KCNQ1OT1 promotes melanoma growth and metastasis

The correlation of KCNQ1OT1, miR-153, and MET with melanoma

To identify lncRNAs involved in melanoma, we performed a cDNA microarray analysis. We collected three pairs of melanoma tissue and adjacent tissues, and a gene expression microarray analysis was performed using the Agilent SurePrint G3 Human Gene Expression 8X60K V2 Microarray Kit. We detected 12 up-regulated and seven down-regulated lncRNAs in melanoma tissues (Table 1). The top lncRNA, KCNQ1OT1, was selected, and its expression was verified by real time PCR. KCNQ1OT1 expression increased in melanoma tissues compared with the paired adjacent normal tissues (Figure 1A).

Figure 1. KCNQ1OT1, miR-153, and MET correlation with melanoma. (A) KCNQ1OT1 levels detected by real time PCR in 30 samples of melanoma and adjacent tissues. Data are presented as means ± SEM. ** P < 0.01 for comparison of tumor vs. adjacent tissues groups. (B) The relationship between KCNQ1OT1 expression and patient survival. (C) The levels of miR-153 were detected by real time PCR in 30 samples of melanoma and adjacent tissues. Data are presented as means ± SEM. ** P < 0.01 for comparison of tumor vs. adjacent tissues groups. (D) Relationship between miR-153 expression and patient survival. Patients with high expression of miR-153 showed longer survival (E) MET levels were detected by western blot in melanoma and adjacent tissues. Data are presented as means ± SEM. ** P < 0.01 for comparison of tumor vs. adjacent tissues groups. (F) MET levels were detected by real time PCR in 30 samples of melanoma and adjacent tissues. Data are presented as means ± SEM. ** P < 0.01 for comparison of tumor vs. adjacent tissues groups. (G) The relationship between MET expression and patient survival. (H) KCNQ1OT1 expression in HACAT, A375, A875 and MuM-2C cells was measured by real time PCR. Data are shown as mean ± SEM. ** P< 0.01 vs. HACAT (I) MiR-153 expression in HACAT, A375, A875 and MuM-2C cells. Data are shown as mean ± SEM. ** P< 0.01 vs. HACAT (J, K) MET expression in HACAT, A375, A875 and MuM-2C cells. Data are shown as mean ± SEM. ** P< 0.01 vs. HACAT.

Kaplan-Meier analysis indicated that patients with high levels of KCNQ1OT1 had worse overall survival (40 months) than those with lower KCNQ1OT1 (60 months; Figure 1B). Melanoma tissues had lower miR-153 expression, and the patients with higher miR-153 levels survived longer (Figure 1C, 1D). MET expression was increased in melanoma tissues, and patients with lower MET expression had a better prognosis (Figure 1E-1G). Compared with HACAT cells, miR-153 expression was decreased in melanoma cell lines (A375, A875, and MuM-2C), while KCNQ1OT1 and MET expression was increased (Figure 1H-1K).

KCNQ1OT1 is a target of miR-153

It is possible that lncRNAs might function as ceRNAs to indirectly regulate miRNAs [15]. There is a negative correlation between KCNQ1OT1 and miR-153 in melanoma (Figure 2A). The lncbase software showed that there are binding sites between KCNQ1OT1 and miR-153 (Figure 2B). The EGFP reporter assay showed that KCNQ1OT1 activity was decreased after cotransfection with miR-153, and increased after cotransfection with miR-153 antisense (Figure 2C). This was not the case when KCNQ1OT1 and miR-153 binding sites were mutated (Figure 2D). Real time PCR assays showed that miR-153 could inhibit KCNQ1OT1 expression (Figure 2E), and that KCNQ1OT1 could inhibit miR-153 (Figure 2F). This result suggests that KCNQ1OT1 has a direct combining effect with the miR-153.

