TCGA data analysis
Gene expression data for 160 EC and 11 normal tissues were downloaded from the Cancer Genome Atlas (TCGA) database and processed using R software (version 3.6.1). Differentially expressed genes were | log2(fold change (FC)) | > 1.0 and adjusted the p-value < 0.05.
Cell culture
The esophageal epithelial cell line HEEC and two esophageal cancer cell lines (Eca-109 and EC9706) were procured from Jennio Biotech (Guangzhou, China). All cells were maintained in DMEM (Life Technologies, Carlsbad, CA, USA) containing 10% FBS (Sigma Aldrich, St. Louis, MO, USA) and 100 U/mL penicillin/streptomycin (Life Technologies, Carlsbad, CA, USA).
Lentivirus, oligonucleotide, plasmid, and transfection
HOXC-AS1 short hairpin RNA (sh-HOXC-AS1), CBP short hairpin RNA (sh-CBP) or negative control (NC) lentivirus were obtained from GenePharma (Shanghai, China). The EC cell lines were infected with the virus using 5 mg/ml polybrene for 48 h. Puromycin (5 µg/ml) was used to select stable cell clones for two weeks. qRT-PCR was performed to assess the knockdown efficiency. The full-length ANLN complementary DNA (cDNA) was cloned into the pcDNA3.1 vector. The mimics and inhibitors of miR-195-5p and their negative control were bought from RiboBio (Guangzhou, China). The plasmids, mimics, or inhibitors were then transfected into Eca-109 and EC9706 cells using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA).
Quantitative real-time reverse transcription polymerase chain reaction
The total RNA of EC cells was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and reverse-transcribed to cDNA using RNA Reverse and MicroRNA Reverse Transcription kits (Applied Biosystems, Foster City, CA, USA). Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) was performed using SYBR Select Master Mix and ABI Prism 7000 Sequence Detection System (Applied Biosystems, Foster City, CA, USA). β-actin and U6 were chosen as references for mRNA and miRNA, respectively. Relative expression was quantified according to the 2−ΔΔCt method. The sequences of the primers used are as follow: miR-195-5p RT primers: GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACGCCAAT, PCR primers: forward 5′-GTACTAGCAGCACAGAAAT-3′, reverse 5′- CTGGGAAGGAGAGAGGGAGA-3′; U6 primers: forward 5′-CTCGCTTCGGCAGCACA-3′, reverse 5′-AACGCTTCACGAATTTGCGT-3′; HOXC-AS1 primers: forward 5′-ACCGAGCTTGAAGAAGTGTAGG-3′, reverse 5′-AAGTGTCGCAGAGATGGAGTTG-3′; CBP primers: forward 5′-CATCTTCCCAACACCTGA-3′, reverse 5′-GTCCCCTTCCACTTTCTT-3′; ANLN primers: forward 5′-CACCTATCACCTTTAAACGCCT-3′, reverse 5′-CAATGACAGGAGGTGACAGAA-3′; β-actin primers: forward 5′-GAGGGAAATCGTGCGTGAC-3′, reverse 5′-TTCTGACCCATTCCCACC-3′.
2.5 Western blot
Radioimmunoprecipitation buffer (Beyotime Biotechnology, Shanghai, China) was used to extract the total protein. Protein concentrations were measured using a BCA Protein Assay Kit (Beyotime Biotechnology, Shanghai, China). Equivalent proteins were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis and subsequently transferred to a polyvinylidene fluoride membrane. the membranes were blocked with a blocking buffer and incubated overnight with the primary antibody targeting ANLN (1:1000; Abcam, Cambridge, MA, USA) and GAPDH (1:3000; Cell Signaling Technology, Beverly, MA, USA) at 4°C. Then, they were probed with the secondary antibody HRP-labeled rabbit IgG (1:5000; Cell Signaling Technology, Beverly, MA, USA) for 1 h at room temperature. The protein bands were detected using enhanced chemiluminescence.
Immunohistochemistry staining
Tissues were fixed in 4% paraformaldehyde, embedded in paraffin, and cut into 4 µm-thick slices. They were dewaxed and rehydrated using graded ethanol. antigen retrieval was incubated in Retrieval Solution, and the sections were probed with primary antibody PCNA (1:1000; abcam, Cambridge, MA, USA) and incubated with secondary antibody (1:3000, abcam, Cambridge, MA, USA). The DAB Kit (Beyotime Biotechnology, Shanghai, China) was applied to detect protein expression, and the nuclei were counterstained using hematoxylin (Sigma Aldrich, St. Louis, MO, USA).
MTT assay
Cells were seeded at 1 × 104 cells per well in a 96-well plate. they were cultivated for 24 h, 48 h, 72 h, and 96 h. Then, 20 µl of MTT reagents (Sigma Aldrich, St. Louis, MO, USA) were added to each well and incubated for 4 h at 37°C. Subsequently, 150 µl of dimethylsulfoxide was added to dissolve the formazan precipitates. The optical density (OD) was measured at 490 nm using a Microplate Reader (Thermo Fisher Scientific, Waltham, MA, USA).
