Critical role for the long non-coding RNA AFAP1-AS1 in the proliferation and metastasis of hepatocellular carcinoma.

Increasing evidence has indicated that dysregulation of long non-coding RNAs (lncRNAs) can contribute to the progression and metastasis of human cancer, including HCC. Previous studies have shown that the lncRNA AFAP1-AS1 plays a critical role in cancer. However, the roles of AFAP1-AS1 in HCC remain to be determined. In the present study, AFAP1-AS1 was found to be increased in HCC tissues, and high AFAP1-AS1 expression was associated with tumor size, TNM stage, vascular invasion, and poor prognosis. Silencing of AFAP1-AS1 significantly reduced cell proliferation, clonal growth, cell migration, and invasion and increased apoptosis in vitro. Furthermore, AFAP1-AS1 silencing markedly reduced tumor growth in a murine allograft model in vivo. The results suggested that AFAP1-AS1 is important in HCC development and serves as a therapeutic target of HCC.

Introduction

Hepatocellular carcinoma (HCC) is the sixth most common diagnosed cancer and the third leading cause of cancer death in the world [1, 2]. Although advances in treatment have been made in HCC in the past decades, surgical resection and liver transplantation are the primary effective approaches to treat HCC, and the overall 5-year survival rate of HCC patients remains very poor due to its advanced tumor stages at the time of diagnosis [3, 4]. Increasing evidence has shown that several genetic or epigenetic alterations contribute to tumorigenesis, and unrestricted cell growth and invasion are the most two key traits of HCC [5-7]. However, limited information is available regarding how to improve the probability of survival. Therefore, a better understanding of the mechanisms of key genes that can be used to provide novel therapeutic strategies is urgently needed for patients with HCC.

Emerging evidence has suggested that non-coding RNAs (ncRNAs) play an essential role in various physiological and pathological processes, including cell proliferation, differentiation, apoptosis, invasion, metabolism, developmental timing, and immune responses [8]. lncRNAs, functional RNA molecules larger than 200 nucleotides in length have been shown to exert their functions as oncogenes or tumor suppressors, and their aberrant expression contributes to carcinogenesis [9-11]. For example, lncRNA GAS5 has been shown to be significantly downregulated in HCC tissues, and the overexpression of GAS5 suppresses HCC cell migration and invasion through negatively regulating the expression of miR-21 [12]. lncRNA HOTAIR has been reported to be upregulated in breast cancer, pancreatic cancer, non-small cell lung cancer, and gastric cancer, and high HOTAIR expression is associated with poor prognosis [13-16].

Previous studies have shown that AFAP1-AS1 is upregulated in esophageal adenocarcinoma, pancreatic ductal adenocarcinoma, lung cancer, and nasopharyngeal carcinoma, and high AFAP1-AS1 expression is associated with lymph node metastasis, perineural invasion, and poor survival [17-20]. However, little is known concerning the potential role of AFAP1-AS1 in the development and progression of HCC. In the current study, we detected the expression of AFAP1-AS1 in HCC and found that AFAP1-AS1 was dramatically increased in HCC tissues compared with matched normal tissues. High AFAP1-AS1 expression was correlated with poor clinicopathological features and poor outcome in HCC patients. Further functional studies of AFAP1-AS1 suggested that knockdown of AFAP1-AS1 could decrease cell proliferation in vitro and in vivo.

Materials and methods

Patients and tissue specimens

HCC tissues and normal tissues were obtained from 156 patients who had undergone surgical resection of HCC between April 2008 and February 2011 at The First Affiliated Hospital of Zhengzhou University, China. No chemotherapy or radiotherapy treatment had been administered to these patients prior to surgery. All collected specimens were immediately frozen in liquid nitrogen and stored at −80 °C until RNA extraction. Tumors and noncancerous tissues were confirmed using histological diagnoses by two experienced pathologists. Written informed consent was obtained from the patients, and this study was approved by the research ethics committee of The First Affiliated Hospital of Zhengzhou University.

