Introduction
Rhabdomyosarcoma (RMS) is a type of soft tissue sarcoma observed occurring in children, which consists of skeletal myoblast-like cells with a high-grade neoplasm [
1]. RMS can be divided into two histopathological subtypes: embryonal rhabdomyosarcoma (ERMS) and alveolar rhabdomyosarcoma (ARMS) [
2]. The 5-year overall survival rates of children with RMS have improved significantly due to the adoption of multimodal therapeutic protocols [
3]. However, children with high-risk RMS usually have low survival rates due to the development of chemoresistance and the metastasis and recurrence of this disease [
4]. Uncovering the molecular mechanisms underlying RMS may assist in identifying novel therapeutic targets and improve the prognosis of patients with this malignancy.
Long noncoding RNAs (lncRNAs) are noncoding RNA constructs > 200 nucleotides in length that act as powerful intermediaries in numerous cellular physiological processes during the development and progression of almost all diseases [
5]. Studies have shown that lncRNAs play roles in regulating cancer stem cells (CSCs) by targeting specific signaling pathways and transcription factors. The importance of lncRNAs as potential therapeutic targets for the elimination of CSCs has been emphasized in many research studies, as lncRNAs have the ability to maintain the characteristics of stem cells and facilitate the development of tumors by regulating gene expression. Some lncRNAs are well established to have tumor-specific expression, and these lncRNAs possess unique regulatory functions in tumor cells, ranging from mediating increases in invasion/migration to mediating recurrence, and have been considered prognostic/diagnostic biomarkers or therapeutic targets [
6‐
9]. lncRNAs regulate tumor progression through a variety of mechanisms, and the function of lncRNAs as competitive endogenous RNAs (ceRNAs) allows them to abolish miRNA-mediated inhibition of target genes by sponging microRNAs (miRNAs/miRs) [
10]. miRNAs are a type of endogenously activated small noncoding RNA, 18–25 nucleotides in length, that bind to the 3’-untranslated regions (3’-UTRs) of their target genes to regulate their expression. They reduce the stability and thus also the translational efficiency of mRNAs [
11]. Therefore, the expression levels of tumor suppressors may be decreased and the expression levels of oncogenes increased by miRNAs during the initiation and/or development of RMS [
12].
Guanine nucleotide exchange factor T (GEFT, ARHGEF25, or p63RhoGE), which is encoded by a gene located on chromosome 12q13.3, is a member of the Rho guanine nucleotide exchange factor family and is typically expressed in excitable tissues, including brain, muscle, and heart tissues. GEFT accelerates GDP/GTP exchange to activate Rho GTPases. It also plays essential roles in skeletal muscle regeneration and myogenic differentiation [
13‐
16]. Our previous studies indicated that GEFT had high expression in RMS and that high GEFT expression was significantly related to poor prognosis, lymph node metastasis and distant metastasis [
17,
18]. GEFT exerts its tumor-promoting effect via positive regulation of the proliferation, migration, invasion, and antiapoptotic capabilities of RMS cells via regulation of the Rac1/Cdc42-PAK signaling pathway to induce EMT [
19]. mTOR is encoded by a gene located on chromosome 1p36.2 and is a member of the PI3K-related kinase family. It is often involved in regulating cell survival, growth, metabolism, protein synthesis, and autophagy, and the mTOR signaling pathway is dysregulated in numerous types of cancer and is frequently associated with carcinogenesis and tumor progression; thus, mTOR represents an ideal and promising therapeutic target. In addition, several studies have shown that lncRNAs are regulators of mTOR signaling in cancers [
20]. In the present study, GEFT was found to positively regulate mTOR expression in RMS cells and to promote tumor progression to some extent through its ability to induce mTOR expression. However, the potential molecular mechanism by which GEFT modulates mTOR expression in RMS remains undetermined.