Figure 2. KCNQ1OT1 is a target of miR-153. (A) Correlation between miR-153 expression and KCNQ1OT1. (B) Prediction that KCNQ1OT1 can specifically bind to the miR-153 by LNCBASE. (C, D) Fluorescence intensity was measured in HACAT cells co transfected with miR-153 or miR-153 AS and KCNQ1OT1 WT/MUT construct. A GFP vector was used as a control. (E) Relative RNA of KCNQ1OT1 was measured in HACAT cells transfected with miR-153 or miR-153 AS. (F) Relative RNA of miR-153 was measured in HACAT cells transfected with KCNQ1OT1 WT, KCNQ1OT1 MUT or si-KCNQ1OT1.

miR-153 can target MET

Correlation analysis showed that miR-153 expression was negatively correlated with MET expression in melanoma (Figure 3A). UA miR-153 binding site within the MET 3' UTR sequence was identified by the miRDB software (Figure 3B). Luciferase reporter assays demonstrated that miR-153 can directly reduce MET expression at the transcriptional level, since the wild-type MET 3' UTR was constructed by HACAT cells co-transfected with a luciferase reporter. Luciferase activity was lower than in the control group. However, luciferase levels were unchanged in cells co-transfected with the MET-MUT luciferase reporter or ASO miR-153 (miR-153 antisense) (Figure 3C, 3D). In A375 cells with miR-153 overexpression, miR-153 expression can inhibit MET expression (Figure 3E, 3F). When miR-153 expression was inhibited in A375 cells, MET expression increased (Figure 3G, 3H).

Figure 3. miR-153 can target MET. (A) Correlation between MET and miR-153 expression. (B) Prediction that miR-153 can specifically bind to the MET 3′ UTR by MIRDB. (C, D) Fluorescence intensity was measured in HACAT cells co transfected with miR-153 or miR-153 as and MET WT/mut construct. Vector was used as a control. (E, F) After transfecting A375 cells with miR-153 mimic, the MET protein and mRNA levels were detected by western blot and real time PCR. Data are shown as mean ± SEM. ** P< 0.01 (G, H) After transfecting A375 cells with miR-153 AS, MET protein and mRNA levels of was detected by western blot and real-time PCR. Data are shown as mean ± SEM. ** P< 0.01.

KCNQ1OT1 suppresses miR-153’s activity on MET

KCNQ1OT1 expression was positively correlated with MET expression in melanoma (Figure 4A). In addition, the stimulatory effect of KCNQ1OT1 on MET expression was analyzed using real time PCR (Figure 4B, 4C). The miR-153 combining sites of MET WT or mutant were co-transfected with KCNQ1OT1 plasmids (WT or MUT) or KCNQ1OT1 knockdown plasmids into HACAT cells. KCNQ1OT1 overexpression enhanced MET expression, while KCNQ1OT1 knockdown reduced MET expression. These results were not observed for the KCNQ1OT1 mutant or when the miR-153 binding sites in the MET 3’UTR were mutated. Western blot and real time PCR revealed that the ectopic KCNQ1OT1 expression increased MET protein and mRNA levels in A375 cells. KCNQ1OT1 depletion decreased MET protein and mRNA levels in A375 cells (Figure 4D-4G).

Figure 4. Overexpression of MET enhances transcription and lncRNA-coated territory of KCNQ1OT1. (A) Correlation between MET expression and KCNQ1OT1. (B, C) Fluorescence intensity was measured in HACAT cells co transfected with KCNQ1OT1, KCNQ1OT1 MUT or si-KCNQ1OT1, and MET WT/MUT construct. Vector was used as a control. (D, E) After transfecting KCNQ1OT1/control in A375 cells, MET level was detected by western blot and real time PCR. Data are shown as mean ± SEM. ** P< 0.01 (F, G) After transfecting si-KCNQ1OT1 or control in A375 cells, MET level was detected by western blot and real time PCR. Data are shown as mean ± SEM. ** P< 0.01.

These data indicate that KCNQ1OT1 may act as a ceRNA for MET by competitively binding to miR-153, which suppresses the repressive activity of miR-153 on the MET 3’UTR.

