Background
Lung cancer is the leading cause of cancer-related deaths worldwide, and ~ 85% of all lung cancers are non-small cell lung cancer (NSCLC) [
1,
2]. Despite improvement in therapeutic strategies, NSCLC patients yet exhibits poor prognosis [
3]. This is predominantly attributed to tumor metastasis [
4], suggesting that elucidation of the mechanisms underlying NSCLC metastasis is becoming a big challenge.
Transforming growth factor β (TGF-β) is highly expressed in NSCLCs [
5‐
7]. Our previous study showed that TGF-β can promote epithelial-mesenchymal transition (EMT) and NSCLC cell invasion [
8,
9]. In fact, there are compelling data that TGF-β/Smad signaling potently contributes to EMT and tumor metastasis in various human cancers [
10,
11]. Recently, we have provided evidence that repression of transcriptional intermediary factor 1 γ (TIF1γ), a regulator of TGF-β/Smad signaling [
12,
13], enhanced TGF-β-induced EMT in NSCLC cells [
14]. In support of this, TIF1γ exerts its repressive activity on TGF-β/Smad signaling and plays an antagonistic role in TGF-β-induced EMT in mammary epithelial cells [
11,
15,
16]. These data strongly suggest that TIF1γ functions as a tumor metastasis suppressor in human cancers, including NSCLC, by inhibiting TGF-β-induced EMT.
CircRNAs, a class of non-coding RNAs, are involved in gene regulation at both transcriptional and post-transcriptional levels [
17]. Most of circRNAs are derived from a single exon or multiple exons and are detected in the cytoplasm [
18,
19]. CircRNAs have been discovered to work as miRNA sponges [
17,
20,
21]. The best-known ones so far include the recently identified circRNA, ciRS-7, which can efficiently tether miR-7, leading to reduced miR-7 activity and increased levels of oncogenic factors in cancer-associated signaling pathways [
22]. Most recently, Hsiao et al. found that circCCDC66 may protect
MYC mRNA from the attack of miRNA-33b and miR-93 to promote colon cancer growth and metastasis [
23]; Han et al. reported that circMTO1 inhibits hepatocellular carcinoma progression by disrupting oncogenic miR-9 and promoting p21 expression [
24]. However, the regulatory mechanisms of circRNAs in cancer need to be extensively validated [
21]. Of more importance, hundreds of circRNAs were regulated in human mammary cells undergoing EMT [
25], suggesting that certain circRNAs play important roles in TGF-β-induced EMT and thus influence cancer metastasis. RNA-binding protein Quaking (QKI) was identified to control biogenesis of > 30% of abundant circRNAs during EMT in response to TGF-β [
25]. Furthermore, QKI is frequently down-regulated in NSCLC tissues and significantly associated with poorer prognosis [
26]. These findings suggested that down-regulated circRNAs may be implicated in NSCLC progression, invasion and metastasis.
Taken together, we hypothesized that there may be several dysregulated circRNAs affecting TIF1γ activity and thereby promoting TGF-β-induced EMT and invasion in NSCLC. To test this, we first performed Human circRNA Array analysis in NSCLC cells before and after they underwent EMT in response to TGF-β, and identified 187 differentially expressed circRNAs. From the viewpoint of prediction, we focus on a down-regulated circRNA (hsa_circ_0008305 in circBase:
http://www.circbase.org) produced from the
PTK2 gene, termed as circPTK2. Intriguingly, we further investigated the regulation and function of circPTK2 in TGF-β-induced EMT and tumor metastasis, as well as a link between circPTK2 and TIF1γ in NSCLC. Our findings show that circPTK2 suppresses TGF-β-induced EMT and tumor cell invasion by controlling TIF1γ in NSCLC, revealing a novel mechanism by which circRNA regulates TGF-β-induced EMT and tumor metastasis.
Discussion
To date, whether and how circRNAs contribute to TGF-β-induced EMT in NSCLC remains elusive. In the present study, we reveal that circPTK2 inhibits TGF-β-induced EMT by up-regulating TIF1γ in NSCLC, and establish a novel mechanistic role of circPTK2-TIF1γ axis in regulating TGF-β-induced EMT (Additional file
11: Figure S8).
