Background
Non-small cell lung cancer (NSCLC) is the major type of lung cancer which is a leading course of cancer-related death worldwide [
1]. Although the treatment of NSCLC has been improved, the 5-years survival rate remains low owing to cancer relapse after surgery or radiotherapy [
2,
3]. Therefore, it is critical to better understand the molecular mechanisms of NSCLC progression and find out biomarkers to identify indolent and aggressive tumors, to provide novel therapeutic strategies.
Increasing evidence have demonstrated that the recurrence of NSCLC is mostly induced by cancer stem cells in tumors [
4‐
6]. Cancer stem cells are involved in cancer initiation, proliferation, invasion, and differentiation, resulting in occurrence of aggressive and metastatic cancers [
7]. Simultaneously, cancer stem cells can bring about multi-drug resistance in NSCLC [
8]. Thus, it is interesting and meaningful to investigate the association of cancer stem cell and NSCLC progression, that would create therapeutic strategies.
Long noncoding RNAs (lncRNAs) are involved in the progression of multiple cancers including NSCLC [
9‐
13]. AFAP1-AS1 (Actin Filament Associated Protein 1 Antisense RNA 1) is a lncRNA which promotes NSCLC cell proliferation by epigenetically suppressing p21 expression [
14]. Linc00673 (long intergenic non-protein coding RNA 673) modulates NSCLC cell proliferation, migration, invasion and epithelial mesenchymal transition via sponging miR-150-5p [
15]. Linc00473 (long intergenic non-protein coding RNA 473), regulated by cAMP/CREB (adenosine monophosphate/cAMP-response element binding protein), and LKB1 (liver kinase B1) inhibits lung cancer and controls tumor growth [
16]. Furthermore, lncRNAs also affect the stemness of lung cancer cells. DGC5 (DiGeorge syndrome critical region gene 5) contributes to cancer cell stemness-like properties by regulating miR-330-5p/CD44 in NSCLC [
17]. Linc00662 (long intergenic non-protein coding RNA 662) increases cancer stem cell-like phenotypes in lung cancer [
18]. FENDFRR (FOXF1 adjacent non-coding developmental regulatory RNA) inhibits cancer cell stemness by repressing expression of MDR1 (multi-drug resistance gene 1) by interacting with the RNA binding protein HuR in NSCLC development [
19]. Linc-ITGB1 (long intergenic non-protein coding RNA integrin subunit beta 1) decreases cancer stemness via down-regulating Snail in NSCLC [
20]. HAND2-AS1 (heart and neural crest derivatives expressed 2 antisense RNA 1) elevates cancer cell stemness of lung cancer cells via binding to TGF-beta1 (transforming growth factor beta1) [
21]. Interestingly, lncRNA ASAP1-IT1 (ArfGAP with SH3 domain, ankyrin repeat and PH domain 1intronic transcript 1) increases cell proliferation, invasion, and metastasis by regulating PTEN/AKT (phosphatase and tensin homolog/AKT serine/threonine kinase 1) axis in NSCLC [
22]. ASAP1-IT1 enhances stemness of cancer cells, and overexpression of ASAP1-IT1 indicates a poor prognosis in patients with bladder cancer [
23]. In addition, ASAP1-IT1 promotes development of cholangiocarcinoma through hedgehog signaling pathway [
24]. However, the role of ASAP1-IT1 on cancer cell stemness in NSCLC is largely unknown.
In this study, we explored the role of ASAP1-IT1 in NSCLC progression. The binding of ASAP1-IT1with miRNAs was predicted using LncBook database (a curated knowledgebase of human long non-coding RNAs) (
https://bigd.big.ac.cn/lncbook/index). We found that miR-509-3p was a potential target of ASAP1-IT1. Previous studies demonstrated that miR-509-3p functions as a tumor suppressor. For instance, miR-509-3p increases platinum drug sensitivity to induce cell apoptosis in ovarian cancer [
25,
26]. MiR-509-3p suppresses cell proliferation and migration by up-regulating XIAP (X-linked inhibitor of apoptosis) in gastric cancer [
27]. MiR-509-3p represses cell proliferation and invasion by decreasing XIAP in glioma [
28]. MiR-509-3p is down-regulated by the oncoprotein HBXIP (late endosomal/lysosomal adaptor, MAPK and MTOR activator 5) via activating NF-κB in hepatoma cells. Additionally, the potential targets of miR-509-3p were predicted using Target Scan tools, and the results showed that YAP1 (Yes associated protein 1) was a downstream target of miR-509-3pin NSCLC cells. YAP1 has been considered as an oncogene in multiple cancers including NSCLC [
29‐
33]. YAP1 positively regulates drug resistance and cancer cell stemness [
29,
30]. Also, YAP1is the main effector of the Hippo signaling pathway involved in human cancers [
34].