KCNQ1OT1 promotes melanoma cell proliferation

MTT assays revealed that the proliferation of A375 cells and A875 cells transfected with KCNQ1OT1 was greater than in the control group (Figure 5A). When si-KCNQ1OT1 was transfected, A375 and A875 cell proliferation decreased (Figure 5B). KCNQ1OT1 promoted cyclin d1 expression; KCNQ1OT1 inhibition decreased cyclin d1 expression (Figure 5C-5F).

Figure 5. KCNQ1OT1 promotes melanoma cell proliferation. (A) After transfecting cells with KCNQ1OT1, proliferation rates of A375 and A875 were determined using MTT assays. Data are presented as means ± SEM. (B) After transfecting cells with si-KCNQ1OT1, the proliferation rates of A375 and A875 were determined using MTT assays. Data are presented as means ± SEM. (C, D) After transfecting KCNQ1OT1/control in A375 cells, the cyclin d1 protein and mRNA level was detected by western blot and real time PCR. Data are shown as mean ± SEM. ** P< 0.01 (E, F) After transfecting si-KCNQ1OT1 or control in A375 cells, cyclin d1 protein and mRNA level was detected by western blot and real time PCR. Data are shown as mean ± SEM. ** P< 0.01.

KCNQ1OT1 promotes melanoma cell metastasis

Transwell results suggest that KCNQ1OT1 can promote melanoma cell invasion and migration (Figure 6A-6H). After KCNQ1OT1 expression decreased, cell invasion and migration also decreased. KCNQ1OT1 can promote MMP2 expression (Figure 6I-6L), which is an enzyme that promotes cell metastasis. To examine the effect of KCNQ1OT1 on melanoma cell metastasis in vivo, A375 cells stably expressing vector (control), KCNQ1OT1, or si-KCNQ1OT1 were injected into nude mice via the tail vein. Liver tissues were obtained 21 days after injection for microscopic histological analysis. Hepatic tumor metastasis increased in mice injected with KCNQ1OT1 cells (Figure 6M left). Hematoxylin and eosin staining confirmed that KCNQ1OT1 expression increased metastatic spread to the livers of the mice more than si-KCNQ1OT1 (Figure 6M middle, right).

Figure 6. KCNQ1OT1 promotes melanoma cell metastasis. (A, B) After transfecting KCNQ1OT1/control in A375 cells and (E, F) A875 cells, transwell assays with or without matrigel were performed. Cells were counted and results represent the mean ± SD of three experiments. ** P < 0.01 (C, D) After transfecting si-KCNQ1OT1 or control in A375 cells and (G, H) A875 cells, transwell assays with or without matrigel were performed. Cells were counted and results represent the mean ± SD of three experiments. ** P < 0.01 (I, J) After transfecting KCNQ1OT1/control or (K, L) si-KCNQ1OT1 in A375 cells, MMP2 protein and mRNA level was detected by western blot and real time PCR. Data are shown as mean ± SEM. ** P < 0.01 (M) 2×10⁶ A375 cells with stable expression of vector (control), KCNQ1OT1, and si-KCNQ1OT1 were injected into nude mice via the tail vein. Livers were dissected and either macroscopically photographed (left) or stained with H&E (middle, Scale bar, 100μm). The right side is the HE staining results of the liver (right).

KCNQ1OT1 suppresses miR-153’s inhibition of proliferation and metastasis

To determine whether KCNQ1OT1 functioned through miR-153 in melanoma cells, KCNQ1OT1 was overexpressed in A375 and A875 cells transfected with miR-153. We found that KCNQ1OT1 could eliminate miR-153’s inhibition of proliferation and metastasis of melanoma cells (Figure 7A, 7B). KCNQ1OT1 also eliminated miR-153’s inhibitory effect on MET, cyclin d1, and MMP2 (Figure 7C, 7D). Our data suggest that KCNQ1OT1 acts as a sponge for miR-153, which enhances MET expression, thereby promoting proliferation and metastasis of melanoma cells.