Cell lines and cell culture

Non-malignant liver cells (LO2), the human embryonic kidney cell line 293 T, and human hepatoma cell lines (SMMC-7721, Bel-7402, MHCC-97 L, and MHCC-97H) were obtained from Shanghai Cell Bank of the Chinese Academy of Sciences (Shanghai, China). All of the cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM; Hyclone, Logan, UT, USA) supplemented with 10 % fetal bovine serum (Invitrogen, Grand Island, NY, USA) and 1 % penicillin G and streptomycin in 37 °C humidified air containing 5 % CO2.

RNA isolation and quantitative real-time polymerase chain reaction (qRT-PCR)

Total RNA was isolated from tissues and cells using Trizol Reagent (Invitrogen) according to the manufacturer’s protocol. RNA concentration and integrity were determined using the NanoDrop2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and standard RNA gel electrophoresis. Real-time PCR was performed using SYBR®Green (TaKaRa, Dalian, China) and the ABI Prism 7900 Sequence Detection System (Applied Biosystems, Foster City, CA, USA) according to the manufacturer’s protocol. The primers used were as follows: AFAP1-AS1, forward 5′-TCGCTCAATGGAGTGACGGCA-3′ and reverse 5′-CGGCTGAGACCGCTGAGAACTT-3′; GAPDH, forward 5′- CACCCACTCCTCCACCTTTG-3′ and reverse 5′- CCACCACCCTGTTGCTGTAG-3′. The fold-change for AFAP1-AS1 was normalized to GAPDH.

Lentiviral infection

Lentivirus-mediated suppression of human AFAP1-AS1 was constructed as previously described [19]. Lentivirus packaging and cell transduction were carried out as previously described [21].

Immunohistochemical staining

Standard immunohistochemical procedures were performed using anti-Ki67 polyclonal antibody (ab66155; Abcam) as previously described [21].

Cell proliferation and clone formation assay

For the cell proliferation assay, 2 × 103 cells in 100 μL of complete culture were seeded in 96-well culture plates with five replicate wells. Next, 10 μL of CCK-8 (Dojindo, Kumamoto, Japan) was added to each well at 24, 48, 72, and 96 h and incubated at 37 °C for another 2 h. The absorbance was measured at 450 nm using a Multiskan® Spectrum system (Thermo Fisher Scientific).

For the clone formation assay, 600 cells were plated into 6-well plates and were maintained in media containing 10 % FBS with the medium being replaced every 3 days. Colonies were fixed with methanol and stained with 0.1 % crystal violet 2 weeks later. The visible colonies were photographed and manually counted.

Apoptosis assay

Flow cytometry was performed to determine the apoptotic rate. Cells were harvested and washed three times with phosphate-buffered saline. Staining with Annexin V-PE and Propidium iodide (PI) was performed using the PE annexin V apoptosis detection kit (BD Pharmingen, San Diego, CA, USA) according to the manufacturer’s recommendations, and the cells were then analyzed using a Cytomics FC-500 flow cytometer (Beckman Coulter, Inc., Fullerton, CA, USA).

Wound healing assay

Cells were plated onto in 6-well plates and cultured to 80 % confluence. Wounds were created with a sterilized pipette tip, and the detached cells were washed off thrice with PBS. Images were taken at 0 and 36 h after the scratching using digital microscopy.

Cell migration and invasion assays

Cell migration and invasion were performed as we have previously described [21]. Briefly, 5 × 104 MHCC-97 L or MHCC-97H cells transduced with si-AFAP1-AS1 or the respective control were added to the upper chamber of an insert coated with or without Matrigel (BD Biosciences, San Jose, CA, USA). Cell migration was allowed to proceed at 37 °C for 24 h, and cell invasion was allowed to occur at 37 °C for 48 h. After removing the cells on the inner surface of the filter membrane with a sterile cotton swab, cells were stained with 0.1 % crystal violet, imaged, and counted using digital microscopy.

Western blotting

Western blot assays were performed as we previously described [21]. The membranes were incubated with anti-BCL-2 antibody (#2876), anti-Bax antibody (#2772), anti-MMP-9 antibody (#3852), and anti-GAPDH antibody (#2118), all from CST (Cell Signaling Technology, Danvers, MA, USA), and subsequently, with the appropriate horseradish peroxidase-conjugated secondary antibody (Beyotime, Zhejiang, China).