In the present study, a novel lncRNA, termed lnc-PSMA8-1 (ENST000000580975), was identified and shown to be activated by GEFT and highly overexpressed in RMS cell lines and tissues, which was indicative of poor prognosis. Next, it was shown that lnc-PSMA8-1 promoted the proliferation and migration of RMS cells and upregulated the expression of mTOR by sponging miR-144-3p. Thus, whether lnc-PSMA8-1, miR-144-3p, and/or mTOR could be considered novel therapeutic targets for RMS and how the lnc-PSMA8-1R/miR-144-3p/mTOR axis regulates RMS progression in vivo will be assessed in future studies.
Materials and methods
Clinical samples
In the present study, 20 paraffin-embedded RMS tissues and 10 normal skeletal muscle tissues were obtained from the First Affiliated Hospital, Shihezi University (Xinjiang, China) and the First Affiliated Hospital, Xinjiang Medical University (Xinjiang, China). The inclusion criteria were a diagnosis confirmed by two pathologists and the lack of systemic or local therapy prior to surgery. The exclusion criteria were a history of a second primary malignant tumor and local recurrence or metastasis. The pathological images of RMS samples are shown in Fig.
S1. All the patients and their families were informed regarding specimen collection, and the patients’ parents/guardians provided written informed consent. All experiments were approved by the Ethics Committee of Shihezi University School of Medicine (No. 2019-021-01).
Cell culture
The ERMS cell lines RD and A204 were obtained from the Cell Bank of the Chinese Academy of Sciences (Shanghai, China) and Fu Xiang Biotechnology Co., Ltd. (Shanghai, China). The ARMS cell lines RH30 and PLA802 were purchased from Shanghai Fu Xiang Biotechnology Co., Ltd. and Shanghai Hong Shun Biotechnology Co., Ltd. The human skeletal muscle cell line HSKMC was purchased from Beijing Be Na Biotechnology Co., Ltd. The above cell lines were cultured in DMEM (Gibco; Thermo Fisher Scientific, Inc.) supplemented with 10% fetal bovine serum (Biological Industries, Israel) and 1% streptomycin-penicillin (Solarbio, China) at 37 °C in a humidified incubator under a 5% CO2 atmosphere.
Cell transfection
Shanghai GeneChem Co., Ltd. designed and synthesized the GEFT and lnc-FAM59A-1 overexpression plasmids, the GEFT interference plasmid, and the empty vector. The siRNAs against human lncRNAs (lnc-CEACAM19-1, lnc-VWCE-2, lnc-GPX7-1, lnc-PSMA8-1) and mTOR, the miR-144-3p mimic, the antisense miR-144-3p inhibitor, and the negative scramble control RNA oligo were purchased from Shanghai GenePharma Co., Ltd. Lipofectamine 2000 (Thermo Fisher Scientific, Inc.) was used for all transient transfections.
RNA preparation and quantitative reverse transcription–PCR (qRT‒PCR)
Using a miRNeasy FFPE Kit or a miRNeasy Mini Kit (QIAGEN GmbH), total RNA was obtained from tissue samples or cultured cell lines, respectively. A Cytoplasmic and Nuclear RNA Purification Kit (Norgen Biotek Corp.) was used to isolate and purify cytoplasmic and nuclear RNA according to the manufacturer’s protocol. Reverse transcription was performed with a miScript II RT Kit (QIAGEN GmbH). cDNA was subsequently subjected to qRT‒PCR analysis on an Applied Biosystems 7500 Real-Time PCR System (Thermo Fisher Scientific, Inc.) using a miScript SYBR Green PCR Kit (QIAGEN GmbH). Subsequently, the samples were amplified by PCR, and the 2
-∆∆Ct method was used to calculate relative gene expression levels. The sequence-specific qRT‒PCR primers targeting miR-144-3p and U6 were designed and purchased from Shanghai GenePharma Co., Ltd. Additional RNA sequence-specific qRT‒PCR primers were acquired from Sangon (Shanghai, China). All of the sequences of the real-time PCR primers are listed in Table
S1.