TIF1γ (alias, TRIM33/RFG7/PTC7/Ectodermin), a regulator of TGF-β/Smad signaling, acts as an “antagonist” by ubiquitinating Smad4 or a “complementary agonist” by competing with Smad4 to regulate TGF-β/Smad signaling [
12,
13]. TIF1γ has been proved to contribute to multiple malignancies [
16,
31‐
33], and TIF1γ is essential for regulating TGF-β signaling [
34,
35] and EMT [
11]. Our previous studies show that TIF1γ expression is frequently reduced in NSCLC and TIF1γ repression enhances TGF-β-induced EMT and NSCLC cell invasion [
14,
36]. Knockdown of TIF1γ increases the expression of Snail [
14], an important downstream transcriptional activator of TGF-β/Smad signaling [
9]. Here, we show that reduced TIF1γ is not just associated with poor survival of NSCLC patients but also positively correlated with circPTK2 expression in NSCLC tissues. Moreover, circPTK2 expression were significantly reduced in NSCLC cells and circPTK2 overexpression augmented TIF1γ expression in NSCLC cells. Thus, for the first time, we established a link between TIF1γ and circPTK2 in NSCLC. Actually, circPTK2 is produced from the
PTK2 gene, which spans seven of its exons. We validated the characterization of circPTK2 in NSCLC cells (Fig.
1c-f). It has been well documented that exon-intron or intron-derived circRNAs promote their parent gene transcription in cell nucleus, but exon-derived circRNAs do not affect the expression of their parent genes [
29]. In the present study, circPTK2 derived from multiple exons of
PTK2 was detected in the cytoplasm (Fig.
1f) and circPTK2 did not influence its parent gene
PTK2 expression (Additional file
8: Figure S6B). To the best of our knowledge, circPTK2 is a circular RNA which function has not yet been defined in human cancers. In this study, we identified that circPTK2 can function as a sponge for miR-429/miR-200b-3p to counter degradation of TIF1γ. Moreover, miR-429/miR-200b-3p promoted TGF-β-induced EMT and cell invasion by inhibiting TIF1γ in NSCLC cells. These data suggests that circPTK2 has potential functional role in TGF-β-induced EMT and NSCLC metastasis.
Although circRNAs’ expression is often low, circRNAs are emerging as oncogenic stimuli or tumor suppressors in cancer [
37]. To date, the mechanistic roles of circRNAs in TGF-β-induced EMT are poorly understood in NSCLC. Therefore, we primarily performed circRNA microarray analysis and identified that circPTK2 was significantly reduced during TGF-β-induced EMT of NSCLC cells. Moreover, circPTK2 overexpression inhibited TGF-β-induced EMT and NSCLC cell invasion, whereas its knockdown had the opposite effect. Especially, circPTK2 was significantly lower in metastatic NSCLC tissues than non-metastatic counterparts, supporting the roles of circPTK2 in NSCLC cell invasion in vitro. Furthermore, the in vivo experiment of metastasis showed that circPTK2 overexpression suppressed NSCLC cell metastasis. Collectively, these results suggested that circPTK2 may function as a tumor metastasis suppressor by controlling TGF-β signaling activity.
