Background
Primary liver cancer is the sixth most commonly diagnosed cancer, with an estimated 905,677 new cases and 830,180 deaths worldwide in 2020 [
1]. China has the heaviest burden of primary liver cancer, with 50% of all global cases [
2]. Hepatocellular carcinoma (HCC) accounts for 85–90% of primary liver cancer incidence [
3]. Despite the wide scope of research on HCC diagnosis and treatment, approximately 60–70% of HCC patients have a risk of recurrence within 5 years, giving rise to poor prognosis and poor quality of life [
4,
5]. Therefore, it is urgent to discover novel prognostic biomarkers and satisfactory diagnostic and therapeutic strategies.
Long non-coding RNAs (lncRNAs) have attracted widespread attention in recent years due to their important role in HCC [
6‐
10]. An increasing number of studies has proven that lncRNAs are associated with the proliferation, migration, invasion, apoptosis, differentiation, angiogenesis, and metabolism of HCC cell lines [
11‐
14]. For instance, LINC00205, lncRNA RHPN1-AS1, and lncRNA TMPO-AS1 directly interact with microRNAs by acting as competitive endogenous RNAs (ceRNAs) to promote the proliferation, migration, and invasion of HCC cells [
15‐
17]. These findings are helpful in exploring the role of lncRNAs in the occurrence and metastasis of HCC and establishing a new approach for identifying lncRNAs as prognostic indicators and therapeutic targets.
In recent years, tissue-specific non-coding RNAs (ncRNAs) have shown important roles in cancer. Expression of these ncRNAs is always restricted to certain normal tissues, and they show tissue-enriched features. MiRNA-122 was the first liver-specific ncRNA discovered, and it showed inhibitory effects on HCC by reducing the metastatic ability of HCC cells in vitro and tumourigenesis and angiogenesis of HCC in vivo [
18]. With respect to lncRNAs, several liver-specific lncRNAs have been identified and shown cancer suppressive effects in HCC. For example, LINC01093, a novel liver-specific lncRNA, inhibits HCC cell proliferation and metastasis in vitro and in vivo by interacting with IGF2BP1 to promote GLI1 mRNA decay [
19]. Our previous studies also showed that two novel liver-specific lncRNAs, FAM99B and LINC02499, may play similar inhibitory effects on the development of HCC [
20,
21]. This evidence indicate that liver-specific lncRNAs are likely to have an important role in HCC.
LINC01146 is located on chromosome 14q31.3. Based on the quantitative RNA sequencing of major human organs and tissues from the Genotype Tissue Expression Project (GTEx) database, we found that the expression of LINC01146 in normal liver tissue was more than 3 times that in any other normal tissue, showing certain tissue specificity [
22]. Based on the role of liver-specific lncRNAs in the development of HCC, we hypothesized that LINC01146 may be related to the occurrence and development of HCC. In the present study, we aimed to detect the expression level of LINC01146 in HCC tissues compared with adjacent normal tissues and investigated the exact effects of LINC01146 in vitro and in vivo. Furthermore, bioinformatic methods were used to explore the possible biological processes and potential pathways of LINC01146 in HCC and provide a scientific basis for subsequent molecular mechanism studies.
Materials and methods
Microarray assay
Five pairs of HCC tissues and their corresponding adjacent normal tissues were used to conduct a high-throughput microarray expression profile by KangChen Biotech (KangChen Biotech Inc, Shanghai, China). The samples were labelled according to the ArraryStar RNA Flash Labelling Kit specifications, and Agilent SureHyb (Agilent Technologies, Palo Alto, Calif.) was used to conduct the hybridization experiments. The specific workflow is described in detail in the article by Guo X [
23].
The Cancer Genome Atlas (TCGA) database
RNA sequencing data and the corresponding clinical information of HCC patients were obtained from the TCGA (
https://cancergenome.nih.gov/) [
24] database. We used RNA expression data in the transcripts per million (TPM) and converted it into the base-2 logarithm for normalization [
25]. The follow-up time and survival state of clinical information were used for Kaplan–Meier analysis. Patients without LINC01146 expression, follow-up time, or survival state were excluded.