Microarray analysis
Total RNA was obtained from GEFT-overexpressing and GEFT-knockdown RMS cells (RD, A204, RH30, and PLA802), amplified, and then used to synthesize fluorescent cRNA. The labeled cRNA was hybridized onto an Affymetrix Genechip® Human Transcriptome Array 2.0 (Affymetrix Inc.). The microarray experiments and data analyses were performed by Beijing Compass Biotechnology Co., Ltd.
Cell proliferation and apoptosis assays
A CCK-8 assay (Dojindo Molecular Technologies, Inc.) was performed according to the manufacturer’s instructions to evaluate cell proliferation. Approximately 4 × 103 cells per well were seeded into four 96-well plates and cultured with DMEM. After 0, 24, 48, or 72 h, 10 µl of CCK-8 reagent per well was added, and the cells were further incubated for 1.5 h at 37 °C. Subsequently, the optical density at 450 nm (OD450) was measured.
An Annexin V-APC/PI Apoptosis Detection Kit (KeyGEN, Chain) was used to analyze apoptosis 48 h post-transfection according to the manufacturer’s instructions. The apoptosis rate of cells was determined with a PAS flow cytometry system (PARTEC, Germany).
Cell invasion and migration assays
A total of 2.5 × 105 cells in 0.2 ml of serum-free DMEM were seeded into the upper chamber of a Transwell insert (8 μm pore size, Costar; Corning, Inc.) containing a membrane coated with Matrigel for the invasion assay and an uncoated membrane for the migration assay (BD Biosciences). After 24 h of incubation at 37 °C for 24 h, the transfected cells that had migrated through or invaded into the insert membrane were fixed and stained using 0.5% crystal violet solution. Subsequently, the number of invaded or migrated cells was determined using an optical microscope (Olympus BX51).
RNA-binding protein immunoprecipitation (RIP)
A total of 5 × 105 RD or RH30 cells were plated in 100 mm cell culture dishes and incubated for 24 h. Subsequently, the cells were transfected with the miR-144-3p mimic or miR-NC. Then, 48 h after transfection, in accordance with the manufacturer’s protocol, a RIP kit was used to assess the binding of endogenous Ago2 to RNA by RIP with an anti-Ago2 monoclonal antibody (Millipore Sigma); IgG was used as the control. Finally, the relative enrichment of lnc-PSMA8-1 and mTOR in the immunoprecipitates was determined by qRT‒PCR.
Luciferase reporter assay
We used the DIANA, RNA22, miRanda and miRWalk2.0 bioinformatics tools to predict the binding sites between lnc-PSMA8-1 and miR-144-3p and between the mTOR 3’UTR and miR-144-3p. Luciferase plasmids that contained the wild-type lnc-PSMA8-1 binding site (lnc-PSMA8-1-WT) or mutated lnc-PSMA8-1 binding site (lnc-PSMA8-1-MUT) or the wild-type mTOR 3’UTR (mTOR 3’UTR-WT), or mutated mTOR 3’UTR (mTOR 3’UTR-MUT), the corresponding empty vector controls, and the Renilla luciferase plasmid were constructed by Shanghai GeneChem Co., Ltd. RD and RH30 cells were seeded into 24-well plates (3 × 104 cells/well); 24 h later, the cells were transfected with 0.1 µl of one of the luciferase plasmids, 0.02 µl of the Renilla luciferase expression plasmid, and 100 nM miR-NC or the miR-144-3p-mimic. After 48 h, Renilla luciferase expression was measured according to the manufacturer’s protocol.
