regulating various cellular processes, such as cell proliferation, differentiation, apoptosis, and invasion [3, 4]. LncRNAs were reported to be involved in tumor initiation and development and play an oncogenic or tumor-suppressive role in various cancers [5, 6]. Many lncRNAs were confirmed to implicate in GC progression and can serve as molecular markers for early diagnosis and therapeutic agent for treatment GC [7, 8].

SBF2 antisense RNA 1 (SBF2-AS1), located at the 11p15.1 locus, has been shown to play critical roles in tumor progression and function as an oncogene in several types of cancers, such as nonsmall lung cancer, cervical cancer, glioblastoma, colorectal cancer, esophageal squamous cell carcinoma, and hepatocellular carcinoma [9-14]. Although a study showed that SBF2-AS1 expression was upregulated in GC tissues [15], the roles and underlying mechanisms of SBF2-AS1 in GC remain largely unknown and need investigation. To this end, the aims of this study were to examine the expression and functional role of SBF2-AS1 in the progression and development of GC and to identify the molecular mechanism of SBF2-AS1 involved in GC progression.

2. Materials and Methods

2.1. Clinical Samples

Sixty pairs of human GC samples and normal adjacent gastric tissues were harvested at the First Hospital of Jilin University, and detail information of the patients were listed in Table 1. All samples were immediately frozen in liquid nitrogen confirmed by two pathologists after informed consent was signed by all patients. Patients who received preoperative chemo/radiotherapy was excluded. All of the experiments of this study were approved by the Institutional Ethics Committee of the hospital and were conducted based on the Declaration of Helsinki.

Table 1

Correlation between clinicopathological features and SBF2-AS1 expression in 60 patients with gastric cancer.

Variables	No. of cases	SBF2-AS1 expression		P value
		High (n %)	Low (n %)
Age (years)				P = 0.589
<60	22	11	11
≥60	38	23	15
Gender				P = 0.1928
Male	36	23	13
Female	24	11	13
TNM stage				P = 0.0147
I-II	46	22	24
III-IV	14	12	2
Tumor size				P = 0.1639
<5 cm	41	26	15
≥5 cm	19	8	11
Distant metastasis				P = 0.008
No	48	23	25
Yes	12	11	1

2.2. Cell Culture and Transfection

Gastric epithelial cell line GES1 and four human cell lines (MKN45, BGC823, MGC803, and SGC7901) were derived from Shanghai Institutes for Biological Science (Shanghai, China). All cells were cultured in the DMEM (Hyclone, Logan, UT, USA) supplemented with 10% fetal bovine serum (FBS; Gibco, NY, USA) at 37°C in a humidified chamber with 5% CO2.

Three small interfering RNA (siRNA) against SBF2-AS1 (si-SBF2-AS21#1, si-SBF2-AS21#2 and si-SBF2-AS21#3) and nontarget siRNA control (si-NC) were bought from GenePharma (Shanghai, China). Overexpression EMS1 plasmid was granted from Dr. Xue Wang(China Medical University). The miR-545 mimics, negative control mimics (miR-NC), and miR-545 inhibitor (anti-miR-545) were obtained from Ribobio (Guangzhou, China). SGC7901 cells were transfected the abovementioned siRNA, plasmid, mimics, or inhibitor using Lipofectamine 3000 (Life Technologies) (Invitrogen, USA), as per manufacturer's instructions.

2.3. RNA Isolation and qRT-PCR

Total RNA was extracted from cultured cells, GC tissues or adjacent normal gastric tissues using Trizol reagent (Thermo Fisher Scientific, Carlsbad, CA, USA). RNA samples were reversely transcribed into complementary DNA using PrimeScript RT.

Master Mix (Takara, Dalian, China) or TaqMan MicroRNA Reverse Transcription kit (Thermo Fisher Scientific), then was quantified using SYBR Select Master Mix (Applied Biosystems, Foster City, CA) or TaqMan microRNA assays kits (Thermo Fisher Scientific) under a 7900HT fast real-time PCR system (Applied Biosystems). Table 2 listed all primes used in this study. The relative expression levels were calculated using a method (2–∆∆Ct) following normalization against U6 for miR-545 or GAPDH for SBF2-AS1 mRNAs.

Table 2

Real-time PCR primers used in this study.