Gene Expression Omnibus (GEO) database
LINC01146 expression in HCC and normal control samples was searched from the GEO (
http://www.ncbi.nlm.nih.gov/geo/) [
26] database. The search keywords were as follows: (long non-coding RNA OR lncRNAs) AND (hepatic OR liver OR hepatocellular) AND (cancer OR carcinoma OR tumour OR neoplasm). We also set the type to “series” and the species to “human”. The inclusion criteria were as follows: (1) each chip had to contain HCC tissues and normal liver tissues; (2) the expression of LINC01146 was detected in at least three cancer tissues and normal tissues; and (3) the expression of LINC01146 data was directly available or calculable.
Tissue samples
We collected HCC tissues and adjacent normal tissues from the Affiliated Cancer Hospital of Guangxi Medical University from January 2016 to December 2019. We included patients who were about to undergo surgical excision and had not previously received additional adjuvant therapy in our HCC cohort study. The clinical features and follow-up information of patients were also collected for the survival analysis. Each patient entering our cohort signed an informed consent form. Our research was approved by the Ethics Committee of Guangxi Medical University.
HCC cell lines and animals
In total, six HCC cell lines were used to detect the expression of LINC01146, including Huh7, Hep3B, HCCLM3, MHCC97H, SNU423, and SNU449. Dulbecco’s modified Eagle’s medium (DMEM), minimum essential medium (MEM), and Roswell Park Memorial Institute 1640 (RPMI-1640) (Gibco, USA) were utilized for cell culture. All HCC cell lines were cultured in a 37 °C incubator containing 5% CO2.
Twenty-four specific pathogen-free (SPF) 4-week-old male nude mice (BALB/c) were housed in the Guangxi Medical University Laboratory Animal Center. The nude mice were randomly divided into 4 groups according to their weight, with 6 mice in each group. All experimental procedures were reviewed and approved by the Ethics Committee of Guangxi Medical University, and all animal experiments were performed in the Guangxi Medical University Laboratory Animal Center [SYXKGUI 2020-0004] in accordance with the welfare and ethical standards of animal experiments in China.
Quantitative real-time polymerase chain reaction (qRT-PCR)
Total RNA of HCC tissues and cell lines was extracted by TRIzol (Invitrogen, USA). Reverse transcription of complementary deoxyribose nucleic acid (cDNA) was conducted according to the PrimeScript RT reagent Kit (Takara, Japan). qRT–PCR was performed using the TB Green TM Premix Ex Taq TM II Kit (Takara, Japan). The primers were as follows: GAPDH forward: 5′-AGCCACATCGCTCAGACAC-3′, GAPDH reverse: 5′-GCCCAATACGACCAAATCC-3′; LINC01146 forward: 5′-TTGAAGGCAGTATGCTTGGTAA-3′, LINC01146 reverse: 5′-TTCCGCAGTGTATCGTGTCC-3′.
Cell transfection
MHCC97H and Huh7 cells were selected to construct LINC01146 stably overexpressing cell lines through lentiviral transfection, while Huh7 and Hep3B cells were selected to construct LINC01146 stably downregulated cell lines through lentiviral transfection (Genepharma, Shanghai, China). The Lv-NC and sh-NC groups served as the negative controls of the overexpression and downregulation HCC cell lines, respectively. After seventy-two hours of lentivirus infection, we used puromycin (2.5 or 3.5 μg/ml) to screen successfully transfected HCC cells. Finally, qRT-PCR was performed to detect the efficiency of overexpression and downregulation of LINC01146 in HCC cell lines. The sequences of sh-NC and sh-LINC01146 were as follows: LINC01146-Homo-NC: 5′-TTCTCCGAACGTGTCACGT-3′; LINC01146-Homo-330: 5′-GGTCTCCAGCTTCGTCAATGT-3′.
Cell proliferation assays
Cell Counting Kit-8 (CCK-8; Dojindo, Japan) was used to investigate the effect of LINC01146 on the proliferation ability of HCC cells. The cells were diluted to 104 cells/ml and seeded into five 96-well plates. Then, we added a mixture of CCK-8 and complete medium (CCK-8: complete medium = 1:10) to each well after 24, 48, 72, 96, and 120 h of incubation. Finally, the absorbance value (OD = 450 nm) of each group was measured with a microplate reader after incubation for another 2 h.
