Background
The incidence and mortality of Hepatocellular carcinoma (HCC) have been continuously rising in recent decades [
1]. The treatment of HCC is a comprehensive treatment mode based on radical resection,still lacks effective molecular therapeutic targets. Though great efforts have been made to improve treatment options, HCC is still associated with a poor prognosis [
1]. Therefore, research on the molecular mechanisms of HCC pathogenesis is urgently needed.
Circular RNAs (circRNAs) are members of newly discovered non-coding RNAs, initially disregarded as functionless products of pre-mRNA splicing errors [
2]. However, an increasing number of circRNAs have been identified and studied, and their roles in organisms have been gradually discovered and considered pervasive regulatory molecules. Numerous studies have pointed out that circRNA is closely correlated with the pathogenesis of tumors, including HCC [
3‐
6]. The classical research mechanisms related to circRNA include molecular sponge, m6A modification, RNA binding protein, translation, etc. [
7‐
11]. In addition, circRNA can also be transported through extracellular vesicles, which has the potential to affect the chemosensitivity of tumor cells and function as targets of chemotherapy drugs for treating malignancies [
12‐
14]. Moreover, the circRNA-based vaccine has been successfully designed and the vaccine can be rapidly generated by in vitro transcription without nucleotide modification, and has strong stability [
10]. All the above-mentioned indicate that circRNA has extensive research value. However, a large number of circRNAs remain to be discovered and studied.
In the present study, we performed high-throughput sequencing on HCC and paired normal liver tissues and identified a significantly upregulated circRNA-a newly discovered circRNA--circPAK1, for the subsequent molecular mechanism exploration. Our data demonstrated that circPAK1 was significantly upregulated in HCC tissue and cell lines, and high levels of circPAK1 develop poor outcomes in HCC patients. We further validated the oncogenic role of circPAK1 through in vitro and in vivo experiments. Moreover, we constructed Chitosan /si-circPAK1 (CS/si-circPAK1) nanocomplexes and its effective inhibition of tumor growth and metastasis brought us new insight into molecular therapy combined with nanometer materials. Mechanistically, we demonstrated that circPAK1 functioned as an oncogene via directly binding to 14–3-3ζ to facilitate YAP nucleus translocation and inactivate Hippo signaling pathway. Importantly, we surprisingly found that circPAK1 can be transported by exosomes through lenvatinib-resistant cells to lenvatinib sensitive cells to decrease the sensitivity of HCC cells to lenvatinib. Taken together, circPAK1 can be taken as a promising therapeutic target in HCC treatment.
Methods
Patient samples
Overall, HCC tissue samples (60 cases) were collected from HCC patients who received a primary surgery attempt between September 2015 and August 2019 at the First Affiliated Hospital of Nanjing Medical University. Patients who lacked detailed clinical pathological information and who received preoperative chemotherapy or radiotherapy were excluded. Written informed consent was obtained from all patients and the study protocol was approved by the Ethical Committee of the First Affiliated Hospital of Nanjing Medical University.
Cell lines and culture conditions
Human HCC cell lines, including Hep-G2, Focus, Hep-3B, MHCC-97 L, HCC-LM3 (LM3), YY8103, Huh-7, and L02 cell lines were purchased from the Chinese Academy of Sciences Cell Bank (CASCB, Shanghai, China). All the HCC cell lines were cultured with DMEM (Gibco, MD, USA). HUVECs were obtained from the American Type Culture Collection (ATCC, VA, USA) and cultured with RPMI-1640 (Gibco, MD, USA). All the cells were supplemented with 10% fetal bovine serum (HyClone, UT, USA) and 1% penicillin/streptomycin at 37 °C with 5% CO2 in an incubator.
Cell line establishing and generation of lenvatinib-resistant cells
The shRNA targeting the junction site or random sequence of human circPAK1 was designed and synthesized to establish the sh-circPAK1 vector, while the lentiviral vectors containing human circPAK1 were also to construct the Lv-circPAK1 vector. The above lentiviral vectors were synthesized by GeneChem (Shanghai, China). After the transfection of lentiviral vectors into target cells, stably transduced cells were selected by puromycin and validated by qRT-PCR. The silencing RNA against YAP (si-YAP) and 14–3-3ζ (si-14-3-3ζ) were synthesized and purchased from Corues Bio (Nanjing, China). The target sequence of shRNA or siRNAs were listed in Table S
1, and the full sequence of circPAK1 was listed in Table S
2. We selected LM3 and Hep-3B cells to induce lenvatinib-resistant HCC cells. Lenvatinib was purchased from MCE (MedChemExpress, NJ, USA). Briefly, cells were exposed to graded drug concentrations (5 μmol/L to 25 μmol/L) step by step to induce lenvatinib resistance. After 4 months of induction, the two lenvatinib-resistant HCC cell lines were generated.