Tumorigenicity in nude mice

The animal experiments were approved by the Committee on the Ethics of Animal Experiments of Zhengzhou University. This study was performed in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. MHCC-97H cells (1 × 107 cells) transduced with the negative control (Scramble) or siAFAP1-AS1 were injected into the flanks of 4-week-old nude mice. The tumor size was measured using hand calipers every week. All of the mice were sacrificed 5 weeks after inoculation. The tumor tissues were removed from each mouse, weighed, imaged, embedded in 10 % paraffin, and subjected to IHC staining.

Statistical analysis

Statistical analyses were performed using SPSS 17.0 software (SPSS Inc., Chicago, IL, USA). All of the data were expressed as the means ± SD (standard deviation), and Student’s t test was used to analyze the differences between two groups. The correlation between AFAP1-AS1 expression and clinicopathological features was evaluated using Pearson χ2 test. The Kaplan-Meier method was performed to evaluate the survival rate in patients with HCC. A P value less than 0.05 was regarded as statistically significant.

Results

AFAP1-AS1 is significantly increased in HCC samples and HCC cell lines

AFAP1-AS1 expression levels in 156 HCC tissue samples and 156 matched normal liver tissue samples were examined by quantitative real-time PCR. AFAP1-AS1 levels in cancer samples were significantly higher than those in the noncancerous samples (P < 0.001; Fig. 1a). Furthermore, qRT-PCR was performed to detect the expression of AFAP1-AS1 in diverse HCC cell lines and a non-malignant liver cell line. As shown in Fig. 1b, the AFAP1-AS1 expression level was significantly increased in HCC cell lines compared with a non-malignant liver cell line (LO2). These results suggested that AFAP1-AS1 might function as an oncogene in HCC.

Fig. 1

AFAP1-AS1 expression is increased in human HCC tissues and cell lines. a The relative expression of AFAP1-AS1 was detected in 156 pairs of primary HCC tissues and their corresponding adjacent tissues. b qRT-PCR analysis was performed to assess the AFAP1-AS1 levels in HCC cells (SMMC-7721, BEL-7402, MHCC-97 L, and MHCC-97H) and LO2. *P < 0.05 and **P < 0.01

Association between AFAP1-AS1 expression and clinicopathological features in HCC

To understand the significance of AFAP1-AS1 overexpression in HCC, we explored the associations between AFAP1-AS1 expression and the patients’ clinicopathological features (Table 1). There was a significant association between AFAP1-AS1 expression and tumor size (P = 0.012), vascular invasion (P = 0.035), and TNM stage (P = 0.01). However, AFAP1-AS1 expression was not associated with other parameters such as age, gender, or liver cirrhosis in HCC patients. Furthermore, according to the median AFAP1-AS1 expression in tumor tissues, the patients were classified into the high AFAP1-AS1 expression group (n = 78) or relative low AFAP1-AS1 expression group (n = 78). The patients with lower AFAP1-AS1 expression had better overall survival (OS) and disease-free survival (DFS) (Fig. 2a, b). These results indicated that AFAP1-AS1 might be a potential prognostic biomarker for HCC patients.

Table 1

Correlation between AFAP1-SA1 expression and the clinicopathological features in HCC patients

Variables	AFAP1-SA1expression level
	Low	High	P value
	n = 78	n = 78
Gender 0.495a
Female	6	3
Male	72	75
Age, y 0.423
≤51	41	36
>51	37	42
Liver cirrhosis 0.375
No	10	14
Yes	68	64
Tumor size 0.012
≤5 cm	64	50
>5 cm	14	28
Tumor number 0.598
Single	69	71
Multiple	9	7
Tumor envelope 0.1997
Yes	45	36
No	33	42
TNM stage 0.010
I	27	13
II/III	51	65
Preoperative AFP (ng/mL) 0.144
≤20	37	28
>20	41	50
Vascular invasion 0.035
No	52	38
Yes	26	40
ALT (units/L) 0.575
≤75	70	72
>75	8	6

