Introduction
Lung cancer is the most commonly diagnosed cancer and the leading cause of cancer death globally [
1]. The overall 5-year survival rate of patients with lung cancer is approximately 15%, which has remained unchanged in the last several decades despite advances in surgical techniques and molecular targeting therapy [
2]. Poor outcomes of lung cancer are associated with diagnosis at advanced stages and the propensity for metastasis. Currently, there are no effective biomarkers for early diagnosis of lung cancer. There is a limited understanding of the molecular pathogenesis of lung cancer [
3,
4]. Therefore, there is an urgent need to identify new biomarkers for early diagnosis and prognosis and to identify new drug targets combating the proliferation and metastasis of lung cancer cells.
Non-coding RNAs (ncRNAs) compose the large majority (approximately 98%) of the human transcriptome [
5,
6]. Long non-coding RNAs (lncRNAs) are a large and diverse class of ncRNAs whose transcripts are longer than 200 nucleotides with limited or no protein-coding capacity [
6‐
8]. Numerous studies have reported that lncRNAs participate in diverse biological functions such as cell proliferation, stem cell differentiation, immune response, and disease pathogenesis [
9‐
11]. The molecular mechanisms by which lncRNAs exert their biological function are diverse and complex [
12‐
14]. For example, H19 expression modulates chromatin and nucleosome assembly, resulting in gene imprinting [
15,
16]. In addition, LINC00673 promotes cell proliferation and progression through sponging miR-150-5p [
17]. Notably, lncRNAs play a vital role in human carcinogenesis. However, the molecular mechanisms underlying the role of lncRNAs in carcinogenesis require further investigation.
In the present study, we identified a novel lncRNA, lung cancer associated transcript 1 (LCAT1). The biological function and molecular mechanism of LCAT1 are unexplored. LCAT1 is markedly upregulated in lung cancer tissues and is associated with poor prognosis. Functional assays demonstrated that LCAT1 promotes lung cancer cell proliferation and progression in vitro and in vivo. Furthermore, mechanistic analysis reveals that LCAT1 functions as a competing endogenous RNA (ceRNA) to regulate the expression and function of Rac family small GTPase 1 (RAC1) through competitively binding with miR-4715-5p. Taken together, LCAT1 is an oncogenic regulator of lung cancer development and progression and is a valuable biomarker and therapeutic target.
Materials and methods
Cell culture
Four human lung adenocarcinoma cell lines (A549, Calu1, H1299, and HOP62) were procured from the American Type Culture Collection (ATCC). The cell lines were maintained in RPMI-1640 medium (Gibco, Waltham, MA). All cell lines were supplemented with 10% fetal bovine serum (FBS; Gibco), 100 U/mL penicillin, and 100 mg/mL streptomycin and grown at 37 °C and 5% CO2.
RNA extraction and RT-qPCR
RNA samples from frozen lung tissue specimens and cultured cells were extracted using Trizol Reagent (Invitrogen, Carlsbad, CA). Complementary DNA (cDNA) from 1 μg total RNA was synthesized using SuperScript II (Vazyme, Nanjing, China). The amplification reaction volume was 10 μL containing SYBR Green PCR Master Mix (Vazyme), 1 μL cDNA, and amplification primers. The actin mRNA was used for normalization. The relative expression of each examined gene was determined in technical triplicates.
Cell transfection
LCAT1 and RAC1 short interfering RNA (siRNAs) and an hsa-miR-4715-5p inhibitor were synthesized by Shanghai Gene Pharma Co., Ltd. (Shanghai, China). An hsa-miR-4715-5p mimic was synthesized by Ribo Co., Ltd. (Guangdong, China) (Additional file
1: Table S1). SiRNAs were transfected at a final concentration of 50 nM using GeneMute™ reagent (SignaGen™ Laboratories, Rockville, MD), following the manufacturer’s instruction.
Cell proliferation assay and colony formation
An equal number of cells were plated in 96-well plates using 5 wells for technical replicates. Cell viability was measured using a cell counting kit-8 (CCK8) kit (Dojindo Laboratories, Kumamoto, Japan). Absorbance was measured at a wavelength of 450 nm. Cell proliferation was also assessed using a Cell-Light EdU DNA cell proliferation kit (RiboBio, Guangzhou, China), following the manufacturer’s instructions. For the colony formation assay, lung cancer cells were seeded into 6-well plates with 5000 cells/well. The cells were cultured for 10 days before they were fixed in formalin and stained with crystal violet. The colonies were counted, and the results were reported as the relative colony number.