In this study, we investigate the role of ASAP1-IT1, and the association of ASAP1-IT1, miR-509-3p and YAP1 in NSCLC progression and cancer cell stemness.
Materials and methods
Clinical specimens
The NSCLC specimens were collected from 83 patients who were treated in the First Affiliated Hospital of Chengdu Medical College (Chengdu, China) from April in 2019 to September in 2020. The collection of clinical samples was approved by the ethics committee of Chengdu Medical College (approved ID: BR20re19), and each participant signed an informed consent form. All the patients were given no treatment before surgery. The collected specimens were stored in a liquid nitrogen tank.
Cell maintenance and transfection
The A549 and A549/R (cisplatin resistant) cells were obtained from China Infrastructure of Cell Line Resource (Beijing, China), and cultured in DMEM (Dulbecco’s Modified Eagle Medium) media (WISENT, Nanjing, Jiangsu, China) in a CO2 incubator at 37 °C. The DMEM media was supplemented with 10% FBS (fetal bovine serum), 100 mg/mL streptomycin and 100 U/mL penicillin (WISENT). The FBS was bought from Thermo Fisher Scientific (Waltham, Massachusetts, USA). All the other cell culture materials were bought from WISENT.
The cell infection was conducted according to the manufacturer’s instruction (Genechem, Shanghai, China). sh-ASAP1-IT1: 5′-GCU GCG ACA AUA GAC AUC GGA GUU U-3′, and sh-NC: 5′-CUC UCG GAA CAU GUC ACA U-3′. The mimic microRNAs and inhibitors were purchased from Ribobio (Guangzhou, China), miR-509-3p-related sequences were listed, Mock, 5′-UCU CCG AAC GUG UCA CGU U-3′; and anti-miR-509-3p, 5′-CCG UGG UUC AUA CUG GUA-3′; miR-509-3p mimic, 5′-UAC CAC AGG GUA GAA CCA CGG-3′. The pmirGLO-ASAP1-IT1-WT (wild type) or -Mut (Mutant), and pmirGLO-Yap1-3′UTR (untranslated region)-WT or -Mut (Mutant), and pcDNA-sh-NC, pcDNA-sh-ASAP1-IT1 were obtained from Thermo Fisher Scientific.
Hematoxylin–eosin (H&E) staining
The NSCLC specimens were fixed in 4% paraformaldehyde, embedded in paraffin and subjected to sectioning. Then, H&E staining was performed as described previously [
10]. All the chemicals and reagents were bought from Servicebio (Wuhan, Hubei, China).
RNA extraction and qRT-PCR (quantitative real time polymerase chain reaction)
The total RNA was extracted using TRIzol reagent (Life Technologies, Rockville, MD, USA). The reverse transcription kit (Thermo Fisher Scientific) was applied to synthesize cDNA (complementary DNA) from the total RNA. Quantitative RT‐PCRs were used to evaluate the levels of miRNAs, lncRNAs, or mRNAs using the SYBR Premix Ex Taq II (TaKaRa, Dalian, China). The qRT-PCR was carried out under the thermal cycling conditions: 95 °C × 5 min, and 40 cycles of 95 °C × 30 s, 60 °C × 30 s, and 72 °C × 1 min. GAPDH (glyceraldehyde-3-phosphate dehydrogenase) was used as the internal control for RNA and lncRNA, and U6 was used as the internal control of miRNAs. The relative RNA levels were calculated following the 2