Preparation of CS/si-circPAK1 nanocomplexes
CS/si-circPAK1 nanocomplexes was designed and synthesized by Shennuoqing Biotechnology (Nanjing, China).
In vivo nude mouse model
A total of 84 female BALB/c nude mice (4–6 weeks old) were purchased from the Model Animal Research Center of Nanjing Medical University (NJMU). The mice were randomly divided into 12 groups of 6 each. All mice were housed in a pathogen-free environment, and animal experiments were authorized by the NJMU Institutional Animal Care and Use Committee.
To evaluate the roles circPAK1 played in vivo, we first randomly chose four groups to establish a subcutaneous tumor model: Two groups of mice were subcutaneously injected with 1 × 106 LM3 cells infected with sh-circPAK1 or sh-NC, the other two groups subcutaneously injected with 1 × 106 Hep-3B cells transfected with Lv-circPAK1 or Lv-NC. Tumor diameters were recorded every 4 days using a caliper. The tumor volume was calculated using the following formula: volume (mm3) = 0.5 × width2 × length. After 32 days, the mice were sacrificed to harvest and weigh the grafted tumors. To evaluate the roles of circPAK1 on lung metastasis, we set another 4 groups to receive tail vein injection transfected cells (LM3 and Hep-3B) to establish a lung metastasis model. The mice were sacrificed after 30 days, and the lungs were separated and stained with hematoxylin and eosin (H&E).
In addition, CS/si-circPAK1 nanocomplexes treatment and non-treatment groups were established. LM3 cells were used to generate subcutaneous xenograft tumor and lung metastasis models according to the above protocol. After 8 days, saline, si-circPAK1 (10 nmol, in vivo-grade cholesterol-conjugated RIG-I siRNA, RiboBio), or CS/si-circPAK1 nanocomplexes (10 nmol) were injected intratumorally (50 μl) or intravenously (200 μl) into the six groups, once every 4 days, respectively. Mice were treated as described above.
Haematoxylin and eosin (H&E) and immunohistochemical (IHC) staining
Mice lung tissues were embedded in Paraffin and cut into 5 μm sections for H&E staining. While mice tumor tissues were fixed with 4% paraformaldehyde, dehydrated using ethanol solution, and then embedded in paraffinand cut into 4 μm sections, incubated with 3% H2O2 solution. Twenty minutes later, blocking the slice with blocking solution for 30 min, and incubating with the corresponding primary antibody at 4 °C overnight. The rest steps were consistent with previously described. Images were captured using a microscope (Leica Microsystems, Germany). The staining results were evaluated in a double-blind manner.
RNA extraction and quantitative real-time polymerase chain reaction (qRT-PCR)
Total RNA was extracted from cells or frozen human tissues using RNA Quick Purification kit (YiShanbio, Shanghai, China) in accordance with the manufacturer’s instructions. Reverse transcription was performed using a cDNA kit (Vazyme Biotech, Nanjing, China) to synthesize the cDNA. All the primer sequences used in this study were listed in Table S
3. qRT-PCR was performed using SYBR Green PCR kits (Vazyme Biotech, Nanjing, China) on the ABI 7900 detection system (Applied Biosystems, CA, USA). and the CT values were determined. The relative expression of circPAK1 and mRNA were calculated using the 2
-ΔΔCt method. GAPDH and U6 were used as internal standards.
Western blot
Proteins were extracted by using RIPA buffer (Beyotime, Shanghai, China) containing protease inhibitors. Protein lysates were separated using 10% sodium dodecyl sulfate-polyacrylamide gels (SDS-PAGE) and subsequently transferred onto polyvinylidene fluoride membranes (Millipore, MA, USA). The membranes were subsequently blocked with fast blocking buffer (Beyotime, Shanghai, China) for 50 min and then incubated with primary antibodies at 4 °C overnight. After incubating with the respective secondary antibodies for 1 h and washing three times every 10 min with Tris-buffered saline with Tween-20 (TBST), the ECL signals were visualised by using ECL Western Blotting Kit (Millipore, MA, USA). Antibodies used in this study were listed in Table S
4.
