LSCC datasets and clinical samples
The fragments per kilobase of per million (FPKM) of LSCC transcriptome, RNA counts data and corresponding clinical data from 123 LSCC patients were downloaded from the TCGA database. Frozen fresh tumor tissues and corresponding adjacent normal tissues were collected from 36 patients with LSCC (median age, 63.39 years; range, 39-80 years), who underwent surgical resection between March 2015 and May 2018 at the Second Hospital of Hebei Medical University. None of the patients received chemotherapy, radiotherapy or other anticancer treatments before surgery. The final diagnosis of patients were independently diagnosed by two pathologists. In addition, the clinicopathological characteristics of the patients analyzed in the present study included details of age, smoking, drinking, TNM stage, lymph node metastasis and tumor differentiation. Written informed consent was obtained from each patient and the process was approved by the Ethics Committee of Hebei Medical University and the Second Hospital of Hebei Medical University.
Data preprocessing and differential expression analysis
The software “edgeR” package of R was used for profiling the expression of differentially expressed lncRNAs (DElncRNAs), miRNAs (DEmiRNAs) and mRNAs (DEmRNAs) in the TCGA database. The thresholds were set as |log2 foldchange(FC) | >1, with the p value< 0.05.
Weighted gene co-expression network analysis of TM4SF19-AS1 and DEmRNAs
TM4SF19-AS1 and DEmRNAs were used for WGCNA analysis to explore the relationship between co-expression modules and clinical factors. We removed the outliers in the sample, and constructed a weighted adjacency matrix of gene expression data by using a power function based on an appropriate soft threshold parameter β. Then, the adjacency matrix was converted into a topological overlap matrix (TOM), and average linkage hierarchical clustering was carried out based on the TOM-based dissimilarity. In this study, the number of genes in each module exceeded 30.
Subcellular location prediction and ROC curve analysis of TM4SF19-AS1
Different cellular localization of lncRNA has different physiological functions. The prediction of subcellular localization is of great significance for the following study. We used the online tool Lnclocator to predict the subcellular location of lncRNA [14]. Through R software, ROC curve analysis was used to evaluate lncRNA as a molecular marker for predicting patient prognosis.
Cell culture and transfection
Laryngeal cancer cell lines (TU177, TU686, TU212 and AMC-HN-8) were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA). TU177, TU686 and TU212 were cultured in RPMI-1640 medium (Invitrogen; Thermo Fisher Scientific, Inc.), and supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher Scientific, Inc.) and 1% penicillin-streptomycin (Invitrogen, Carlsbad, CA). AMC-HN-8 was cultured in DMEM medium (Invitrogen; Thermo Fisher Scientific, Inc.), and supplemented with 10% FBS (Invitrogen; Thermo Fisher Scientific, Inc.) and 1% penicillin-streptomycin (Invitrogen; Thermo Fisher Scientific, Inc.). All cells were cultured in a humidified chamber at 37˚C with5% CO2.
For small interfering (si) RNA knockdown experiments, TM4SF19-AS1 siRNA (si-TM4SF19-AS-1 and si-TM4SF19-AS-2) and negative control (NC) were synthesized and purchased from Shanghai GenePharma Co., Ltd. Cells cultured in 6-well plates at 40% confluence (4x105 cells. per plate) were transfected using Lipofectamine®3000 reagent (Invitrogen; Thermo Fisher Scientific, Inc.), and were harvested after 48 h of incubation at 37˚C.
The miR-153-3p mimics, inhibitors and the corresponding NCs (all 40 pg/µl) were purchased from Shanghai GenePharm Co., Ltd, and transfected into laryngeal cancer cells (2x105) using Lipofectamine®3000 (Invitrogen; Thermo Fisher Scientific, Inc.) for 8 h at 37˚C. Then, the culture medium was replaced with fresh DMEM supplemented with 10% FBS at 8 h post-transfection. Subsequent experiments were performed 24 h post-transfection.
Cell counting kit-8 (CCK-8) assay
Cell counting kit-8 (CCK-8) (Sangon Biotech, Inc.) assay was used to detect the proliferation of laryngeal cancer cells under different treatments. Briefly, the transfected cells concentration was adjusted to 2.5x103 cells/well and inoculated into 96 well plate at 37˚C. 10 μl CCK-8 was added to the wells at 24, 48 and 72 h post-inoculation. Before measuring the optical density (OD), the original culture medium of each well was replaced with a mixture of 10 μl CCK-8 and 100 μl of culture medium, and then the cells were incubated at 37˚C for another 2 h. The OD of each well was analyzed at a wavelength of 450 nm (620 nm as reference) using a microplate reader (BioTek, Inc.).