Flow cytometry analysis of cell cycle
The cells were harvested and washed with phosphate buffer saline (PBS). The pellet was then resuspended, fixed in 70% prechilled methanol, and stored overnight at 4 °C. The cells were washed again with PBS followed by addition of 200 μL staining solution (0.1% [v/v] Triton X-100, 1 μg/mL DAPI in PBS). The final mixture was incubated for 30 min in the dark before flow cytometry analysis. The experiments were performed in triplicate and repeated 3 times.
Invasion and migration assays
In vitro migration and invasion assays were performed using transwell chambers. Lung cancer cells were transfected with siRNA or negative control for 24 h. The cells were cultured with serum-free RPMI 1640 medium for 24 h, then detached and resuspended in serum-free RPMI 1640 medium. Cells were concentrated to 3 × 104 cells in 300 uL cell suspension and then added to the upper chamber for the migration assay or the upper chamber coated with Matrigel for the invasion assay. The RPMI 1640 medium supplemented with 10% FBS was added to the bottom chamber. Cells that migrated or invaded into the bottom chamber were stained with 0.1% crystal violet. Images were captured from each membrane and the number of migratory cells was counted under a microscope.
5′ and 3′ RACE assay
A 5′ RACE assay and 3′ RACE assay were performed to determine the full length of LCAT1 using a SMARTer RACE cDNA Amplification kit (Clontech, Takara, Japan), following the manufacturer’s instructions.
Subcellular fractionation
We harvested 2 × 107 cells, washed them with ice-cold PBS, and then resuspended the cells in the ice-cold cytoplasmic lysis buffer (0.15% NP-40, 10 mM Tris pH 7.5, 150 mM NaCl) for 5 min on ice. The lysates were transferred into ice-cold sucrose buffer and centrifuged at 13,000 g for 10 min at 4 °C. The supernatant (~ 700 μL) was collected as the cytoplasmic fraction.
Luciferase assay
The whole sequence of LCAT1 (or RAC1 3′ UTR) was inserted into the psiCHECK2 basic construct. 293 T cells were transfected with 0.5 μg reporter construct and 50 nM siRNA (or miRNA mimic) per well using Lipofectamine 3000 (Invitrogen, Cat# L3000–015). After 12 h of transfection, we replaced the transfection medium with complete culture medium. After 48 h culture, the cells were lysed with passive lysis buffer (Promega, Cat# E1910), and the reporter gene expression was assessed using a Dual Luciferase reporter assay system (Promega, Cat# E1910). All transfection assays were carried out in triplicate.
Western blot
Cells were suspended in lysis buffer (50 mM Tris-HCl PH 8.0, 1% SDS, 1 mM EDTA, 5 mM DTT, 10 mM PMSF, 1 mM NaF, 1 mM Na
3VO
4, and protease inhibitor cocktail), and then denatured in boiling water for 10 min. The cellular lysates were centrifuged at 13,000 rpm for 30 min. The protein concentration was determined using a BCA assay (Thermo Fisher Scientific, Waltham, MA, USA). Equal amount of proteins (40 μg) was used to perform sodium dodecyl polyacrylamide gel electrophoresis (SDS-PAGE) using 10% gel. The proteins were then transferred onto a polyvinylidene fluoride (PVDF) membrane. The membrane was blocked with 5% skim milk and incubated with the antibodies. The antibodies used included rabbit anti-Wee1, anti-Cyclin B1, anti-Cyclin D1, anti-cyclin E1, anti-PAK1 and anti-RhoA, mouse anti-Rac1, anti-CDK6 and anti-Cyclin A2 (Additional file
1: Table S1). Immunoreactive bands were developed by enhanced chemiluminescence reaction (Pierce) following standard protocols.
In vivo assay
Briefly, 5–6 week old female athymic nude mice (BALB/c Nude) were used for the xenograft model. A549 cells stably expressing shCtrl or shLCAT1 were dissociated using trypsin and washed twice with sterilized PBS. Then, 0.2 mL of PBS containing 3 × 106 cells was subcutaneously inoculated into the flank of mice. Mice were monitored every 3 days for tumor growth, and the tumor size was measured using a caliper. Three weeks after inoculation, the mice were sacrificed adhering to the policy on the humane treatment of tumor-bearing animals. To further investigate the effect on tumor invasion in vivo, 2 × 106 scramble or shLCAT1 cells were injected intravenously into the tail vein. Five minutes following injection, 1.5 mg luciferin (Gold Biotech, St Louis, MO, USA) was administered to monitor metastases using an IVIS@ Lumina II system (Caliper Life Sciences, Hopkinton, MA, USA). Two-sample t-test with two-tailed P-values was performed to detect the difference in tumor metastasis between the two groups. All experiments were performed in accordance with the Guide for the Care and Use of Laboratory Animals (NIH publication 80–23, revised 1996), with the approval of the Zhejiang University, Hangzhou, China.