−ΔΔCT method. The PCR primers were list in Table
1. All experiments were performed in quadruplicate, and each assay was repeated independently for 3 times.
Table1
The used PCR primers in this study
U6 | TGC GGG TGC TCG CTT CGG CAG C | GTG CAG GGT CCG AGG T |
miR-509-3p | UAC CAC AGG GUA GAA | CTC TAC AGC TAT ATT GCC AGC CA |
GAPDH | CAC CCA CTC CTC CAC CTT TG | CCA CCA CCC TGT TGC TGT AG |
Cyclin A1 | ATA ACG ACG GGA AGA GCG G | CAG GGT ACA TGA TTG CGG GA |
Cyclin B1 | CAG GTT GTT GCA GGA GAC CA | CAT GGC AGT GAC ACC AAC CA |
PCNA | CGC CCT GGT TCT GGA GGT AA | GGC TGA GAC TTG CGT AAG GG |
Bcl-2 | TTC TTT GAG TTC GGT GGG GT | GAA ATC AAA CAG AGG CCG CAT |
Bax | GGG TTG TCG CCC TTT TCT AC | AGT CGC TTC AGT GAC TCG G |
YAP1 | TGC TGT CCC AGA TGA ACG TC | GGT TCA TGG CAA AAC GAG GG |
ASAP1-IT1 | AAA CAT CAT CCC CAG AGT GG | GCC TTG CTC ACC TCT GAA AC |
SOX2 | CAT GAA GGA GCA CCC GGA TT | ATG TGC GCG TAA CTG TCC AT |
CD44 | GCC ACC AGA GCT ATT CCC AA | GGT CTT CGC CCA GCC TTT CT |
CD133 | GCC ATG CTC TCA GCT CTC C | TCC TGA AAA GGA GTT CCC GC |
Western blot
Total protein samples were prepared from the tissues or cells using RIPA (radio immunoprecipitation assay) buffer (Beyotime) for 30 min. The lysates were centrifuged at 12,000×g for 15 min to obtain the supernatants, and they were de-natured at 98 °C for 20 min. 50 μg proteins were used for sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) (Bio-Rad, Hercules, CA, USA). All the prepared gels were transferred to the 0.22 μm PVDF (polyvinylidene difluoride) membranes (Thermo Fisher Scientific) for 2 h, and the proteins-carried PVDF were blocked with 1% bovine serum albumin. Then, the PVDF membranes were incubated with the primary antibody overnight in a 4 °C refrigerator. The membranes were incubated with the HRP (horseradish peroxidase)-conjugated secondary antibody diluted at 1:50,000 (Bioworld Technology, Nanjing, China; Goat Anti-Rabbit IgG, Cat No. BS10550; Goat Anti-Mouse IgG, Cat No. BS12471) for 1 h. The anti-YAP1 (Cat No. MA5-32117), anti-β-Actin (Cat No. PA1-183-HRP), anti-Bax (Cat No. MA5-14003), anti-Bcl-2 (Cat No. MA5-11757), and Cleaved-caspase-3 (Cat No. MA5-32134) were bought from Thermo Fisher Scientific.
Cancer stem cells were sorted from A549 cells or transfected-A549 cells by sphero-cyst medium [
10], and the sorted cancer stem cells from A549 were named as A549-derived stem cells. The 3 × 10
4 cells were seeded in 6-well ultra-low cluster plates (Thermo Fisher Scientific). They were maintained in DMEM/F12 serum free medium (Thermo Fisher Scientific) containing epidermal growth factor (20 ng/mL), beta-fibroblast growth factor (20 ng/mL), insulin (4 μg/mL), and B27 (2%). All reagents were from Sigma. Finally, the number of spheres was counted under an inverted microscope (Leica, Oskar-Barnack-Straße, Germay) post 10 days incubation. The biomarkers of cancer stem cells SOX2, CD34, and CD133 were used to identify the cancer stem cells using qRT-PCR and Western blot.
The A549 cancer stem cells were isolated using magnetic bead kit, and 3 × 104 stem cells were seeded in six-well plates with ultra-low adhesion. They were cultured in sphere formation media for a week, and post another 20 days, the number of spheres was calculated under a microscope.
Cell apoptosis and cell cycle analysis
To determine cell apoptosis of A549-dereived stem cells and other cells, cells were collected at 80 g × 4 °C × 5 min for annexin-V/FITC (fluoresceine isothiocyanate)/PI (propidium iodide) staining after 48 h infection with the indicated plasmids or miRNAs. Briefly, cells were incubated with annexin-V and PI for 10 min and 5 min, respectively, in a dark room using the annexin V-FITC/PI staining kit (Beyotime, Beijing, China). Finally, the cell cycle was evaluated using the Beckman Coulter Navios EX flow cytometry (Beckman, Shanghai, China).
For analyzing cell cycle, the cells were cultured in 12-well plates (Thermo Fisher Scientific). After transfection with the indicated miRNAs or plasmids for 48 h, they were subjected to suspension and fixation in 75% ethanol at 4 °C for 12 h. Then, they were washed with PBS (phosphate‐buffered saline) for 3 times. Afterwards, they were resuspended in 500 μL staining buffer containing propidium iodide (5 mg/mL)/RNase (10 mg/mL) at 37 °C for 30 min in a dark room. Finally, cell apoptosis rate was evaluated using the flow cytometry. Each treatment group consisted four wells, and each assay was repeated for 3 times independently.
