Cells and cell culture
The human ESCC cell lines KYSE-140, KYSE-410, KYSE-510 were obtained from ATCC. YES-2, TE12, KYSE30lm3, KYSE30luc, KYSE450lm2, and KYSE450luc were gifted by Prof. Zhihua Liu (Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical Collage). The KYSE30luc and KYSE450luc cell lines were obtained by labeling the KYSE30 and KYSE450 cells with luciferase reporter genes, which were injected into immunodeficient mice (SCID/Beige) via the tail vein. After 2–3 months, the lungs were taken out under aseptic conditions, minced and digested, and the primary culture of ESCC cells in lung metastases was carried out. These cells were injected secondly into SCID/Beige via the tail vein. KYSE30luc cells were screened for three rounds, while KYSE450luc cells were screened for two rounds, and finally a subset of cells with strong lung metastatic ability (KYSE30lm3 and KYSE450lm2) were obtained and cultured in RPMI-1640 medium supplemented with 15% FBS and 100 µg/mL G418 [35]. KYSE-140, KYSE-410, KYSE-510, YES-2, and TE12 were maintained in RPMI-1640 supplemented with 10% FBS. SP2/0 myeloma cells were maintained in RPMI-1640 supplemented with 20% FBS. All cells were grown at 37°C with 5% CO2, 95% air atmosphere.
Small interfering RNA (siRNA) synthesis, vector construction, and transfection
The full-length sequence of human TMEM16A eukaryotic plasmid (pLVX-PURO-ANO1) and prokaryotic plasmids (pGEX-4T-1-ANO1-T1-T4) were synthesized by Sangon Biotech (Suzhou, China). The vector pLVX-puro-MOCK and pGEX-4T1-GST were purchased from Public Protein/Plasmid Library (Nanjing, China). The genetically encodable biosensor of intracellular perchlorate concentration monitored by pCDNA3.1-Hygro EYFP H148Q/I152L was purchased from addgene (USA). The siRNAs, including si-EGFR1#1 (CUCCAGAGGAU GUUCAAUATT), siEGFR-#2 (GCCUUUGAGAACCUAGAAATT) and control siRNA (UUCU CCGAACGUGUCACGUTT) were synthesized by GenePharma (Shanghai, China). The shRNA of lentiviral knockout plasmids, including PLVX-TMEM16A-shRNA#1 (GCCGACGAAGAAG ATGTACCA), PLVX-TMEM16A-shRNA#2 (CAGCATCTATTTGACTTGTC) and PLVX-Non- silencing-shRNA (TTCTCCGAACGTGTCACGT) were provided by Beijing Syngentech. (Beijing, China).
Plasmids were transfected with Lipofectamine2000 (Invitrogen, USA) for KYSE30luc and KYSE450luc cells. siRNA was transfected with buffer Mate (GenePharma) for tumor cells. All transfections were performed according to the manufacturer’s instructions. The cells were collected and used for Western blot assays 48h after transfection.
Antibodies and proteins
Anti-TMEM16A (ab190803, WB 1:500, CO-IP 1:200), Anti-JNK1/JNK2/JNK3 (ab179461, WB 1:1000) and anti-JNK1/JNK2/JNK3 (phospho T183/T183/T221) (ab124956, WB 1:500) were purchased from Abcam. Anti-pEGFR-Tyr 992 (2235, WB 1:1000), anti-pEGFR-Tyr 1068 (#3777, WB 1:1000), anti-EGFR (#4267, WB 1:2000, CO-IP 1:500), anti-Akt (#14702, WB 1:2000), anti-phospho-Akt (Ser473) (#4060, WB 1:1000), anti-phospho-PI3 Kinase p85 (Tyr458)/p55 (Tyr199) (#4228, WB 1:1000), and anti-PI3K p85(#4257, WB 1:1000) were purchased from CST. Anti-GAPDH (10494-1-AP, WB 1:2000) was purchased from Proteintech. Recombinant human EGFR protein (aa 668–1210, His & GST Tag) was purchased from Sino Biological.
RNA extraction and quantitative RT-PCR (qPCR)
Cells were harvested in Trizol® reagent (Invitrogen), and total RNA was isolated according to the manufacturer’s instructions. Single-stranded cDNA was synthesized from 5 µg total RNA using M-MLV reverse transcriptase (Invitrogen), with an oligo(dT)18-mer and Random primers, in a final reaction volume of 20 µL. The resulting complementary DNA was subjected to Real-time PCR using SYBR Green qPCR Master Mix (Promega). GAPDH was used as an internal standard. Primers used for TMEM16A, forward: 5’-ACTACCACGAGGATGACAAGC-3’, reverse: 5’-TCTCTGCACAGCACGTTCC-3’; for EGFR, forward: 5’- AGGCACGAGTAA CAAGCTCACT-3’, reverse: 5’- ATGAGGACATAACCAGCCACC − 3’; for GAPDH, forward: 5’-CATCAAGAAGGTGGTGAAGCAG-3’, reverse: 5’-CGTCAAAGGTGGAGGAGTGG-3’.