Library preparation for RNA sequencing
Transcriptome analysis of LCAT1 knockdown and scrambled control lung cancer cells was conducted using RNA sequencing (RNA-seq) as described previously [
18]. Briefly, total RNA was isolated using TRIzol according to the manufacturer’s instructions (Invitrogen). cDNA libraries were prepared using a TruSeq RNA Sample Preparation Kit (Illumina). Libraries were quantified using qPCR according to the Illumina’s qPCR quantification guide to ensure uniform cluster density. Samples were multiplexed with 12 samples per lane and paired-end sequenced with an Illumina HiSeq X10 (Additional file
2: Table S2).
Analysis of RNA-seq data
Transcriptome data were mapped with Tophat v2 using the spliced mapping algorithm [
19]. A set of both known and novel transcripts was constructed and identified using Cufflinks [
20]. Gene expression was quantified using fragments per kilobase of transcript per million reads mapped (FPKM). Finally, differentially expressed genes were obtained by paired t-test with false discovery rate (FDR) < 0.05.
Prediction of lncRNAs from RNA-seq data of lung tumor tissues
To predict novel lncRNAs in lung cancer, we downloaded the RNA-seq binary sequence alignment map (BAM) files of 485 lung adenocarcinoma tissues and 56 adjacent normal tissues from The Cancer Genome Atlas (TCGA). Our process of predicting lncRNAs followed a previously described workflow with modifications [
21]. Briefly, transcripts with single exon or length < 160 bp were filtered. The protein coding potential of the remaining transcripts was evaluated by PhyloCSF based on the alignment with genomes of chimp, rhesus, mouse, guinea, pig, cow, horse and dog [
22]. The transcripts with PhyloCSF scores greater than 50 were removed for their high coding potential. Meanwhile, transcripts with complete branch length (CBL) > 0 and open reading frame (ORF) of > 150 amino acids were removed. The transcripts with CBL scores equal to 0 due to poor sequence alignments were also removed if they contained an ORF with more than 50 amino acids. Finally, we used blastx with repeats masked to analyze the remaining transcripts and removed those with a median of the E-value <1e-18. The coding potential of the identified lncRNAs was further evaluated by CAPT [
23] and CPC2 [
24] with default parameters.
Human lung cancer samples
To evaluate the expression of LCAT1, 25 paired lung adenocarcinoma tissues and corresponding adjacent normal lung tissues were obtained from the surgical specimen archives of the Sir Run Run Shaw Hospital of Zhejiang University (Additional file
3: Table S3). Tissue specimens were snap-frozen in liquid nitrogen and stored at − 80 °C for RNA extraction. Hematoxylin and eosin (H&E) slides was reviewed by a pathologist to confirm the diagnosis. The study was conducted in accordance with the International Ethical Guidelines for Biomedical Research Involving Human Subjects. All subjects provided informed consent to participate in the study.
Analysis of copy number variation at the RAC1 locus
The level 3 data of the copy number variation (CNV) of the TCGA lung adenocarcinoma samples generated from Affymetrix SNP 6.0 was downloaded through GDC data portal (
https://portal.gdc.cancer.gov/). The CNV value of RAC1 was defined as the segment mean whose absolute value was the largest among all segments covering RAC1 gene. The samples with CNV value less than 1 were retained for further analysis.
Statistical analysis
For comparison of two groups, a two-tailed Student’s t test was used. Comparison of multiple groups were made using a one- or two-way ANOVA. All experiments were repeated at least 3 times, and representative experiments are shown. Difference was considered statistically significant at P < 0.05.
Discussion
Emerging studies have shown that lncRNAs play a critical role in cancer [
38‐
40]. Although a large number of lncRNAs have been identified in the human genome, only a very few have been experimentally validated and functionally annotated in lung cancer [
41‐
44]. In the present study, we identified a novel lncRNA, LCAT1, which is markedly upregulated in lung cancer tissues. Importantly, higher expression of LCAT1 is highly predictive of the shorter survival in patients with lung cancer, suggesting that LCAT1 is a potential prognostic biomarker for lung cancer. Both in vitro and in vivo assays demonstrated that LCAT1 exhibited strong oncogenic activity by promoting lung cancer cell proliferation, migration, and invasion.