There are multiple and diverse molecular mechanisms of TGF-β-induced EMT in human cancers [
38,
39]. In fact, it is not surprising because various molecules participate in TGF-β signaling, which is a potent inducer of EMT. Unexceptionally, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are also implicated in TGF-β signaling and EMT [
40‐
42]. As exemplified, miR-145 and miR-203 repressed SMAD3, a downstream effector in canonical TGF-β/Smad signaling, then inhibited TGF-β-induced EMT in NSCLC cells [
43]. In the present study, miR-429/miR-200b-3p acted as invasion-promoting miRNAs to promote TGF-β-induced EMT in NSCLC cells. Our results are different from the previous findings where miR-429/miR-200b-3p was recognized as anti-metastatic miRNAs in glioma and renal cell carcinoma [
44,
45]. However, Lang et al. reported that miR-429 promoted the metastasis of NSCLC cells [
46], supporting our results obtained in NSCLC cells. This can be explained by the idea that miRNAs may exert distinct roles depending on the cellular context, which is probably attributed to the availability of specific targets or downstream effectors [
47]. Moreover, the invasion-promoting phenotype of miR-429/miR-200b-3p overexpression was copied by knockdown of TIF1γ, which promoted TGF-β-induced EMT in NSCLC cells [
14]. In fact, our data and a public data set (GSE36681) suggests that miR-429/miR-200b exerts a tumor-promoting role in NSCLCs (Additional file
12: Table S4 and Additional file
13: Figure S9A-F). It has been proposed that TGF-β induces EMT by driving the expression of ZEB transcription factors, which in turn inhibit miR-200 family members via a double-negative feedback loop [
48]. However, on TGF-β1 stimulation, miR-429/miR-200b-3p levels were still unchanged in time-independent manner, albeit a dynamic alteration of ZEB1/ZEB2 expression in A549 cells (Additional file
14: Figure S10A-D). In support of this, Zhang et al. reported that miR-200 family members were not altered by TGF-β1 in A549 cells [
28]. More importantly, we here provided the first evidence that TGF-β promotes EMT via circRNAs in NSCLC, albeit circPTK2 may be one of several circRNAs affecting TGF-β-induced EMT. Interestingly, TGF-β was able to down-regulate circPTK2 expression but failed to alter miR-429/miR-200b-3p levels in NSCLC cells. This result is consistent with that circPTK2 is frequently reduced in NSCLC tissues (Fig.
6h and
j), where increased expression of TGF-β has been detected [
6,
7,
27]. More recently, Conn et al. identified that formation of > 30% of abundant circRNAs was regulated by QKI during TGF-β-mediated EMT in human mammary cells [
25]. Zong et al. reported that QKI is frequently reduced in NSCLC [
26]. The two investigations on QKI might provide an explanation for why TGF-β diminished circPTK2 expression in NSCLC cells. Interestingly, QKI plays an important role in TGF-β-mediated downregulation of circPTK2 (Additional file
15: Figure S11A-D).
More interestingly, another circRNA hsa_circ_0003221 (also named after circPTK2), with a spliced sequence length of 625 nt in circBase (
http://www.circbase.org), has been reported to promote the proliferation and migration of bladder cancer cells [
49]. Although hsa_circ_0003221 and hsa_circ_0008305 are derived from the same parent gene
PTK, they exert different functions. In fact, this is not surprising because they could have distinct mechanisms depending on the cellular context or downstream target molecules.
In summary, our findings show that circPTK2 (hsa_circ_0008305) inhibits TGF-β-induced EMT through regulating TIF1γ and NSCLC cell metastasis, as well as establish a positive relationship between TIF1γ and circPTK2 in NSCLC, revealing a novel mechanism by which circRNA regulates TGF-β-mediated EMT and tumor metastasis, and suggesting that overexpression of circPTK2 could provide a therapeutic strategy for advanced NSCLC.
Methods
Cell lines and cell culture
Human lung normal epithelial cell BEAS-2B, and NSCLC cells A549, H1299, H1650, SPC-A1, and Calu3 (lung adenocarcinoma cells) and H226, H520, and SK-MES-1 (lung squamous carcinoma cells) from Cell Bank of Chinese Academy of Sciences were cultured in RPMI 1640 medium (HyClone, South Logan, UT, USA) supplemented with penicillin/streptomycin, L-glutamine and 10% fetal bovine serum (FBS, Invitrogen, Carlsbad, CA, USA) at 37 °C in a humidified atmosphere with 5% CO
2. A549 and H226 cells were induced by TGF-β1 to undergo EMT as per our description [
9,
14].
Tissue samples
Seventy-three fresh NSCLC tissues and paired adjacent noncancerous lung tissues (Additional file
10: Table S3) were collected after informed consent from patients in the First Affiliated Hospital of Soochow University. Histological and pathological diagnostics for NSCLC patients were evaluated based on the Revised International System for Staging Lung Cancer. Patients received neither chemotherapy nor radiotherapy before tissue sampling. As listed in Additional file
10: Table S3, metastatic tissues (
n = 41) were from NSCLC patients with local lymph node metastasis (T
1-4 N
1-2 M
0) or distant organ metastasis (T
1-4N
anyM
1), and non-metastatic tissues (
n = 32) were from NSCLC patients without any metastasis (T
1-4N
0M
0). The samples were snap-frozen in liquid nitrogen and stored at − 80 °C before RNA extraction. This study was approved by the Ethics Committee of Soochow University.