Figure 7. miR-153 mediates the effect of KCNQ1OT1 on proliferation and metastasis in melanoma cells. (A) After transfecting with control, miR-153, or KCNQ1OT1 and miR-153, A375 and A875 cell proliferation was detected using an MTT assay. Data are shown as mean ± SEM. (B) After transfecting control, miR-153, or KCNQ1OT1 and miR-153 in A375 cells, a transwell assay without matrigel was performed. Cells were counted and results represent the mean ± SD of three experiments. ** P < 0.01 (C, D) Western blot and real time PCR was used to detect indicant proteins in A375 cells. ** P < 0.01 (E) After transfecting with control, AS-miR-153, or si-KCNQ1OT1 and miR-153 AS, A375 and A875 cell proliferation was detected using an MTT assay. Data are shown as mean ± SEM. (F) After transfecting control, ASO-miR-153, or si-KCNQ1OT1 and miR-153 AS in A375 cells, a transwell assay without matrigel was performed. Cells were counted and results represent the mean ± SD of three experiments. ** P< 0.01 (G, H) Western blot and real time PCR were used to detect indicant proteins in A375 cells. ** P< 0.01.

Informed consent

All methods were carried out in accordance with relevant guidelines and regulations. The study protocol was approved by Ethics Committee of the General Hospital of Shenyang Military Region and Human Clinical Trial Committee. The procedures were approved by ethics committee according to the Chinese Community guidelines. Written informed consent was obtained from all patients.

Ethical approval

The study protocol was approved by Medical Ethics and Human Clinical Trial Committee.

Tissue specimens and cell culture

Thirty melanoma and adjacent tissues were obtained from the cancer center of the General Hospital of Shenyang Military Region. Samples were collected from 30 patients (13 men, 17 women). Ages ranged from 29 to 81 years old, with an average age of 54.8 (Table 2). HACAT, A375, A875, and MuM-2C cell lines were obtained from American Type Culture Collection (Manassas, VA, USA). Cells were cultured in DMEM (Invitrogen, Carlsbad, CA, USA) containing 10% FBS (Invitrogen, Carlsbad, CA, USA). All cells were cultured at 37 °C with humidified atmosphere of 5% CO₂.

Microarray

The SurePrint G3 Human Gene Expression 8X60K Microarray version 2 (Agilent Technologies) was used to analyze differences in lncRNA or mRNA levels in melanoma tissues and adjacent tissues. Total RNA was prepared using an RNeasy Mini Kit (Qiagen).

Real time PCR

RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA, USA) [14], and was reverse transcribed to cDNA by a RT reaction kit (Promega, Madison, WI, USA). Real-time PCR was performed by SYBR Green PCR master mix (TAKARA, Japan) on Mx 3000P real time PCR System. All reactions were performed at least three times. A dissociation step was conducted to generate a melting curve to confirm amplification specificity. GAPDH was used as the reference gene, and primer sequences are in Table 3.

Transfection

Lipo2000 transfection reagent (Ribobio, China) was used according to the manufacturer’s protcol. All the sequences were bought from Ribobio. KCNQ1OT1, including the miR-153 target sites, was amplified from the KCNQ1OT1 expression plasmid using the primers shown in Table 1, and then cloned into restriction sites of pcDNA3.1 vector (Ribobio, China). The resultant plasmid was named KCNQ1OT1. The KCNQ1OT1 fragment with mutations in the miR-153 response elements was inserted into pcDNA3.1 and named KCNQ1OT1 MUT (miR140-5p). The siRNA of KCNQ1OT1 was annealed and cloned into the vector pSilencer 2.1-U6 neo (Ribobio, China) to construct the knockdown plasmids. Similarly, the MET 3′UTR, which contains miR-153 target sites, was cloned into the same restriction sites, and the mutant forms of the KCNQ1OT1 or MET 3′UTR were obtained according to the methods described above. MiR-153/control and miR-153 antisense/control were bought from Ribobio China. The transfection efficiency was tested by real time PCR. Primer sequences are found in Table 4.