EdU incorporation assay
EdU (Beyotime, Shanghai, China) assay was also used to evaluate the cell proliferation ability. AMC-HN-8 cell was seeded in 6-well plates with slides and cultured for 24h. After transfection for 24 h, the cell proliferation was tested according to the EdU kit protocol. Then it was incubated with 10 μM EdU working solution for 2 h, fixed with 4% paraformaldehyde, permeabilized with 0.3% Triton X-100 and incubated with DAPI solution to stain nuclei. Imagines were obtained with the fluorescence microscope (Olympus, Tokyo, Japan).
Wound healing assay
Following 48 h transfection, cells were cultured into 6-wellplates until 90% confluence. A vertical lines was drawn with a 200µl sterile micropipette tip against the ruler, and the cells were incubated in serum-free medium for an additional 24 h. Images of the wound were taken at 0 and 24 h respectively.
Transwell assay
A 24-well transwell chamber (8-µm pore size; BD Biosciences) was used for migration assays. After 48 h of transfection, 2.5x104 cells per well were plated into the upper chamber containing 200 µl serum-free medium. Then the upper chamber was placed in the lower chamber with 600 µl of medium containing 20% FBS. After 24 h of incubation, the cells on the upper surface of the upper chamber were removed, and the cells on the bottom side of the upper chamber were fixed with 4% paraformaldehyde and stained with 0.5% crystal violet. Transwell chambers coated with 30 µg Matrigel (BD Biosciences, CA, USA) were used for invasion assays. The number of migratory cells was counted in five randomly selected regions in each well at 200x magnification using inverted microscope.
Bioinformatics prediction and dual-luciferase reporter assay
The web tools StarBase v3.0 was used to predict the potential binding sites of TM4SF19-AS1 and ITGAV transcripts on miR-153-3p [15]. PsiCHECKTM-2 reporter plasmids (Promega, Madison, WI, USA) containing the wild type (WT) and mutated (MUT) sequences for the 3’ untranslated region (3’UTR) of TM4SF19-AS1 and ITGAV. The empty plasmid served as a control. After that, the constructed luciferase vectors were co-transfected with miR-153-3p mimics or miR-NC into HEK 293T cells. Following incubation for 48 h, the luciferase activity was tested using the Dual-Luciferase Reporter Assay System (Promega) following the manufacturer’s protocol. Firefly luciferase activity was normalized to Renilla luciferase activity.
Real-time quantitative reverse transcription PCR (qRT-PCR)
The total RNA in LSCC tissues and 4 cell lines were extracted using a Trizol kit (Solarbio). The concentration and purity of total RNA samples were determined by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). The RNA was synthesized into complementary DNA (cDNA) according to the instructions of the FastQuant RT kit (KR106; Tiangen). qRT-PCR analysis was performed on ABI-7500 using Go Taq® qPCR Master Mix (Promega, Madison, WI). The primer sequences of these genes were as follows: TM4SF19-AS1 forward, 5ʹ- GGT CTG CAC AGG TCT GAC TTC-3ʹ and reverse, 5ʹ-CCC CAC CAT GCG TTA TGC TT TT-3ʹ; ITGAV forward, 5ʹ-GTT TCA GTG TGC ACC AGC AG-3ʹ and reverse, 5ʹ-AAG GCC ACT GAA GAT GGA GC-3ʹ; 18S forward, 5ʹ-CGC CGC TAG AGG TGA AAT TC-3ʹ and reverse, 5ʹ-CCA GTC GGC ATC GTT TAT GG-3ʹ.
Western blot analysis
The total cell protein was extracted using radioimmunoprecipitation assay (Beyotime Biotechnology, Shanghai, China) containing protease inhibitors (Roche, Guangzhou, China). Protein concentration was determined using a BCA kit (Pierce, Appleton, WI). Equal amounts of the protein samples were separated using 10% SDS-poly acrylamide gel electrophoresis (SDS-PAGE) and electro-transferred onto a polyvinylidene difluoride membrane (PVDF; Millipore, Billerica, MA, USA). The membranes were blocked with tris-buffered saline (TBS) containing 5% skimmed milk at 37˚C for 2 h. Then primary antibodies against ITGAV (dilution of 1:1000) and GAPDH (dilution of 1:1000) incubated with the membrane at 4˚C overnight. On the second day, the membrane was washed three times and subsequently incubated with secondary antibody marked by horseradish peroxidase for 1 hour at 37 ˚C. Finally, an enhanced chemiluminescence assay kit was used to observe the protein bands, and the Image J software was used to quantify the protein signal through densitometric analysis.
Statistical analyses
ROC curve analysis was performed in SPSS 22.0 to evaluate the diagnostic value of TM4SF19-AS1. GraphPad Prism 7 was used to analyze the expression correlation between lncRNAs, miRNAs and mRNAs. Two tailed Student's t-tests were used to compare test and control groups between cell lines or tissues. Independent-samples t-test was used to analyze the correlation between gene expression level and clinicopathological data. A p value less than 0.05 was considered a statistically significant difference. The rest of the statistical analysis and drawing were performed using the software package in the statistical software environment R software 4.0.0.