Cell counting kit‐8 (CCK-8) assay
The A549-dereived stem cells or A549 cells were plated into a 96-well plate (Thermo Fisher Scientific) at the density of 4 × 103 cells per well for determination of cell viability. CCK‐8 reagent (Sangon, Shanghai, China) were added into medium after the cells were cultured 36 h. After incubation for 1 h at 37 °C, the formation of water‐soluble formazan was examined in a microplate reader (Bio-Rad) with the light length of 450 nm. All experiments were performed in quadruplicate, and each assay was repeated independently for 3 times.
Dual luciferase reporter assay
To determine the effects of miR-509-3p on luciferase activity of pmirGLO-ASAP1-IT1, 2 × 104 A549 cells per well were seeded in 24-well plates. They were co-transfected with pmirGLO-ASAP1-IT1-WT (wild type), pmirGLO-ASAP1-IT1-Mut (Mutant), as well as Mock (negative control), miR-509-3p mimic, and anti-miR-509-3p. To examine the effects of miR-509-3p on luciferase activity of pmirGLO-Yap1-3′UTR, the cells were co-transfected with pmirGLO-Yap1-3′ UTR-WT, pmirGLO-Yap1-3′ UTR-Mut (Mutant), as well as Mock, miR-509-3p mimic, and anti-miR-509-3p. After transfection for 48 h, they were collected and lysed. The supernatants were used for measurement of luciferase activity using the Dual-Luciferase Assay Kit on GloMax 20/20 Luminometer following the manufacturer’s instructions (Promega, Madison, USA). All experiments were performed in quadruplicate, and each assay was repeated independently for 3 times.
RNA immunoprecipitation (RIP) assay
RIP assay was conducted to examine the interaction between ASAP1-IT1 and miR-509-3p using the RIP RNA-binding protein immunoprecipitation kit Magna (Millipore, Massachusetts, USA). Briefly, the cell lysate was incubated with anti-Ago2 (argonaute-2), and anti-IgG was used as a negative control. The antibodies were purchased from Bioworld Technology (Nanjing, China). At last, the collected immunoprecipitated RNA samples were used to determine ASAP1-IT1 and miR-1301-3p content by qRT-PCR analysis. All experiments were performed in quadruplicate, and each assay was repeated independently for 3 times.
Mouse tumorigenesis assay
The A549-dereived stem cells were infected with the mentioned shRNAs or plasmids as indicated. Post 48 h infection, the A549-dereived stem cells were collected at 80 g × 4 °C × 5 min. Afterwards, 4 × 106 cells were inoculated into 5-week-old nude mice. The BALB/c nude mice were bought from the Model Animal Research Center of Nanjing University (Nanjing, China), and divided randomly with 3 mice in each group. The animal experiments were approved by the research ethics committee of Chengdu Medical College (approved animal protocol No. CMC20LM22). The tumor volume was calculated every 3 days using the formula, tumor volume = (length × width2)/2. All the tumor-carried nude mice were sacrificed on the 24th day post inoculation.
Statistical analysis
Statistical analysis was conducted using SPSS software package (version 20.0, SPSS Inc., NY, USA) and GraphPad Prism 6 (GraphPad Software, CA, USA). A p value < 0.05 was considered statistically significant. The data were obtained from three independent experiments, and all data were expressed as mean ± standard deviation (S.D.). The statistical significance was examined using Two-tailed Student’s t-test for two-group comparisons and one-way analysis of variance (ANOVA) test with post-hoc analysis for multi-group comparisons.
Discussion
Increasing evidence have demonstrated that cancer stem cells participate in the aggressive and destructive behaviors of lung cancers including NSCLC, a main cause of cancer-induced death worldwide [
2,
3,
35,
36]. The cancer stem cells significantly increase the recurrence of NSCLC after surgery or radiotherapy [
4‐
6]. The cancer stem cells possess the properties of self-renewal, cancer initiation, and cancer progression [
7]. Cancer stem cells also aggravate multi-drug resistance in lung cancer [
8]. Therefore, exploring cancer stem cell-related potential molecular mechanism in NSCLC progression is critical, as it would contribute to the treatment of patients with NSCLC.