Real-time quantitative reverse transcriptase PCR (qRT-PCR)
RNA was isolated using TRIzol (Thermo Fisher Scientific, Carlsbad, CA, USA). cDNA synthesis and qRT-PCR analysis were performed as described by us [
50] with some modification. Primers are listed in Additional file
16: Table S5. U6 levels were used to normalize miR-429/miR-200b-3p expression. β-actin was endogenous control for
TIF1γ mRNA,
Snail mRNA,
PTK2 mRNA and circPTK2. Relative expression of each RNA was determined using the ΔΔ
Ct method. Each qRT-PCR analysis was done in triplicate.
Western blot analysis
Cells were lysed and subjected to western blot analysis as described by us [
51]. Antibodies were as follows: mouse anti-TIF1γ (Santa Cruz Biotechnology, Santa Cruz, CA, USA), mouse anti-E-cadherin, anti-N-cadherin and anti-Vimentin (BD Biosciences, San Jose, CA, USA), mouse anti-Snail (Cell Signaling Technology, Danvers, MA, USA), mouse anti-β-actin and anti-mouse secondary antibodies (Santa Cruz Biotechnology). Molecular sizes of TIF1γ, E-cadherin, N-cadherin, Vimentin, Snail and β-actin proteins shown on the immunoblots are 150kD, 120kD, 130kD, 57kD, 29kD and 43kD, respectively. Each experiment was carried out in triplicate.
CircRNA microarray analysis
Total RNA from A549 cells treated without and with TGF-β1 was used for Arraystar Human circRNA Array (Arraystar Inc., Rockville, MD, USA). CircRNA microarray analysis was performed as described [
52]. CircRNAs (fold change ≥1.5 and
P-value < 0.05) were considered to be differentially expressed between two groups. Each group (cells treated with TGF-β1 for 0 h or 24 h, respectively) was analyzed in triplicate.
Northern blot with denaturing agarose gels
Digoxin-labeled DNA probes (351 nt), spanning the back-splice junction of circPTK2, were prepared from cDNA using PCR DIG Probe Synthesis Kit (Roche, Mannheim, Germany). PCR primers were as follows: 5’-GAATATGGCTGACCTAATAGA-3′ (forward); 5’-ACACTTGAAGCATTCCTTATC-3′ (reverse).
Total RNA (15 μg) denatured in formaldehyde was resolved on 1% agarose-formaldehyde gel and transferred onto a Hybond-N+ nylon membrane (GE Healthcare, Buckinghamshire, UK). Membranes were crosslinked, pre-hybridized in DIG Easy Hyb (Roche), and hybridized with DIG-labeled DNA probes overnight. After stringent washing, the membranes was incubated with alkaline phosphatase (AP)-conjugated anti-DIG antibodies (Roche). Immunoreactive bands were visualized using chemiluminescent substrate CSPD (Roche) followed by exposure to X-ray film.
Prediction of miRNA targets
CircRNA/miRNA interaction was predicted with miRNA target prediction software (Arraystar’s home-made) based on TargetScan and miRanda. TargetScan (Release 7.1,
http://www.targetscan.org) or miRBase (Release 21,
http://www.mirbase.org) were employed to identify the miRNA targeting sites in
TIF1γ 3’-UTR.