Western blot analysis
Western blotting was used to measure the protein expression levels of mTOR and p-mTOR. Equal quantities of proteins were loaded into each lane of an SDS gel, separated using SDS‒PAGE, and transferred to PVDF membranes, which were then blocked with 5% BSA for 2 h. Since the positions where all protein blots appeared were quite stable and for obtaining clearer western blot bands, we set the upper and lower boundaries of the membranes according to protein molecular weight, and the left and right boundaries were according to different cell lines or other experiments. Therefore, all the blots were cropped.
prior to hybridization with primary antibodies. Subsequently, the membranes were incubated with primary antibodies overnight at 4 °C. The following antibodies were used: anti-β-actin (OriGene Technologies, Inc.), anti-mTOR, and anti-p-mTOR (both from Cell Signaling Technology, Inc.). Following six washes, the membranes were incubated with a secondary antibody (OriGene Technologies, Inc.) for a duration of 2 h and were then washed. Signals were visualized using chemiluminescence solution (Thermo Fisher Scientific, Inc.).
Statistical analysis
SPSS 26.0 software was applied for statistical analysis. All data obtained from at least three separate experiments are presented as the means ± SDs. GraphPad Prism software was used to draw graphs. Differences with P < 0.05 were regarded as statistically significant (*P < 0.05, **P < 0.01, and ***P < 0.001).
Discussion
Approximately 7% of all pediatric malignancies are soft tissue sarcomas, of which 50% of cases are RMS [
3]. Radiation, combination chemotherapy, and surgery are commonly used approaches to treat RMS [
21]. Over the past 50 years, several low-risk RMS patients have exhibited excellent outcomes, as shown by cooperative group trials [
22]. Patients with distant metastases, who are at the greatest risk, have a maximum two-year event-free survival (EFS) rate of < 20% [
23]. Despite a cooperative group trial being conducted in 1972, the outcome of those patients has not improved for five decades, highlighting the need to improve our understanding of the molecular mechanisms underlying this disease [
24].
Approximately 2% of human genetic material encodes proteins, while the vast majority is transcribed into ncRNAs [
25,
26]. Despite the annotation of thousands of lncRNAs in recent years, only a small fraction of them have undergone functional characterization [
27].
ncRNAs can regulate chromatin function, influence the stability and translation of mRNAs within the cytoplasm, and interfere with signaling pathways through lncRNA–DNA, lncRNA–RNA, and lncRNA–protein interactions during pretranscriptional, transcriptional, or posttranscriptional processes [
28]. It is possible that lncRNAs, which play crucial roles in almost all diseases, may eventually serve as therapeutic targets. There are theoretical advantages to this possibility. The high degree of specificity of lncRNA profiles across tissues and the regulation of cellular networks by lncRNAs suggests that targeting lncRNAs may have an advantage over targeting proteins in avoiding potentially harmful unintended consequences. Additionally, the lack of translation, fast degradation, and low expression levels of lncRNAs may allow more rapid effects with lower doses [
10]. Therefore, searching for potential lncRNA therapeutic targets in rhabdomyosarcoma is a highly promising endeavor.
The GEFT gene is located on chromosome 12q13.3-24.1 and was validated to be overexpressed in RMS and associated with survival and prognosis. GEFT leads to metastasis and tumorigenicity in RMS by activating EMT induced by Rac1/Cdc42 signaling [
17,
18,
29]. Here, microarray analysis was used to identify GEFT-regulated lncRNAs. In this study, knockdown of GEFT resulted in upregulation of lnc-CEACAM19-1, lnc-VWCE-2, lnc-GPX7-1, and lnc-PSMA8-1, and overexpression of GEFT resulted in downregulation of lnc-FAM59A-1, attenuating the malignant phenotypes of RMS cells. Then, it was found that lnc-PSMA8-1 was activated by GEFT and highly overexpressed in RMS cell lines and tissues, which was indicative of poor prognosis.
An increasing number of studies have shown that lncRNAs with multiple complementary miRNA binding sites function as ceRNAs or miRNA sponges, reducing miRNA function and indirectly targeting mRNAs, thus affecting the occurrence and development of tumors [
30‐
33]. Wang et al. [
34] demonstrated that the lncRNA HULC induced the phosphorylation of CREB by functioning as a ceRNA for miR-372 to reduce the translational repression of its target gene, PRKACB. Chen et al. [
35] showed that LINC01234 in gastric cancer cells modulated CBFB expression by competitively binding to miR-204-5p. Yuan et al. [
36] found that lncRNA-ATB was activated by TGF-β and accelerated hepatocellular carcinoma cell invasion by serving as a ceRNA for miR-200s to modulate the expression of ZEB1/2, ultimately inducing EMT.