It has been reported that a variety of lncRNAs are involved in the progression of NSCLC [
14,
15,
37,
38]. As reported in previous studies, ASAP1-IT1 is upregulated in NSCLC and promotes cancer proliferation, invasion and migration [
22]. Consistent with this report, our preliminary sequencing data shows that ASAP1-IT1 was one of the top 20 up-regulated lncRNA in NSCLC with poor clinical outcome (data not shown). Moreover, ASAP1-IT1 was validated to be upregulated in NSCLC tumors, cancer cells, and A549 cell spheres. Cancer stem cells was reported to efficiently affect multi-drug resistance in NSCLC [
8,
39‐
42]. Here we demonstrated that knockdown of ASAP1-IT1 significantly suppressed cancer cell stemness of NSCLC cells and increase chemoresistance to cisplatin in NSCLC cells. ASAP1-IT1 was also overexpressed in A549/R cells, suggesting that ASAP1-IT1 could be associated with cisplatin resistance. Knockdown of ASAP1-IT1significantly inhibited cancer stem cell colony formation and A549 cancer cell stemness. Further studies demonstrated that knockdown of ASAP1-IT1 suppressed expression of stem cell biomarkers SOX2, CD34, and CD133 in A549-dereived stem cells. Then, downregulating ASAP1-IT1 expression decreased expression of cell growth-associated genes Cyclin A1, Cyclin B1, and PCNA, and elevated expression of cell apoptosis related genes Bax and caspase-3 and reduced anti-apoptotic Bcl-2 expression in A549-dereived stem cells. The in vivo experiments proved that knockdown of ASAP1-IT1 significantly inhibited tumor growth in nude mice. Thus, these in vitro and in vivo findings suggested that ASAP1-IT1 acted as an oncogene to regulate cancer cell stemness, cell growth and cell apoptosis in NSCLC. Down-regulation of ASAP1-IT1 could be a good strategy to fight against NSCLC.
LncRNAs exert their activity in cancers often by functioning as sponges of miRNAs [
15,
43]. In this study, ASAP1-IT1 was firstly predicted to interact with miR-509-3p. The interaction between ASAP1-IT1 and miR-509-3p was proved by luciferase RIP assays. Previous studies have revealed that miR-509-3p inhibits tumor growth in multiple types of cancers. For example, miR-509-3p improves sensitivity of cancer cells to platinum in ovarian cancer [
23,
24,
44], and it depresses cell proliferation and invasion via down-regulating X-linked inhibitor of apoptosis in glioma [
28]. MiR-509 promotes hepatoma progression by activating NF-κB (nuclear factor kappa B) signaling pathway. However, the role of miR-509-3p in the stemness of NSCLC has not been investigated. In consistent with previous studies, miR-509-3p was significantly down-regulated in NSCLC tissues, NSCLC cells, A549 spheres, and in A549/R cells. Overexpression of miR-509-3p suppressed sphere formation and cell growth, and increased cell apoptosis of A549-dereived stem cells. Also, overexpression of miR-509-3p decreased expression of SOX2, CD44, and CD133, and enhanced expression of Bax and caspase-3 while repressed Bcl-2 expression in cancer cells. Furthermore, overexpression of miR-509-3p suppressed tumor growth in nude mice. These results implied that miR-509-3p was a tumor suppressor, and overexpression of miR-509-3p could offer a novel approach to prevent NSCLC progression. Furthermore, overexpression of ASAP1-IT1 significantly blocked overexpression of miR-224-3p-mediated inhibition of cancer stem cell-like properties and cell growth of A549-dereived stem cells both in vitro and in vivo. Additionally, overexpression of ASAP1-IT1 abolished miR-509-3p-induced cancer cell apoptosis of A549-dereived stem cells both in vitro and in vivo, indicating that the interaction between ASAP1-IT1 and miR-509-3pis involved in regulation of cancer cell stemness and NSCLC progression.
Bioinformatics analysis showed that miR-509-3p could target the 3′UTR of YAP1, which is an oncogene in the Hippo signaling pathway involved in human cancers [
34]. Pan et al
. reported that miR-509-3p attenuates ovarian cancer cellular migration and formation of multi-cellular spheroids by targeting YAP144. Our study also demonstrates that miR-509-3p abrogates cancer cell stemness via downregulation of YAP1. Our results were in consistent with the previous studies which supported that YAP1 is an oncogene and aggravates drug resistance and cancer cell stemness in NSCLC [
29‐
33,
45,
46]. Moreover, we also observed that interaction of ASAP1-IT1 with miR-509-3p led to reciprocally inhibition. These findings demonstrated that YAP1 is involved in ASAP1-IT1/miR-509-3p interaction and plays an important role in cancer cell stemness and progression of NSCLC.
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