Target gene	Prime(5′-3′)
U6	F: TCCGATCGTGAAGCGTTCR: GTGCAGGGTCCGAGGT
miR-545	F: TCAGTAAATGTTTATTAGATGAR: GTGCAGGGTCCGAGGTATTC
SBF2-AS1	F: CACGACCCAGAAGGAGTCTACR: CCCGGTACCTTCCTG TCATA
EMS1	F: AGCCGTCGCCCTGTACGACTR: GTACCGGCCCTTGCACACCC
GAPDH	F: AAGGTGAAGGTCGGAGTCAAR: AATGAAGGGGTCATTGATGG

F: forward; mRNA: messenger RNA; PCR: polymerase chain reaction; R: reverse.

2.4. Cell Proliferation Assay

Cell proliferation was assessed by Cell Counting Kit-8 assay (CCK8, Promega, Madison, WI, USA) assay. Briefly, the transfected cells (5000 cells per well) were seeded in 96-well plates and grown at 37°C and 5% CO2 atmosphere for 24 h-72 h. In specific time (24 h, 48 h, and 72 h), 20 μl of CCK8 solution was added to each well and cultured another for 4 h. The absorbance at 450 nm was recorded using a microplate reader (Bio-tek, USA).

2.5. Wound Healing Assays

Transfected cells were suspended and seeded into in 12-wells plates. After the cells attached to the bottom and formed a monolayer, linear wounds were scratched at the center of the monolayer using a pipette tip. After washed off with PBS thrice, cells were cultured in a free-serum medium for 24 h. The wounds were photographed at 0 h and 24 h under a microscope (Olympus, Japan), and the widths of each scratch wound were recorded.

2.6. Cell Invasion Assay

Transwell inserts (Corning, NY, USA) were applied to examine invasion assay in vitro. Transfected cells were resuspended in 100 μl FBS-free medium at a final density of 1 × 106 cells/ml and seeded into the upper chambers of transwell inserts precoated with Matrigel (BD, San Jose, CA, USA). The lower chambers were filled with 600 μl medium containing 20% FBS. After incubation at 37°C for 48 h, invaded cells on the lower surface of the transwell membrane were fixed with 20% methanol and stained with 0.1% crystal violet. The invaded cells were imaged and recorded in five randomly selected fields using a light microscope equipped with a digital camera (Olympus Corporation, Tokyo, Japan).

2.7. Bioinformatics Prediction and Luciferase Reporter Assay

A publicly available algorithm (StarBase v2.0) was used to predict SBF2-AS1 that interact with miRNAs. The sequence of SBF2-AS1 containing a putative binding site of miR-545 was synthesized and inserted into the luciferase-reporter psiCHECK2 vector (Promega, Madison, WI, USA) and named as WT-SBF2-AS1. The putative binding site of SBF2-AS1 was mutated using a QuikChange XL Site-Directed Mutagenesis kit (Agilent Technologies, Santa Clara, CA, USA) and named MT-SBF2-AS1. For luciferase reporter assay, SGC7901 cells were cotransfected with WT/MT SBF2-AS1 and miR-545/miR-NC using Lipofectamine 3000. The luciferase activity was determined at 48 h post-transfection using the Dual-luciferase Reporter Assay System (Promega) as per manufacturer's instructions.

2.8. RNA Immunoprecipitation (RIP) Assay

RIP was carried out using the EZMagna RIP kit (Millipore, Billerica, MA, USA) based on provided instructions. SGC7901 cells were harvested and lysed in complete RIP lysis buffer. Then, whole cell extract was incubated with RIP buffer containing magnetic beads conjugated with Ago2 antibody (Abcam, USA) and normal mouse IgG (as a control) according to the manufacturer's protocol. After the beads were washed with wash buffer, the protein was removed using Proteinase K (30 min at 55°C). Purified RNA was subjected to qRT-PCR analysis to demonstrate the presence of SBF2-AS1 and miR-545.

2.9. Statistical Analysis

All results were expressed as mean ± standard deviation (SD) from at 3 replicates measurements and were analyzed using version 19 SPSS statistical software (SPSS, Chicago, IL, USA). Differences between groups were analyzed using the Student's t test or one-way analysis of variance (ANOVA). Spearman's correlation coefficient was used to assess correlations with SBF2-AS1, EMS1, and miR-545. Kaplan-Meier method and log-rank test were used to the analysis survival time of the patients. A statistically significant difference was defined as follows: ∗P < 0.05, ∗∗P < 0.01.