Fluorescent reporter assays

HACAT cells were co-transfected with miR-153/control, miR-153 AS/AS-NC, EGFP-KCNQ1OT1 WT/MUT, or MET WT/MUT plasmid in 48-well plates. GFP (Clontech, Mountain View, CA, USA) was used as control. Forty-eight hours later, cells were lysed in 200 μl lysis buffer per well. The fluorescence intensity of GFP was measured by an F-4500 Fluorescence Spectrophotometer (Hitachi, Tokyo, Japan). The primers of MET WT/MUT, EGFP-KCNQ1OT1 WT/MUT were designed by Shengong, Shanghai. This experiment was performed in triplicate.

MTT assays

Cells were plated in 96-well plates. The medium was replaced 24 hrs later, and the transfection was conducted. MTT solution was added to the well at 0, 12, 24, 36, and 48h after starting the culture. The medium was removed at 4 hours after incubation. The remaining MTT formazan was dissolved in 150 μl of DMSO. Each well’s absorbance was measured at 490 nm. This experiment was performed in triplicate.

Cell migration and invasion assay

The transwell chambers (Corning, USA) were coated with or without 20 µl matrigel (1:4, BD Bioscience, USA). The transfected cells were trypsinized and suspended in 100 µl of DMEM without serum, which was transfected to the upper chamber. A total of 600 µl culture medium with 10% FBS was added to the lower chamber. Twenty-four hours after incubation, the numbers of cells which pass through the membrane were counted under a microscope. This experiment was performed in triplicate.

Western blot analyses

Proteins from the tissue and cells were isolated with RIPA (Beyotime, Shanghai, China) containing protease inhibitor. Each protein sample (30 μg) was separated by 10% SDS-PAGE, and then transferred onto a PVDF membrane. The membrane was blocked with 5% nonfat dry milk in TBST for 1 h at room temperature. The proteins were probed with specific antibodies: cyclin d1 (sc-4074), mmp2 (sc-13594), and MET (sc-8057). The proteins were detected using the ECL detection system (UVP Inc., Cambridge, UK) with enhanced chemiluminescence detection reagents. To confirm equal protein loading, the gels were stripped and reprobed with antibodies against GAPDH (Santa Cruz, California, Texas).

Nude mice xenografts

Five- to six-week-old female, athymic nude BALB/c mice (Vital River Laboratory Animal Technology Co. Ltd., Beijing, China) were used to study metastasis, in which 2×10⁶ cells mixed with 1ml saline were injected into the tail vein. The experiment was divided into three groups (the cell lines that stably overexpressed KCNQ1OT1, the cell lines of si- KCNQ1OT1 and the control group) with six mice in each group. At day 21 following tumor cell injection, liver samples were collected for histological examination.

All experimental procedures involving animals were conducted in accordance with the Guide for the Care and Use of Laboratory Animals (NIH publication no. 80-23, revised 1996) and were performed according to the institutional ethical guidelines for animal experiments.

Histopathology

Liver specimens were fixed with 4% paraformaldehyde. The fixation time depended on the size of the tissue block and the tissue type. Serial sections (2 μm) were cut using a microtome and affixed onto positively charged slides. All slides were incubated at 60°C for a few hours to allow the sections to adhere to the slides. Tissues were deparaffinized and rehydrated through graded xylene and alcohol. Hematoxylin–eosin staining procedures were performed according to routine protocols.

Statistical methods

Each assay was performed in triplicate and repeated three times independently. All data was analyzed with Graph PRISM 6.0 (GraphPad, Inc.). Continuous variables were analyzed by the Student’s t-test or one-way variance. The overall survival rate was calculated by the Kaplan–Meier method. The comparison of differences was performed with the log-rank test, and P<0.05 indicated significance.