CCK-8 cell proliferation assay
Cell Counting Kit-8 was performed as we described before [
15].
For colony formation assay, cells were plated at a density of 600 cells per well into 6-well plates and cultured in complete media for approximately 10 days. After 10 days, the colonies were fixed using formaldehyde and then stained with 0.1% crystal violet (Vicmed, China). These colonies were subsequently photographed and counted visually.
EdU proliferation assay
The EdU proliferation assay was performed using an EdU kit (Beyotime, Shanghai, China). Briefly, cells were inoculated in 96-well plates at a density of 1 × 104 cells per well, then cultured for 12 h and incubated with EdU for 2 h. The rest steps are performed according to the manufacture’s instructions. After staining for nucleic acids with DAPI (Beyotime, Shanghai, China), images were acquired by using an inverted fluorescence microscope (Nikon, Tokyo, Japan).
Transwell assay
The invasion and migration assay were performed using trans-well chambers (Corning, USA) pre-covered or uncovered with Matrigel (BD Biosciences, USA), respectively. Briefly, 5 × 104 cells were seeded onto the upper chamber, while 600ul medium with 10% FBS was provided in the lower chamber. After 24-36 h of incubation, cells on the upper membrane surface were scraped off, the invaded and migrated cells were fixed with methanol and stained with 0.1% crystal violet for 30 min. Images were acquired by using an inverted microscope.
Wound healing assay
Cells were seeded onto 6-well plates. When the confluence of cells reached more than 80%, the monolayers were scratched by a 200 μL pipette, and the cell debris was removed by washing with PBS. After that, cells were cultured with medium without FBS. Images of cell migration were captured at the same locations at 0 h, 24 h and 48 h.
Cell cycle and apoptosis analysis
Cell cycle and apoptosis analysis were performed as we described before [
15].
RNA pull-down assay and mass spectrometry
RNA pull-down was performed using a kit (Thermo Fisher Scientific, CA, USA). The biotinylated circPAK1 probe and control probe were designed by RiboBio (Guangzhou, China), and the probe sequences were listed in Table S
5. Approximately 1 × 10
7 LM3 cells were lysed and then incubated with biotinylated probes for 4 h at 4 °C. After that, incubated with 50 μL of streptavidin-coated magnetic beads at room temperature for 1 h. Then, the beads-probe-protein complex was washed with wash buffer. The retrieved proteins were boiled in a SDS buffer and separated using SDS-PAGE, followed by staining with fast silver stain kit (Beyotime, Shanghai, China). The protein bands in circPAK1 probe group in comparison with control group were analyzed by Q Exactive mass spectrometer (Thermo Fisher Scientific, CA, USA).
RNA immunoprecipitation (RIP) assay
RIP was performed using Magna RIP RNA Binding Protein Immunoprecipitation Kit (Millipore, MA, USA) according to the manufacturer’s protocols. Antibodies including anti-IgG (Millipore, MA, USA), anti-YAP (Proteintech, Wuhan, China) and anti-14-3-3ζ(Proteintech, Wuhan, China) were listed in Table S
4. The relative interaction between circRNA and proteins were assessed by qPCR, and normalized to input.
Co-immunoprecipitation (co-IP) assay
To evaluate the binding between LATS2, YAP and 14–3-3ζ, proteins were immunoprecipitated by using a IP kit (Thermo Fisher Scientific, CA, USA) according to the manufacture’s protocols and then assessed by immunoblotting.
Cytoplasm and nucleus fractionation
Cytoplasm and nucleus fractionation was performed with Nuclear and Cytoplasmic Protein Extraction Kit (Beyotime, Shanghai, China) in accordance with the manufacturer’s instructions (Beyotime, Shanghai, China). Cytoplasm and nucleus fractionations of protein and RNA were analyzed by western blot and qPCR respectively, to determine the level of YAP.
Fluorescence in-situ hybridization (FISH)
Briefly, after the fixation and permeabilization of HCC cells, Hybridization with circPAK1 probe (Sequence is shown in Table S
5) (RiboBio, Guangzhou, China) was performed with a Fluorescent in Situ Hybridization Kit (RiboBio, Guangzhou, China) in accordance with the manufacturer’s instructions. Fluorescence images were acquired using a confocal laser scanning microscopy (Zeiss, Jena, Germany).