3. Results

3.1. SBF2-AS1 Is Upregulated in GC Tissues and Cell Lines

To explore the functional role of SBF2-AS1 in the progression of GC, the expression of SBF2-AS1 in GC tissues and cell lines was examined by qRT-PCR. As shown in Figure 1(a), SBF2-AS1 expression was significantly upregulated in clinical GC samples compared with the normal adjacent gastric tissues. When compared with the normal human gastric epithelial cell line GES1, all four human cell lines (MKN45, BGC823, MGC803, and SGC7901) showed higher expression of SBF2-AS1 (Figure 1(b)), with the highest expression found in SGC7901 cells; thus, it was selected for all subsequent experiments. These results suggested that SBF2-AS1 may play a role in promoting the development and progression of GC.

Figure 1

SBF2-AS1 is upregulated in GC tissues and cell lines. (a) The expression level of SBF2-AS1 in GC tissues and adjacent normal gastric tissues was measured by qRT-PCR. (b) The expression level of SBF2-AS1 was measured in human gastric epithelial cell line GES1 and four human cell lines (MKN45, BGC823, MGC803, and SGC7901) by qRT-PCR. (c) Kaplan-Meier overall survival curves were established based on the SBF2-AS1 expression levels. ∗P < 0.05 and ∗∗P < 0.01.

3.2. Increased SBF2-AS1 Is Associated with TNM Stage and Poor Prognosis of GC

To further explore the significance of SBF2-AS1 overexpression in GC, we examined the correlation between SBF2-AS1 expression and clinical-pathological features. The 60 gastric cancer patients were divided into two groups based on the mean of relative SBF2-AS1 expression (7.1) in GC tissues: high SBF2-AS1 group (n = 34, HOXA-AS2 expression ≥7.1) and low SBF2-AS1 group (n = 26, SBF2-AS1 expression <7.1). As shown in Table 1, SBF2-AS1 was positively correlated with the advanced TNM stage and distant metastasis of GC. But SBF2-AS1 expression was independent of the gender and age of GC patients and the tumor size (Table 1, All P > 0.05). Moreover, patients with high SBF2-AS1 expression had poorer overall survival compared with a patient with low SBF2-AS1 expression (P < 0.001) (Figure 1(c)). These results imply that SBF2-AS1 may serve as a novel prognostic marker for GC.

3.3. Knockdown of SBF2-AS1 Inhibits GC Cell Proliferation, Migration and Invasion

To investigate the functional role of SBF2-AS1 in GC cells, we designed three different SBF2-AS1 siRNAs to transfect SGC7901. qRT-PCR analysis was performed at 48 h posttransfection and revealed that si-SBF2-AS1#1 had higher efficiency of interference than that in si-SBF2-AS1#2 and si-SBF2-AS1#3 (Figure 2(a)), so we chose si-SBF2-AS1#1 (also called si-SBF2-AS1) subsequently for the following experiments. CCK8 assays showed that SBF2-AS1 depletion significantly inhibited cell proliferation of SGC-7901 cells (Figure 2(b)). Wound healing assay revealed that knockdown of SBF2-AS1 significantly decreased the migratory ability of SGC7901 cells compared with the si-NC group (Figure 2(c)). In addition, the invasion of SGC7901 cells was also suppressed by SBF2-AS1 knockdown when compared with the si-NC group, as determined by Transwell invasion assay (Figure 2(d)). These results implied that knockdown of SBF2-AS1 inhibits GC progression.

Figure 2

Knockdown of SBF2-AS1 inhibits GC cell proliferation, migration, and invasion. (a) The expression of SBF2-AS1 was examined in SGC-7901 cells transfected with si-NC, si-SBF2-AS1#1, si-SBF2-AS1#2, or si-SBF2-AS1#3 by qRT-PCR. (b-d) Cell proliferation, migration, and invasion were determined in SGC7901 cells transfected with si-NC or si-SBF2-AS1 by CCK8, wound healing and transwell invasion assays. ∗P < 0.05 and ∗∗P < 0.01.