ALT alanine aminotransferase, TNM tumor-node-metastasis,

aFisher’s exact tests and Χ 2 tests for all other analyses

Fig. 2

Kaplan-Meier analysis of HCC survival rates in relation to AFAP1-AS1 expression. The overall survival a and disease-free survival b rates of HCC patients with high (n = 78) and low (n = 78) levels of AFAP1-AS1 expression. The P values were determined using the log-rank test

Knockdown of AFAP1-AS1 inhibits HCC cell proliferation in vitro

To explore the biological significance of AFAP1-AS in HCC, we transfected lentivirus-mediated siRNA into MHCC-97 L and MHCC-97H cells, which had high endogenous AFAP1-AS levels. As shown in Fig. 3a, the expression of AFAP1-AS was significantly decreased compared with that of the negative control (SCR). Cell proliferation assays were performed to investigate the effect of AFAP1-AS on cell viability using the CCK-8 assay. Our results showed that knockdown of AFAP1-AS expression significantly suppressed cell growth in MHCC-97 L and MHCC-97H cells compared with that in the respective controls (Fig. 3b). Furthermore, colony formation assays showed that downregulation of AFAP1-AS could significantly inhibit colony formation in MHCC-97 L and MHCC-97H cells (Fig. 3c). In addition, AFAP1-AS silencing induced an increase in the apoptosis levels using the Annexin V Apoptosis Assay (Fig. 3d). These data suggest that AFAP1-AS plays a critical role in HCC cell proliferation in vitro.

Fig. 3

Knockdown of AFAP1-AS1 decreases HCC cell proliferation in vitro. a qRT-PCR was performed to detect the expression of AFAP1-AS1 in MHCC-97 L and MHCC-97H cells transduced with SCR or siAFAP1-AS1. The effects of knockdown of AFAP1-AS1 in cells on cell proliferation b colony formation c and apoptosis d were examined. *P < 0.05 and **P < 0.01

Knockdown of AFAP1-AS1 inhibits HCC cell migration and invasion

Unrestricted cell growth and motility are the two most important traits of cancers. Thus, wound healing assay and transwell assays were performed to evaluate the cell motility capability. As determined by the wound healing assay, knockdown of AFAP1-AS1 markedly inhibited the migratory ability of the MHCC-97 L and MHCC-97H cells (Fig. 4a). The transwell assay also showed that motility was significantly decreased in cells transduced with siAFAP1-AS1 compared with that in the negative control (Fig. 4b). To explore whether AFAP1-AS1 exerts its functions through the proliferation- and apoptosis-related genes that are known to be involved in cancer, we examined the expression of Ki67, Bcl-2, Bax, and MMP9. As shown in Fig. 4c, knockdown of AFAP1-AS1 resulted in a dramatic decrease in Ki67, Bcl-2, and MMP9 levels and an increase in Bax levels. Taken together, the data strongly suggest that AFAP1-AS1 promotes HCC cell proliferation and invasion through mediating proliferation- and apoptosis-related gene expression in vitro.

Fig. 4

The effects of AFAP1-AS1 knockdown on cell invasion. a Representative images of wound-healing assay showed that the migration ability of MHCC-97 L and MHCC-97H cells transduced with SCR or siAFAP1-AS1 at 0 h and 48 h time point, respectively. b The Boyden chamber assay was employed to examine the invasion ability of MHCC-97 L and MHCC-97H cells transduced with SCR or siAFAP1-AS1, respectively. c The expression of Ki-67, BCL-2, Bax, and MMP-9 in MHCC-97 L and MHCC-97H cells transduced with SCR or siAFAP1-AS1 was determined by western blotting. **P < 0.01