RNA sequencing
To identify differentially expressed circRNAs, circRNA sequencing was performed using 3 paired HCC tissues and adjacent normal tissues. The tissue quality control, sample preparation and circRNA sequencing were performed by Huada Gene (Shenzhen, China). To explore the influence of circPAK1 knockdown on global gene expression profiles, circPAK1-knockdown and control LM3 cells were lysed in Trizol. The RNA sequencing was analyzed by Tiangen Biotech (Beijing, China).
Exosome isolation
Exosomes were isolated from CM by differential ultracentrifugation. Briefly, cells were cultured in DMEM with 10% exosome-free FBS (Absin, Shanghai, China). When the confluence of cells reached more than 80%, CM was collected and centrifuged at 300 g for 10 min. Subsequently, cells and debris were removed through 2 × 103 g centrifugation for 20 min and 1 × 104 g centrifugation for 30 min. The resulting supernatant was pre-cleared through 0.22 μm filters (Millipore, MA, USA), followed by ultra-centrifugation at 1× 105 g for 70 min. Repeat the previous step and the exosomes can be collected. For exosomal RNA extraction, exosomes were pre-treated with RNase, and an equal number of exosomes were used for RNA extraction.
Transmission electron microscopy (TEM)
Exosomes were examined by electron microscopy using negative staining and quantified using the NanoSight NS300 instrument (Malvern Instruments Ltd. UK) equipped with NTA 3.0 analytical software (Malvern Instruments Ltd. UK).
Discussion
HCC is still one of the most lethal malignant tumors, which seriously influences the quality of human life [
41]. With the improvement of diagnosis and treatment options, the 5-year survival rate of postoperative HCC increased to a certain extent. Surgical intervention is still the primary treatment option for HCC. However, for radical resection is only suitable for HCC at an early stage, while the early symptoms of HCC are not typical and patients are often diagnosed at an advanced stage, so the treatment options are limited and the therapeutic effects are unoptimistic.
Molecular-targeted therapies are to design the corresponding therapeutic drugs aiming at the established carcinogenic sites (which can be a protein or a gene fragment inside the tumor cells). Despite the remaining molecular-targeted drugs for HCC have gained a lot benefits, drug resistance is still the main reason that affects the efficiency of chemotherapeutic drugs [
42,
43]. Therefore, there is an urgent need to identify other effective molecular therapy targets.
Accumulating studies prove that circRNAs play a crucial role in the progression of various malignancies [
4‐
7]. The biological functions of circRNAs are diverse, mainly including serving as miRNA sponge, translating, modulating alternative splicing and transcription, interacting with RNA binding proteins (RBPs), translocating, etc.
In this study, we performed high-throughput sequencing and combined with a series of filter conditions, a significantly upregulated circRNA, circPAK1, was finally identified. Clinically, circPAK1 was significantly upregulated in HCC tissues, and high expression of circPAK1 negatively correlates with tumor size, LN metastasis, TNM stage and MVI. Functionally, a series of in vitro and in vivo experiments demonstrate that circPAK1 could promote the proliferation, invasion and metastasis of HCC. We also noticed that overexpression of circPAK1 leads to apoptosis inhibition and angiogenesis of HCC.
Gene-targeted therapy provides a promising option for treating malignancies that are insensitive to chemotherapy. Nanomedicines encompass various nanocarriers with sizes ranging between 10 nm and 1000 nm. They are highly useful owing to their small size and particle dimension, high aspect ratio, encapsulation ability, and the opportunity to functionalize the surface to deliver loaded cargos, including plasmid DNA, small interfering RNA and mRNA [
44‐
46]. Herein, we generated CS/si-circPAK1 nanocomplexes with Chitosan material to simulate gene-targeted therapy. Surprisingly, by subcutaneous xenograft and lung metastasis models, we found that the application of CS/si-circPAK1 nanocomplexes could inhibit the growth and metastasis of HCC effectively, even better than animal grade si-circPAK1. These findings may bring us inspiration in the construction of HCC circPAK1-targeted drugs.