3.4. SBF2-AS1 Interacts with miR-545 in GC Cells

Given that lncRNA-miRNA interactions implicated in the functional role of lncRNAs in cancer, the potential miRNA that interacts with SBF2-AS1 was explored using the Starbase2.0 software. miR-545 was found to have putative binding sites indicated in Figure 3(a). Importantly, dual-luciferase reporter assay confirmed that overexpression of miR-545 by transfection with miR-545 mimic obviously decreased the luciferase activity of the reporter containing WT-SBF2-AS1, rather than MT-SBF2-AS1 in SGC7901 cells (Figure 3(b)). To further assess if SBF2-AS1 and miR-545 interact in a manner that is dependent upon Ago2, RIP was performed and revealed that SBF2-AS1 and miR-545 to be preferentially enriched among Ago2-containing microribonucleoproteins (Figure 3(c)). Moreover, we found that silencing SBF2-AS1 significantly increase miR-545 expression (Figure 3(d)), whereas overexpression of miR-545 declined SBF2-AS1 expression in SGC7901 cells (Figure 3(e)). In addition, we also investigate the relationship with SBF2-AS1 and miR-545 in GC tissues and found that there is a negative correlation between SBF2-AS1 and miR-545 expression in GC tissues by the Spearman's correlation test (r = −0.383, P = 0.003; Figure 3(f)).

Figure 3

SBF2-AS1 directly interacts with miR-545 in GC cells. (a) The predicted miR-545 binding sites in SBF2-AS1 (WT-SBF2-AS1) and the designed mutant sequence (MT-SBF2-AS1) were shown. (b) Luciferase reporter assay was examined in SGC7901 cells cotransfected with WT/MT-SBF2-AS1 and miR-NC/miR-545 mimic. (c) The interaction between miR-545 and SBF2-AS1 was determined in SGC7901 with RIP assay. (d) The expression of miR-545 was determined in SGC7901 cells transfected with si-NC or si-SBF2-AS1 by qRT-PCR. (e) The expression of SBF2-AS1 was measured in SGC7901 cells transfected with miR-NC and miR-545 mimic. (f) The correlation between SBF2-AS1 and miR-545 was analyzed by Spearman's correlation analysis. ∗P < 0.05, ∗∗P < 0.01.

3.5. SBF2-AS1 Depletion Inhibits GC Progression by Regulating miR-545/EMS1 Axis

EMS1 was identified as a direct target of miR-545 in GC. As both SBF2-AS1 and EMS1 are direct miR-545 targets, we next tested whether they competed for binding to miR-545. We found that knockdown of SBF2-AS1 significantly decreased EMS1 expression in SGC-7901 cells, while transfection of miR-545 inhibitor or EMS1 plasmid partially reversed this trend (Figure 4(a)). In addition, we found that EMS1 expression was increased in GC tissues, and its expression was positively correlated with SBF2-AS1 (Figure 4(b)) and negatively correlated with miR-545 (Figure 4(c)). To determine whether SBF2-AS1 depletion-mediated inhibitory effects on GC cells were indeed through targeting miR-545/EMS1, a rescue experiment was performed in SGC7901 cells transfected with si-NC, si-SBF2-AS1, si-SBF2-AS1+miR-545 inhibitor (anti-miR-545) or si-SBF2-AS1+overexpression EMS1 plasmid. As shown in Figure 4(a), the increased miR-545 expression resulted by SBF2-AS1 knockdown was reserved by miR-545 inhibitor. Additionally, the decreased capacity of cell proliferation, migration, and invasion mediated by SBF2-AS1 depletion in SGC7901 cells was partially abrogated by inhibition miR-545 or EMS1 overexpression (Figure 4(d)–4(f)).

Figure 4

SBF2-AS1 depletion inhibits GC progression by regulating miR-545 axis. (a) The expression level of EMS1 was measured by qRT-PCR in SGC7901 cells transfected with si-NC, si-SBF2-AS1, si-SBF2-AS1+miR-545 inhibitor (anti-miR-545), or si-SBF2-AS1+EMS1. (b) The correlation between EMS1 and SBF2-AS1 was analyzed by Pearson's correlation analysis. (c) The correlation between EMS1 and miR-545 was analyzed by Pearson's correlation analysis. (d-f) Cell proliferation, migration, and invasion were determined in SGC7901 cells transfected with si-NC, si-SBF2-AS1, si-SBF2-AS1+anti-miR-545, or si-SBF2-AS1+EMS1. ∗P < 0.05, ∗∗P < 0.01.