Multiple types of cancer exhibit dysregulated mTOR signaling, and this pathway is frequently associated with carcinogenesis and tumor progression. According to reports, cancers with abnormal mTOR activation account for > 70% of all cases [
37]. Therefore, targeting mTOR expression may serve as a novel strategy for the management of refractory RMS. lncRNAs can modulate mTOR activity in several ways as important modulators of mTOR signaling [
20]. Thus, here, we examined whether the lncRNAs that regulate the role of GEFT also promote RMS progression by functioning as ceRNAs to regulate mTOR expression. We determined that lnc-PSMA8-1, one of the four GEFT-activated lncRNAs, positively regulated mTOR expression in RMS cell lines and was expressed mainly in the cytoplasm. According to the ceRNA hypothesis, lnc-PSMA8-1 possibly acts as a ceRNA to indirectly regulate mTOR expression. The bioinformatics results showed that miR-144-3p may play a bridging role between lnc-PSMA8-1 and mTOR.
Related studies have confirmed that multiple target sequences, including the 3’-UTR of mTOR, are regulated by miR-144-3p in several complex tumors. For example, Huo et al. [
38] revealed that mTOR expression was downregulated by miR-144-3p in human salivary adenoid carcinoma, inhibiting cell proliferation and inducing apoptosis. Iwaya et al. [
39] demonstrated that the progression of colorectal cancer was associated with the downregulation of miR-144, which targets mTOR. Ren et al. [
40] revealed that miR-144 had a suppressive effect on the proliferation of osteosarcoma cells and induced apoptosis through the direct regulation of mTOR expression.
Hence, we assessed whether lnc-PSMA8-1, activated by GEFT, modulates mTOR expression by competitively binding to miR-144-3p to regulate biological behaviors of RMS cells. Our studies revealed that the expression of lnc-PSMA8-1, miR-144-3p, and mTOR in RMS tissues was consistent with the expression patterns suggested by a ceRNA-based lncRNA–miRNA–mRNA regulatory network. Mechanistic verification was also performed, which confirmed that lnc-PSMA8-1 modulated mTOR expression by competitively binding to miR-144-3p. The results of cell functional assays suggested that lnc-PSMA8-1 promoted cell proliferation, invasion, and migration and inhibited apoptosis in RMS cell lines through miR-144-3p via regulation of mTOR activity. These results collectively suggest that lnc-PSMA8-1 promotes RMS progression through competitively binding to miR-144-3p to regulate the expression of mTOR.
Notably, the of ceRNA hypothesis considers that all types of RNA transcripts interact via miRNA response elements [
31]. Therefore, studies on lncRNAs acting as ceRNAs have primarily focused on the prediction and identification of lncRNA-targeted miRNAs. However, an often overlooked concept is that a ceRNA’s subcellular localization affects its accessibility to miRNAs. miRNAs are localized primarily in the cytoplasm, and lncRNAs can perform biological functions in the nucleus and in the cytoplasm [
41‐
44]. lncRNAs with a nuclear localization typically control pretranscriptional or transcriptional processes. lncRNAs localized in the cytoplasm often act as ceRNAs that sponge miRNAs, thereby indirectly controlling the expression of target mRNAs at the posttranscriptional level [
45]. Therefore, determining the subcellular localization of lncRNAs is necessary. The results of the bioinformatic analysis and cell fractionation assays in the present study confirmed that lnc-PSMA8-1 is localized primarily in the cytosol, and it regulates mTOR at the posttranscriptional level. In our study, we show that lnc-PSMA8-1 is an important modulator of mTOR.
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