Colony formation assays were conducted to investigate the effect of LINC01146 on the proliferation ability of HCC cells. The cells were diluted to a density of 250 cells/ml and cultured in a six-well plate until most clones had more than 50 cells. Afterwards, the cells were fixed with methanol and stained with 0.1% crystal violet for another 30 min. Finally, the treated cells were scanned, and the number of clones in each group was calculated as the average number in three parallel wells.
Transwell assays
Transwell chambers with 8 μm pore filters (Costar, Corning, NY) were utilized to explore the effect of LINC01146 on the migration and invasion abilities of HCC cells. The specific experimental procedure was described in our previous article [
21]. The cells with serum-free medium were seeded into the upper chambers, and complete media with 20% serum was added to the lower chambers. After 48 or 72 h, the cells were fixed with methanol and stained with 0.1% crystal violet, followed by observation and counting under an inverted microscope.
Flow cytometric assays
Flow cytometry was performed to assess the cell cycle distribution in different groups. Huh7 cells were digested and washed with PBS twice when the density of cells reached 80–90% in six-well plates. Then, the cells were fixed with cold 75% ethanol overnight at 4 °C. After centrifugation, the fixed cells were washed with precooled PBS and then with periodic reagents. Afterwards, the cells were incubated with PI/RNase Staining Buffer (BD Pharmingen™, USA) at room temperature for 15 min, and the cycle distribution was immediately measured by flow cytometry.
To detect the apoptotic rate, the cells were digested by ethylenediaminetetraacetic acid (EDTA)-free trypsin, washed with precooled PBS and then with 1× buffer. The cells were later double stained with PE Annexin V and 7-AAD according to the instructions of the PE Annexin V Apoptosis Detection Kit I (BD Pharmingen™, USA). The cell apoptosis rate was analysed by flow cytometry within 1 h.
In total, 2 × 107 MHCC97H cells and 5 × 107 Huh7 cells were suspended in a 2 ml mixture (1:1, v/v) of serum-free medium and Matrigel (Costar, Corning, NY). Then, 0.2 ml of cell suspension was injected subcutaneously into the left axilla of the nude mice. The formed tumour was measured with a Vernier caliper every 5 days, and the tumour volume was calculated as follows: V = 1/2ab2, where V represents the volume of the tumour, while a and b represent the longest and shortest diameter of the tumour, respectively. Thirty and 25 days after the inoculation of MHCC97H and Huh7 cells, respectively, the nude mice were sacrificed by cervical dislocation, followed by removal, weighing, and measurement of the tumour tissues. Each tumour was then placed in 4% paraformaldehyde for fixation for 24 h.
Haematoxylin–eosin (HE) staining and immunohistochemical (IHC) staining
For HE, after deparaffinization and rehydration, the sections were stained with haematoxylin for 8 min followed by 5 dips in 1% acid ethanol (1% HCl in 70% ethanol) and then rinsed in distilled water. Then, the sections were stained with 1% eosin aqueous solution for 4 min followed by dehydration with graded alcohol and clearing in xylene [
27]. Finally, the sections were sealed with neutral adhesive and observed under a microscope.
For IHC, after incubating with antigen retrieval solution and 3% H
2O
2 for 15–20 min, the slides were rinsed with water and incubated with the primary antibody Ki-67 (Abcam, Cambridge, MA; 1:200) for 1 h at 37 °C. Then, the slides were incubated with the biotinylated secondary antibody and DAB followed by haematoxylin staining [
28]. Finally, the slices were dried and sealed with neutral gum. The results were analysed by Image-Pro Plus 6.0 software.
LINC01146 pathway analysis
To reveal the basic molecular mechanisms of LINC01146 in HCC, we conducted a pathway enrichment analysis on the coexpressed genes of LINC01146. WebGestalt (
http://www.webgestalt.org/) [
32] was used to conduct Gene Ontology (GO) functional annotation, and KOBAS 3.0 (
http://kobas.cbi.pku.edu.cn/kobas3) [
33] was utilized to construct Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. The STRING (
http://string.embl.de/) [
34] database was applied to construct a protein–protein interaction (PPI) network.