4. Discussion

A body of evidence suggested that lncRNAs play crucial roles in carcinogenesis and development of human GC and function as a tumor suppressor or oncogene [16, 17]. Therefore, exploring the biological role of lncRNAs and clinical significance may contribute to find diagnosis and prognosis maker and therapy target for this malignancy. LncRNA SBF2-AS1 has been reported to be involved in occurrence and development in several types of cancers [10-14]. However, the expression level and biological role of SBF2-AS1 in GC remains largely unclear. In the present study, we examined the expression levels of SBF2-AS1 in GC tissues and cell lines and found that the expression of SBF2-AS1 was upregulated in GC tissues and cell lines compared with adjacent normal tissues and normal gastric epithelial cell line GES1, which was consistent with previous result [15]. In particular, patients with advanced TNM stages or distant metastasis had a high expression of SBF2-AS1. Importantly, the high expression of SBF2-AS1 indicated poor overall survival of patients with GC. These results implied that HOXA-AS2 may be a potential clinical marker in GC prognosis.

To explore the biological function of SBF2-AS1 in GC progression, loss-of-function assay we performed in SGC7901 cells. Our results revealed that knockdown of SB2-AS1 resulted in significant inhibition of cell proliferation, migration, and invasion in SGC7901 cells. These data indicated that SBF2-AS1 depletion suppressed the progression of GC and SBF2-AS1 may function as an oncogene in GC.

LncRNA exerts its role in cancers by acting as competing endogenous RNAs (ceRNAs) to absorb miRNA, leading to affect the biological role of miRNA in cancer [18, 19]. SBF2-AS1 has been reported to function as ceRNA sponging multiple miRNA, such as miR-188-5p [20], miR-619-5p [12], miR-361-5p [10], and miR-140-5p [21]. Here, we select miRNAs that interact with SBF2-AS1 through starbase2.0. Among miRNAs, we selected miR-545 as an object base on its biological function in cancers [22-24]. MiR-545, a known tumor suppressor, has been reported to be downregulated in multiple cancers including gastric cancer [25]. We further verified that SBF2-AS1 could directly bind to miR-545 and serve as a miR-545 sponge in GC cells via luciferase reporter activity and RIP assays. In addition, we also found that there is a negative correlation between SBF2-AS1 and miR-545 expression in GC tissues (r = −0.383, P = 0.003). Importantly, the decreased capacity of cell proliferation, migration, and invasion mediated by SBF2-AS1 depletion was partially abrogated by miR-545 inhibitor. These results implied that SBF2-AS1 functioned as a ceRNA for sponging miR-545.

Growing evidence indicated that lncRNAs can serve as critical elements of the ceRNA network via binding miRNAs to regulate target gene expression of miRNAs [18, 19]. EMS1 was confirmed as a target of miR-545 in GC progression [25]. EMS1 has been reported to function as an oncogene that promotes tumorigenesis and metastasis via impacting on proliferation, migration, and invasion in multiple tumor cells including GC [25, 26]. Here, our result demonstrated that SBF2-AS1 could indirectly regulate the expression of EMS1 by way of sponging to miR-545. The tumor-suppressive effect of SBF2-AS1 depletion was able to be restored by overexpression of EMS1 in GC cells. Moreover, EMS1 was found to be upregulated and positively associated with SBF2-AS1 expression in CRC tissues, as well as negatively correlated with miR-545 in CRC cells. These results suggested that SBF2-AS1 exerted an oncogenic role in human GC progression by regulating miR-545/EMS1 expression.

Some limitations exist in this study. First, enough GC samples are needed to further investigate the clinical significance of SBF2-AS1. Second, in vivo experiments need to be performed to clarify the SBF2-AS1 role in GC growth and metastasis. Third, lncRNA could target multiple miRNA or mRNA; thus, the detailed regulatory mechanisms of SBF2-AS1 on GC progression should be further explored in future research.

In conclusion, the present study demonstrated that SBF2-AS1 was upregulated in GC tissues and cell lines and was associated with poor prognosis. SBF2-AS1 may function as a ceRNA sponging for miR-545, which consequently contributed to promote GC cell proliferation and invasion. These findings indicated that SBF2-AS1 may serve a potential therapeutic target for GC treatment.