5-ethynyl-2′-deoxyuridine assay
Cell proliferation was measured using the 5-ethynyl-2′-deoxyuridine (EdU) assay kit (RiboBio, Guangzhou, China). Briefly, cells were inoculated into a 24-well plate and cultured for 48 h. Cells were then incubated with EdU for 2 h. Then, the cells were fixed, permeabilized, incubated with Apollo® 567, and stained using 4′,6-diamidino-2-phenylindole (Thermo Fisher Scientific, Waltham, MA, USA). The EdU positive cells were observed under a fluorescence microscope (Olympus, Tokyo, Japan).
Transwell invasion assay
Cell invasions were carried out using a 24-transwell chamber with 8 µm pore size (Corning Costar, Cambridge, MA, USA) coated with Matrigel (Corning Costar, Cambridge, MA, USA). EC cells were seeded in the upper chamber using a serum-free medium. The DMEM medium containing 10% FBS was added to the lower chamber. After incubating for 24 h, the invaded cells in the lower chamber were fixed and stained using paraformaldehyde and 0.1% crystal violet, respectively. Then, the cells were counted and photographed under a microscope with a digital camera (Olympus, Tokyo, Japan).
Wound healing assay
Cells were seeded in a 6-well plate at a density of 1×105 cells per well and cultured to a 90% confluence state. Cells were scratched off using a 200 µl pipette tip. The cells were cultured for 24 h after washing. Images of wound closure were captured at 0 h and 24 h under the microscope with a digital camera (Olympus, Tokyo, Japan). The images were analyzed using ImageJ software.
Dual-Luciferase reporter assay
The wild (wt) and mutant (mut) types in HOXC-AS1 and 3′-untranslated region (UTR) of ANLN containing miR-195-5p binding site (HOXC-AS1-wt/mut, ANLN-3′UTR-wt/mut) were subcloned into psiCHECK-2 plasmids (Promega, Madison, WI, USA). Cells were co-transfected with HOXC-AS1-wt, HOXC-AS1-mut, ANLN-3′UTR-wt/mut, or ANLN-3′UTR-mut, and miR-195-5p, or control mimics using Lipofectamine 2000. they were harvested after 48 h. The luciferase activity was assessed using the dual-luciferase assay kit (Promega, Madison, WI, USA).
RNA immunoprecipitation assay
An RNA immunoprecipitation (RIP) kit (Millipore, Bedford, MA, USA) was utilized to detect the binding relationship between HOXC-AS1 and miR-195-5p. briefly, cells were lysed with RIPA lysis buffer (JRDUN, Shanghai, China). The lysates were incubated overnight with magnetic beads conjugated with Ago2 or control IgG antibody at 4°C. The magnetic bead-protein complexes were collected treated with proteinase K to digest protein complexes and recovered the RNAs from the beads. Immunoprecipitated RNA was purified and quantified using qRT-PCR.
In vivo model
All animal procedures were performed in accordance with the Guidelines for the Care and Use of Laboratory Animals with the approval of the Ethics Committee of the First Affiliated Hospital of Xiamen University (No. 202109899). Nude mice were used for this study. The animals were sourced from Xiamen University Laboratory Animal Center (Xiamen, Fujian, China). Eca-109 cells (1×107 cells/ml) infected with sh-HOXC-AS1 or NC lentiviruses were subcutaneously inoculated into the axilla of the nude mice. Tumor size was measured every 6 d. Tumor volume was calculated using the formula V = width2×length×1/2. After four weeks, the nude mice were euthanized by using CO₂ inhalation, and the tumors were collected and weighed. For the lung metastasis model, 2 × 106 NC or sh-HOXC-AS1 stable Eca-109 cells co-transfected with with a Luc-lentivirus (GenePharma, Suzhou, China) which expresses luciferase were injected into the tail veins of mice. After 6 weeks, mice were evaluated lung metastasis ability using an in vivo imaging system (IVIS, PerkinElmer, Waltham, USA). After mice were sacrificed, the lungs were collected and lung metastasis was measured by hematoxylin-eosin (H&E) staining. Dmetrix software by combining the number and area of lung metastatic nodules in each mouse were calculated the metastatic foci.
ChIP assay
ChIP assays were performed with Eca-109 and EC9706 cells via ChIP Assay Kit (Thermo Fisher Scientific). In brief, Eca-109 and EC9706 cells with 1% of formaldehyde were incubated for 10 minutes to form DNA-protein cross‐links, and then cross‐linked chromatin DNAs were broken into 200 to 1000 bp‐sized segments by using an ultrasound machine. Anti‐H3K27ac antibody, anti‐CBP, antibody or IgG antibody (Abcam) was used to precipitate the chromatin the lysate. ChIP samples were analyzed via RT‐qPCR.
RNA fluorescence in situ hybridization (FISH)
Cy3-labeled HOXC-AS1 probe was purchased from GenePharma Ribo Bio (Guangzhou, China). FISH was performed using a FISH kit (Ribo Bio). EC cells were incubated with cy3-labeled HOXC-AS1 at 37℃ overnight after fixation. Nuclei were stained with DAPI. Finally, the Spinning Disc Laser Confocal Microscope (Dragonfy 200, Oxford Instruments Andor, USA) was utilized to determine the locations of HOXC-AS1 in EC cells.
Statistical analysis
Statistical analyses were performed using SPSS21.0 (SPSS Inc., Chicago, IL, USA). The data were presented as mean ± standard deviation. Differences between the two groups were compared using the student’s t-test. Differences among multiple groups were analyzed using the two-way analysis of variance. Statistical significance was set at P < 0.05.