Statistical analysis
The median value was used as the cut-off value to distinguish between high- and low-expression groups, and Student’s t test was performed to compare the expression levels of LINC01146 in HCC tissues and normal tissues. The chi-square test was performed to explore the relationship between LINC01146 expression and the clinical features of HCC patients. Kaplan–Meier analysis and the log-rank test were used to assess the association between LINC01146 expression and the overall survival (OS) time of HCC patients. Cox regression models were utilized to explore the independent prognostic risk factors for HCC patients. The above statistical analyses were all conducted using SPSS 22.0 software, and P < 0.05 was considered statistically significant. GraphPad Prism 8.0 was used to draw graphs.
Meta-analysis was conducted to integrate the GEO chip results using STATA 13.0 software. The chi-squared and I2 tests were used to explore the heterogeneity between studies. When I2 < 50% or P > 0.1, no significant heterogeneity existed among studies, and the fixed effect model was used for meta-analysis. Otherwise, the random-effect model was selected. A forest plot was utilized to obtain the combined effect value, including the standard mean deviation (SMD) and 95% confidence interval (CI). When SMD < 0 and P < 0.05, the expression of LINC01146 was considered downregulated in HCC tissues compared with adjacent normal tissues. Otherwise, the expression of LINC01146 was considered upregulated or unaltered in HCC tissues compared with adjacent normal tissues. Sensitivity analysis was used to evaluate the robustness of the meta-analysis results. The funnel graph and Egger’s test were applied to evaluate reporting bias, with P > 0.1 deemed to indicate no apparent reporting bias.
Discussion
In the present study, we identified LINC01146 as a novel liver-specific lncRNA. We showed that LINC01146 was decreased in HCC tissues and expression of LINC01146 was negatively related to the aggressive clinical features and poor prognosis of HCC patients. Furthermore, overexpression of LINC01146 inhibited the proliferation, migration, and invasion while promoting the apoptosis of HCC cells in vitro. In contrast, downregulation of LINC01146 exerted the opposite effects. Moreover, overexpression of LINC01146 inhibited the tumour growth of HCC cells in vivo, while downregulation of LINC01146 played the opposite role in vivo. All of the above results indicated that LINC01146 may play a cancer-inhibiting role in HCC progression.
HCC patients with aggressive clinical features are prone to recurrence, metastasis, and poor prognosis. Previous studies have shown that MVI indicates the metastasis of HCC, and patients with positive MVI have a poor prognosis [
35,
36]. The increase in tumour size is one of the signals of metastasis in HCC patients and is directly proportional to the risk of metastasis in HCC patients [
37]. Additionally, the presence of satellite nodules in the pathological diagnosis of HCC patients shows invasion of cancer cells and suggests poor prognosis of HCC patients and increased proneness to symptom recurrence [
38,
39]. A great deal of evidence suggests that lncRNAs can serve as molecular targets to predict the prognosis of HCC patients, such as lncRNA DGCR5, lncRNA GAS5-AS1, lncRNA miR210Hg, and lncRNA SNHG16 [
40‐
43]. In our study, we found for the first time that low expression of LINC01146 was associated with aggressive clinical features, including tumour size, tumour number, MVI, satellite nodules, DNA content of HBV, and BCLC grade. In addition, we found that low expression of LINC01146 was associated with poor prognosis in HCC patients. These results suggested that low expression of LINC01146 may affect the progression and prognosis of HCC patients and may serve as a tumour inhibitor and a prognostic molecular marker for HCC patients.
In the present study, we identified LINC01146 as a liver-specific lncRNA enriched in normal liver tissues based on the GTEx database and involved in the proliferation, migration, invasion, and apoptosis of HCC cells. Recently, more studies have shown that tissue-specific lncRNAs play an important role in the development of cancers. For instance, two tissue-specific lncRNAs, PCAT18 and LINC01133, were enriched in normal stomach tissues and downregulated in gastric cancer (GC) [
44]. PCAT18 acts as a cancer inhibitor by impairing the viability, invasion, and migration of GC cells [
45]. LINC01133 inhibits the proliferation, migration, and epithelial–mesenchymal transition (EMT) of GC cells by silencing the Wnt/β-catenin pathway [
46]. LncRNA TINCR plays a tissue-specific role in normal skin, placenta, and oesophageal tissues [
47]. Several studies have reported that TINCR plays a cancer suppressive role in lung cancer, breast cancer, and prostate cancer by inhibiting biological characteristics, such as proliferation, migration, and invasion of cancer cells [
48‐
50]. These findings suggest that tissue-specific lncRNAs may play an inhibitory role in tumourigenesis.