Increasing evidence suggests the existence of a widespread interaction network involving ceRNAs, in which ncRNAs could regulate target RNA by binding and titrating them off their binding sites on protein coding messengers [
45]. LncRNA functions are closely related to their subcellular localization. In the present study, we determined that LCAT1 is mainly localized to the cytoplasm and interacts with Ago2 in lung cancer cells, suggesting that LCAT1 may function as an endogenous miRNA sponge. Bioinformatics analysis and luciferase reporter assays revealed that miR-4715-5p is a target of LCAT1. In addition, the expression of miR-4715-5p was enhanced in lung cancer cells upon LCAT1 knockdown, which confirmed our hypothesis. However, the function of miR-4715-5p in cancer is rarely studied. In this study, we demonstrated that overexpressing miR-4715-5p in lung cancer cell lines could inhibit cell proliferation and induce cell-cycle arrest at G1-G0 phase. Our findings revealed the significance of the interaction between LCAT1 and miR-4715-5p in lung tumorigenesis given that LCAT1 exerts oncogenic function partly via sponging miR-4715-5p in lung cancer cells.
We first used bioinformatics analysis to predict miR-4715-5p targets, followed by validation using a luciferase assay. We found that RAC1 was the strongest target and was directly regulated by miR-4715-5p. Whereas the expression level of miR-4715-5p was affected by the endogenous level of LCAT1. RAC1 is widely expressed in human tissues and regulates cell proliferation and cell motility [
46,
47]. Overexpression of RAC1 is involved in multiple human cancers such as breast cancer and liver cancer [
48,
49]. Therefore, we assumed that LCAT1 could modulate RAC1 mRNA level by competitively sponging miRNA-4715-5p, thereby enhancing lung cancer cell proliferation and invasion. Consistent with our hypothesis, we found that RAC1 expression was upregulated in lung cancer tissues compared to normal tissues. Higher RAC1 expression were significantly associated with poor prognosis in lung cancer patients. Depletion of RAC1 inhibited cell proliferation and motility. Moreover, we identified its downstream target, PAK1, which partly mediated RAC1 function. Both RAC1 and PAK1 were downregulated in cells overexpressing miR-4715-5p and in LCAT1 knockdown cells.
Interestingly, increased copy number was observed at the RAC1 locus in lung cancer, which consequently upregulated its mRNA expression. We also observed that lung cancer patients with normal or low copy number of RAC1 tended to have higher LCAT1 expression. These data suggested that two mechanisms potentially mediate the RAC1 expression in lung cancer: one is through genomic amplification which causes elevated RAC1 expression and the other is through the upregulation of LCAT1 which competitively sponges miRNA-4715-5p to regulate the RAC1 mRNA expression. In the second mechanism, miR-4715-5p serves as a mediator between LCAT1 and RAC1. Overexpression of LCAT1 in lung tumor can sponge more miR-4715-5p and thus leads to less miRNA-mediated mRNA decay of RAC1 by miR-4715-5p. This promotes the aggressive growth of tumor and ultimately influences patients’ survival (Fig.
8g). We estimated pairwise correlations among three genes in our lung cancer tissues. There was a weak positive correlation between LCAT1 and RAC1, and a negative correlation between miR-4715-5p and LCAT1/RAC1 in lung cancer tissues (Additional file
9: Figure S6). These trends are in good agreement with our proposed model (Fig.
8g).
Finally, our data demonstrated that EHop-016, a small molecule inhibitor of Rac GTPase, could decrease lung cancer cell viability. The combination of EHop-016 and paclitaxel exhibited better efficacy than the respective monotherapy for treating lung cancer cells. This suggests that EHop-16 could potentially be used as an adjuvant to improve the therapeutic effect of paclitaxel in lung cancer patients with high expression of LCAT1. It is also worth noting that LCAT1 was upregulated in a distinct subgroup of lung cancer patients that don’t have actionable mutations in EGFR, ALK, ROS or NRAS. In other words, there is a lack of targeted therapy in this subgroup of lung cancer patients characterized by LCAT1 overexpression. Therefore, there is an urgent need to develop an effective combination therapy of RAC1 inhibitor and paclitaxel for this subgroup of cancer patients.
In conclusion, our study identified a novel lncRNA associated with poor prognosis in lung cancer. LCAT1 is an oncogenic regulator that promotes cell proliferation and metastasis. It induces competitive binding with miR-4715-5p, resulting in the upregulation of RAC1 and PAK1 (Fig.
8g). LCAT1 overexpression defines a distinct subgroup in lung cancer patients with poor prognosis. This subgroup of patients usually don’t have actionable mutations in EGFR, ALK, ROS or NRAS. Thus, there is a lack of targeted therapy in the subgroup of lung cancer patients characterized by LCAT1 overexpression. Our findings suggest that the LCAT1-miR-4715-5p-RAC1/PAK1 axis could be a valuable target for lung cancer prognosis and therapies. The novel strategy for treating lung cancer using a combination of paclitaxel and EHop-016 warrants further investigation, especially in the subgroup of lung cancer patients exhibiting LCAT1 overexpression.
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