Knockdown of AFAP1-AS1 suppresses tumor growth in vivo

To further determine whether AFAP1-AS1 silencing affects tumorigenesis, MHCC-97H cells transduced with SCR or siAFAP1-AS1 were subcutaneously inoculated into nude mice. All of the mice were sacrificed 5 weeks after injection, and tumors derived from the AFAP1-AS1-silencing group developed more slowly than those from the SCR group (Fig. 5a). Consistent with tumor size, the average tumor weight in the siAFAP1-AS1 group was significantly lower than that in the SCR group (Fig. 5b). Tumor growth in the knockdown AFAP1-AS1 group was slower than that in the SCR group (Fig. 5c). Furthermore, qRT-PCR was performed to detect the expression of AFAP1-AS1 in the xenograft tumor tissues. Our results showed that the levels of AFAP1-AS1 expression in tumor tissues formed in the siAFAP1-AS1 group were lower than those of the tumors formed in the SCR group (Fig. 5d). In addition, immunostaining revealed that the tumors derived from the siAFAP1-AS1 group showed weaker Ki-67 expression than that in tumors from the SCR group (Fig. 5e). These data further supported the role of AFAP1-AS1 in HCC cell growth in vivo.

Fig. 5

AFAP1-AS1 silencing inhibited tumor growth in a xenograft mouse model. a Representative photographs of tumors are shown. Tumor weight b and tumor growth curves c in mice are shown for MHCC-97H cells transduced with SCR or siAFAP1-AS1. d qRT-PCR was used to detect the average expression of AFAP1-AS1 in xenograft tumors. e Representative images of IHC staining showed the expression of Ki67 in xenograft tumor tissues from the siAFAP1-AS1 group or SCR group. **P < 0.01

Discussion

Accumulating evidence has shown that lncRNAs are associated with many functions in various aspects of cell biology, and increasing attention has been paid to their roles in tumors [9-11]. Previous studies have demonstrated that AFAP1-AS1, localized in the antisense DNA strand of the AFAP1 gene, regulates the invasion and metastasis of lung cancer and PDAC cells [18, 19]. Recently, Hao et al. provided evidence that AFAP1-AS1 mediated cell malignant behavior by affecting the expression of several small GTPase family members and molecules in the actin cytokeratin signaling pathway in nasopharyngeal carcinoma [20]. However, the expression and functions of AFAP1-AS1 in HCC remain unclear. In the current study, we provided the first evidence that AFAP1-AS1 was significantly upregulated in HCC tissues compared with that in adjacent normal tissues, and high AFAP1-AS1 expression in HCC patients was associated with an increased tumor size, vascular invasion, advanced TNM stage, and poor prognosis, findings that were consistent with those in previous studies. These findings suggested that AFAP1-AS1 acts as an oncogene in the progression of HCC.

Because high AFAP1-AS1 expression was associated with tumor size in HCC, we surmised that AFAP1-AS1 might play a key role in tumor cell proliferation. To further elucidate the functions of AFAP1-AS1 in HCC, we knocked down AFAP1-AS1 in MHCC-97 L and MHCC-97H with high endogenous AFAP1-AS1 expression using RNAi-mediated suppression. Our results showed that AFAP1-AS1 knockdown could significantly inhibit HCC cell proliferation and invasion in vitro. In addition, flow cytometric analysis indicated the inhibitory effect of AFAP1-AS1 silencing on the proliferation of HCC cells by inducing apoptosis. Similarly, the gain- and loss-of-function strategies for AFAP1-AS1 expression resulted in changes in cell proliferation and apoptosis in esophageal cancer [17] and migration and invasion in pancreatic cancer and nasopharyngeal carcinoma [19, 20]. It is well known that aberrant BCL-2 and Bax expression is involved in cancer [22]. As we expected, AFAP1-AS1 silencing led to a decrease in Ki-67, BCL-2, and MMP-9 and an increase in Bax. In addition, AFAP1-AS1 knockdown significantly inhibited tumor growth in vivo, confirming the vitro experiments.

In conclusion, our results showed that AFAP1-AS1 is remarkably upregulated in HCC tissues and is significantly correlated with the malignancy status and poor prognosis. Furthermore, AFAP1-AS1 silencing suppressed cell proliferation and induced cell apoptosis at least partly through regulating proliferation- and apoptosis-related genes. However, dysregulation of AFAP1-AS1 is only the tip of iceberg; more studies on the functions of AFAP1-AS1 in HCC are needed.