The negative correlation between the expression of LINC01146, MVI, and satellite nodules prompted us to hypothesize that LINC01146 may be involved in the proliferation, migration, invasion, and apoptosis of HCC cells. Rapid proliferation is one of the most important biological characteristics of HCC cells [
51]. LncRNAs can affect the proliferation of HCC cells by targeting key regulatory factors in different pathways. For instance, lncRNA MALAT1 promotes HCC cell proliferation by regulating expression of the oncogenic transcription factor B-MYB to facilitate cell cycle progression [
52]. Overexpressed lncRNA SNHG16 sponges hsa-miR-93 and inhibits the proliferation of HCC cells [
53]. The upregulation of lncRNA FAM83H-AS1 promotes HCC cell proliferation through the Wnt/β-catenin pathway [
54]. Previous studies also revealed that HCC patients harbouring cancer cells with high migration and invasion activities often have increased aggressiveness, recurrence, and poor survival. For example, lncRNA MYLK-AS1 facilitates HCC progression and angiogenesis by promoting the invasion and metastatic abilities of HCC cells in vivo through targeting the miR-424-5p/E2F7 axis and activating the VEGFR-2 signalling pathway [
55]. LncRNA HAND2-AS1 inhibits the proliferation, migration, and invasion of SNU-398 cells by mediating the downregulation of ROCK2 protein in HCC [
56]. Silencing of LINC00240 suppresses the migration and invasion of HCC cells by promoting miR-4465 and inhibiting the HGF/c-Met signalling pathway [
57]. In the present study, by overexpressing and knocking down LINC01146, we found that LINC01146 inhibited the proliferation, migration, and invasion abilities of HCC cells in vitro and promoted their apoptosis. Additionally, LINC01146 inhibited the growth of tumours in vivo. These results suggest that LINC01146 may play a cancer-inhibiting role in HCC by reducing biological characteristics of HCC cells, such as proliferation, migration, and invasion, and promoting apoptosis.
Previous studies have reported that lncRNAs influence the occurrence and progression of tumours by participating in a variety of pathways. We found that the coexpressed genes of LINC01146 were mainly involved in “metabolic pathway”, “complement and coagulation cascade”, “retinol metabolism”, “caffeine metabolism” and other pathways. The reprogramming of cell energy metabolism, which provides an energetic basis for the unrestricted proliferation and metastasis of cancer cells, is widely recognized as an emerging cancer marker. Metabolic reprogramming plays a key role in promoting tumour survival and proliferation to sustain the increasing metabolic demands of cancer cells [
58,
59]. In recent years, complement and coagulation cascades have played crucial roles in the carcinogenesis and progression of cancer [
60‐
62]. Complement cascades contribute to the development of the major features of carcinogenesis, including the maintenance of cell proliferation, inhibition of apoptosis, and promotion of cell invasion [
63]. In addition, many bioinformatic studies have shown that retinol metabolism plays an important role in the occurrence and development of HCC [
64‐
66]. Caffeine has also been reported to have an antitumour effect and can protect liver function. Edling et al. found that caffeine blocks the proliferation of HCC and pancreatic cancer adenocarcinoma cells by inhibiting the PI3K/Akt pathway [
67]. Moreover, Okano et al. reported that caffeine inhibits the proliferation of HCC cells by activating the MEK/ERK/EGFR signalling pathway [
68]. We also found a strong correlation between the expression levels of
FETUB/
TTR and LINC01146 in HCC. However, we only discovered this relationship through the TCGA database and did not verify it through experimental methods, which requires further study.
In conclusion, LINC01146 is downregulated in HCC tissues and negatively correlated with aggressive clinical features and poor prognosis of HCC patients. It may serve as a prognostic biomarker for HCC patients and a cancer suppressor by repressing the proliferation, migration, and invasion abilities of HCC cells, while promoting the apoptosis of HCC cells.
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