Luciferase reporter assay
A series of constructs containing
TIF1γ 3’-UTR and circPTK2 exon11 were generated using psiCHECK2 dual luciferase vector (Promega, Madison, WI, USA). Different fragments (Additional file
4: Table S2) were directly synthesized (GENEWIZ Inc., Suzhou, China), subcloned into the psiCHECK-2 vector to create various constructs. Each construct was subsequently cotransfected with miR-429 mimic (5’-UAAUACUGUCUGGUAAAACCGU-3′) or miR-200b-3p mimic (5’-UAAUACUGCCUGGUAAUGAUGA-3′) and a negative control (miR-NC, 5’-UUCUCCGAACGUGUCACGUTT-3′) into A549 and H226 cells. All the transient transfections, including miR-429 inhibitor (5’-ACGGUUUUACCAGACAGUAUUA-3′) or miR-200b-3p inhibitor (5’-UCAUCAUUACCAGGCAGUAUUA-3′) and anti-miR-NC (5’-CAGUACUUUUGUGUAGUACAA-3′), were performed using Lipofectamine 2000 (Invitrogen). After 48 h, cells were harvested, and luciferase activities were determined by the Dual-Luciferase Reporter Assay Kit (Promega). Results are presented as relative
Renilla luciferase activities, which are normalized to firefly luciferase activities. Each experiment was performed in triplicate.
RNA-binding protein immunoprecipitation (RIP) assay
RIP assay was performed using EZ-Magna RIP Kit (Millipore, Billerica, MA, USA). The AGO2-RIP experiments were performed in A549 cells transiently overexpressing miR-429/miR-200b-3p or miR-NC. Briefly, cells were lysed using RIP lysis buffer with proteinase and RNase inhibitors (Millipore), and the RIP lysates were incubated with RIP buffer containing magnetic beads conjugated with human anti-Ago2 antibody or nonspecific mouse IgG antibody (Millipore). Each immunoprecipitate was digested with proteinase K, and the immunoprecipitated RNAs were subjected to RT-PCR and gel-staining analyses to detect circPTK2 enrichment. Each RIP assay was repeated three times.
RNA pull-down analysis
RNA pull-down analysis was performed as previously described [
53] with some modification. Briefly, the RIP lysates from A549 cells were incubated with biotin (Bio)-labeled oligonucleotide probes against circPTK2 (
Bio-5’-TTAAACCAACATCTTTTCTGACACAGAGACGGCG-3′, RiboBio, Guangzhou, China) for 2 h at 25 °C. CircPTK2/miRNA complexes were captured with Streptavidin-coupled Dynabeads (Invitrogen). CircPTK2/miRNA/beads complexes were incubated with RIP wash buffer (Millipore) containing proteinase K for 1 h at 25 °C. CircPTK2 and miR-429/miR-200b-3p in the pull-down were determined using qRT-PCR analysis. The retrieved circPTK2 or miR-429/miR-200b-3p were evaluated as the percentage of pull-down to input. Each experiment was performed in triplicate.
Fish
Cells were cultured on coverslips, fixed and permeablized as previously described by us [
14]. Subsequently, the coverslips were hybridized in hybridization buffer (Geneseed Biotech, Guangzhou, China) with digoxin (Dig) and biotin (Bio)-labeled single-stranded DNA probes at 37 °C overnight. Digoxin-labeled probes (
Dig-5’-CATCTTTTCTGACACAGAGACGGCG-3′-
Dig) specific to circPTK2 back-splice region and biotin-labeled probes against miR-429/miR-200b-3p (for miR-429,
Bio-5’-ACGGTTTTACCAGACAGTATTA-3’-
Bio; for miR-200b-3p,
Bio-5’-TCATCATTACCAGGCAGTATTA-3’-
Bio) were prepared (Geneseed Biotech). The signals were detected by Cy3-conjugated anti-digoxin and FITC-conjugated anti-biotin antibodies (Jackson ImmunoResearch Inc., West Grove, PA, USA). Cell nuclei were counterstained with 4,6-diamidino-2-phenylindole (DAPI). Finally, the images were obtained on a Zeiss LSM 700 confocal microscope (Carl Zeiss, Oberkochen, Germany). Each experiment was performed three times.