To clarify what mechanism circPAK1 exercised in HCC progression, we then performed RNA-seq and found that Hippo signaling pathway was highly correlated with the downstream of circPAK1. The hippo pathway is an important signaling transduction pathway in the development of organisms, especially in regulating organ size and inhibiting tumorigenesis and immune response. An indispensable function of the Hippo pathway inhibits the activity of YAP, a putative oncogene whose activity is regulated by phosphorylation and subcellular localization. When the Hippo pathway is activated, YAP is phosphorylated by LATS1/2 kinase and isolated in cytoplasm by binding to 14–3-3 protein, thus leading to the inactivation of YAP [
31]. In contrast, the inactivation of Hippo pathway will cause the none-phosphorylated YAP translocate to the nucleus, accordingly interacting with various transcription factors, including members of the transcriptional enhancer factor (TEF) family, which is also called the TEA domain (TEAD) family (TEAD1–4) [
30,
47]. TEAD family proteins are widely expressed in tissues, and the YAP/TEAD complex is vital in regulating the expression of genes related to cell proliferation and apoptosis [
47]. Our results demonstrate that circPAK1 has a significant regulatory effect on the nucleus translocation of YAP; meanwhile, the downstream effectors of YAP, CTGF and CYR61, were downregulated after the knockdown of circPAK1, but upregulated when circPAK1 overexpression.
Based on the previous study of circRNA in delivering YAP into the nucleus by binding to YAP directly to promote the EMT of CRC [
32], we performed RIP to validate whether circPAK1 has similar biological effects. However, the RIP assay failed to confirm this interaction, this made us speculate that there may exist other RBPs mediate the YAP nucleus translocation indirectly. To validate this speculation, we designed the specific probe of circPAK1 and performed the RNA pulldown assay to determine the RBPs of circPAK1. Although the key molecules in the hippo pathway are not involved among these pull-down proteins, it is worth noting that 14–3-3ζ protein showed a strong binding ability with circPAK1. We further confirmed the existence of this binding by RIP and WB. 14–3-3 family proteins play a key regulatory role in signal transduction, checkpoint control, apoptosis and nutrition sensing channels [
48,
49]. The binding of 14–3-3 will shade the special sequence of the target protein and then affect the localization phosphorylation state, stability and intermolecular interaction of the target protein [
48‐
51]. The dysregulation of 14–3-3 is highly correlated with the occurrence and development of tumor [
52]. At least seven subtypes of 14–3-3, β, γ, ε, σ, ζ, τ and η, have been found in mammals. The spatio-temporal expression patterns of different 14–3-3 protein subtypes were found during the growing development and acute response to extracellular signals and drugs, indicating that although the sequences of 14–3-3 protein subtypes are similar, they may have different functions [
51]. Our results showed that circPAK1 competitively binds to 14–3-3ζ with YAP,thus impairing the recruitment and cytoplasm fixation of 14–3-3ζto YAP, consequently promoting the nucleus transportation and the amplification of downstream target genes of YAP.
As a multikinase inhibitor, lenvatinib was approved by the US Food and Drug Administration (FDA) for unresectable HCC patients in 2018. However, drug resistance is still the major hurdle that limits the application and efficiency of Lenvatinib [
43]. Therefore, it is extremely important to elucidate the detailed mechanisms for chemoresistance. Multiple lines of evidence have suggested that circRNAs play a pivotal role in regulating drug resistance. For example, Xu et al. [
13] reported that they found circRNA, which they named circSORE, could induce sorafenib resistance to HCC. Zhang et al. [
53] demonstrate that circMED27 promotes HCC resistance to lenvatinib. Liu et al. [
54] revealed that ectopic expression of circKCNN2 in HCC cells enhanced the therapeutic effect of lenvatinib. These results suggest that circRNAs are involved in the regulation of chemoresistance. Since the RNA-seq results showed that the VEGF pathway is also associated with circPAK1, and circPAK1 has been shown to promote angiogenesis in our functional experiments, we speculate that circPAK1 may affect the chemosensitivity of HCC. Surprisingly, circPAK1 was overexpressed in lenvatinib resistance cell lines than their parental cells, and the knockdown of circPAK1 increased the lenvatinib sensitivity of lenvatinib resistance cells, indicating that circPAK1 is crucial for maintaining lenvatinib resistance.
Additionally, we demonstrated a novel mechanism that exosomes released by lenvatinib resistant cells could mediate circPAK1 transfer and transmission of lenvatinib resistance, and this finding is consistent with the recently reported studies on the transmission of chemotherapy resistance by tumor-derived exosomal circRNAs [
12,
13,
55]. Our findings may make exosomal circPAK1 a promising biomarker in liquid biopsy for the early identification of lenvatinib resistance and provide new ideas for overcoming lenvatinib resistance.
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