Establishment of NSCLC cells transiently and stably overexpressing circPTK2
To establish A549 and H226 cell lines transiently overexpressing circPTK2, we subcloned full-length of 584-bp circPTK2 into a pLCDH-ciR lentiviral expression vector (Geneseed Biotech) to generate pLCDH-circPTK2-copGFP(T2A)Puro construct. The subcloned sequence containing front circular frame (SA), back circular frame (SD) of circRNA biogenesis and full-length of circPTK2, 5’-TGAAATATGCTATCTTACAG-circPTK2-GTGAATATATTTTTTCTTGA-3′, was directly synthesized (GENEWIZ Inc.). Cells was transiently transfected with the construct using Lipofectamine 2000. The empty vector was used as negative control. After transfection for 48 or 72 h, cells were harvested for additional more experiments.
To generate A549 cells stably overexpressing circPTK2, we cotransfected the above-mentioned construct or empty vector with packaging plasmids psPAX2 and pMD2.G (Geneseed Biotech) into HEK 293 T cells using Lipofectamine 2000 (Invitrogen). After HEK 293 T cells were cultured for 48 h, the packaged lentiviruses were harvested. A549 cells were infected with the virus and cultured for 3 days. Finally, A549 cells were selected with 0.5 μg/ml of puromycin (Sigma-Aldrich, St. Louis, MO, USA) for in vivo experiments of metastasis.
RNA interference for circPTK2 knockdown
CircPTK2 was specifically knockdown using siRNA (si-circPTK2, 5’-GUGUCAGAAAAGAUGUUGGUU-3′), which was designed by CircInteractome (
http://circinteractome.nia.nih.gov) and synthesized (GenePharma, Shanghai, China) to target circPTK2 back-splice junction. Scramble siRNA (5’-CACAGUCAAAAGAUGUUGGUU-3′) was used as a negative control. A549 and H226 cells were transfected with 100 pmol of siRNA using Lipofectamine 2000 (Invitrogen). After 48 or 72 h, cells were harvested for qRT-PCR analysis of circPTK2 and linear
PTK2 mRNA expression or for other experiments.
Transwell migration and invasion assays
Transwell assays were conducted to evaluate cell migration and invasion abilities as described by us [
14]. Briefly, A549 and H226 cells transiently overexpressing miR-429/miR-200b-3p or circPTK2 were incubated with TGF-β1 (5 ng/ml) in Transwell plates (BD Biosciences) for 24 h and 48 h. Then cells were allowed to migrate through an 8-μM pored membrane or invade through Matrigel-coated membrane. Migrated and invasive cells were stained and counted under a light microscope. Transwell assays were done in triplicate.
Female BALB/c nude mice (4–6 weeks, 18–20 g) were purchased from the Laboratory Animal Center of Soochow University, and were bred and maintained in specific pathogen-free conditions. Mice were divided into two groups, including circPTK2 overexpression group and control group (6 mice per group). CircPTK2-overexpressed and control A549 cells (3 × 10
6 cells/mouse) in PBS were intravenously (i.v.) injected into the tail vein of mice. TGF-β1 (4 μg/kg bodyweight) was injected intraperitoneally (i.p.) every 5th day post cell inoculation as previously described [
27] to facilitate TGF-β-induced cancer cell invasion. Fifty-six days post-inoculation, the mice were sacrificed and their lung, liver and heart tissues were histologically analyzed with H&E staining for the presence of metastasizing tumor cells. Before H&E staining, the number of metastatic nodules established in lung, liver and pericardium was counted. To monitor tumor cells metastasized to lung, bioluminescent imaging was performed using an IVIS® Spectrum in vivo imaging system (Caliper Life Sciences, Hopkinton, MA, USA). Approximately 15 min before imaging, the mice were injected i.p. with D-luciferin sodium salt (Yeasen Biotech, Shanghai, China) in PBS (15 mg/ml) at a dose of 150 mg/kg bodyweight. Following air anaesthesia with isoflurane, live images were acquired using photography and photons emitted from active luciferase within a region of interest (ROI) were quantified using Living Image® 4.0 software (measured in photons/sec/cm
2/steradian). Animal studies were approved by the Ethics Committee of Soochow University.
Statistical analysis
Difference between two groups was assessed using paired or unpaired t test (two-tailed). Pearson’s correlation test was used to determine the association between two groups. Results were presented as mean ± SEM. P values of < 0.05 were considered significant. Statistical analyses were performed using GraphPad Prism 5.02 software (GraphPad, San Diego, CA, USA).