RNA transcriptome sequencing
The KYSE30lm3 and KYSE30luc cells were cultured for 48h with complete medium. Then the cells were collected and the total RNA was extracted using TRIzol reagent (Invitrogen). The genomic DNA was removed using DNase I. RNA degradation and contamination was monitored on 1% agarose gels. Then RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280 = 1.8 ~ 2.2, OD260/230 ≥ 2.0, RIN ≥ 8.0, 28S:18S ≥ 1.0, > 1 µg) was used to construct sequencing library. RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instruction (Illumian, San Diego, CA). The transcriptome library was prepared following TruSeq™ RNA sample preparation Kit from Illumian (San Diego, CA) using 1 µg of total RNA. Fastp (https://github.com/OpenGene/fastp) was used for quality control and read mapping. To identify DEGs between two different groups, the expression level of each gene was calculated according to the TPM method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances. GO (Gene Ontology, http://www.geneontology.org) and KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/) were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at P-adjust ≤ 0.05compared with the whole-transcriptome background.
Migration and Invasion assay
For migration assay, 5×104 KYSE30lm3/KYSE30luc and 2×105 KYSE450lm2/KYSE450luc cells were plated in 24-well Transwell plates with inserts (8-µm pore size, Corning) and were incubated at 37°C for 24h. Invasion assays were carried out in a 24-well Transwell unit on polycarbonate filter coated with Matrigel (Corning). Cell inserts were fixed with 4% PFA for 30 min, followed by PBS wash and 1% crystal violet staining to allow visualization. Nine random fields were captured per sample at 10× magnification. The ratio of the average stained area to the field of view of each sample was calculated by Image J. All experiments were performed in triplicate.
Generation and purification of anti-TMEM16A monoclonal antibodies
BALB/C mouse were used for immunization. TMEM16A eukaryotic plasmid mixed with In vivo-jetPEI (Polyplus) transfection reagent was used as antigen. Ten days after the last boost the sera of the immunized mice were tested for the TMEM16A specific antibody by ELISA, and the spleen cells were isolated and fused with myeloma cells to obtain hybridomas. Limited dilution was performed as standard step to selected hybridoma cell clones. We used 293T-TMEM16A cell as coating antigen of primary screening, and GST-T16A-T1-T4 prokaryotic protein and GST protein (400 ng/mL) recombinant protein as coating antigen in the next few rounds of screening. Antibodies were prepared by intra-peritoneal injection of hybridomas into 8-week-old BALB/C female mice. One week before the hybridoma injection, 500 µL of incomplete Freund's adjuvant was injected. After 10–15 days, the ascites was collected, and protein G agarose beads were used for antibody purification. After being concentrated by PEG20000, antibodies were dialyzed by PBS and identified with SDS-PAGE.
Immunoprecipitation and Co-immunoprecipitation
KYSE30lm3 cells were lysed with IP buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl ,1mM EDTA and 0.5% NP-40) containing protease inhibitors (Roche, USA), and the lysates were used for IP with appropriate antibodies as well as protein G-Sepharose (GE Healthcare, USA). The precipitants were separated by SDS-PAGE and subjected to Western blotting with specific antibodies.
Western blot assay
For western blot analysis, cells were collected and lysed with 40 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1% (v/v) Triton X-100, 1 x cocktail of protease inhibitors and PMSF. Protein samples (20 µg per lane) were separated and transferred to a NC membrane. After blocking with 5% non-fat milk, the membranes were incubated with primary antibodies at 4°C overnight. HRP-conjugated sheep anti-rabbit or anti-mouse IgG secondary antibodies (Vector, Burlingame, CA) were incubated for 1 h at room temperature. The protein bands were detected using the Super Enhanced chemiluminescence detection kit (Applygen Technologies Inc, Beijing, China).
Multiplex IHC
Immunofluorescence staining was performed using a Multiplex mIHC kit (TSA-RM-275, Panovue, China). Chips were heated at 60°C for 20 min. After dehydrated, chips were incubated with formalin solution and 3% H2O2 for 10 min. Following antigen retrieval with pH 8.0 EDTA, the slides were blocked with 5% goat serum (ZLI-9056, ZSGB-BIO) for 1 h. Anti-EGFR antibody and anti-TMEM16 antibody as primary antibodies and then incubated with fluorescent antibodies. The chips were rinsed with washing buffer after each step. Following TSA deposition, the chips were again subjected to HIER to strip the tissue-bound primary/secondary antibody complexes and ready for labeling of the next marker. These steps were repeated until two markers were labeled and finally added with spectral 4’6-diamidno-2-phenylindole (DAPI) at 1:500 dilution. The chips were mounted in ProLong Diamond Anti-fade Mountant and cured in the dark at room temperature for 24 h. All images were acquired for each case using a Vectra 3 pathology imaging system and analyzed using inform software.
Measurement of TMEM16A chloride channel activity with MQAE
MQAE (S1082, Beyotime) is a fluorescently-labeled deoxyglucose analog that is used primarily to detect chloride channel activity in living cells. Briefly, the cells were cultured on glass-bottomed cell culture dishes (801002, NEST, China). The cells were subsequently loaded with 1 mM MQAE in the dark for 2 h at 37°C, and washed twice with the MQAE effluent to remove the unbound probe and re-added with 1 mL of MQAE effluent. Culture dishes were placed on the stage of the laser confocal microscope. The effluent was aspirated after selecting the field of view, and 500 µl of MQAE buffer with NaI (50 mM) was added. The focal length was adjusted at the excitation wavelength of 405 nm, and after 2 seconds of baseline fluorescence intensity in the field of view, 500 µl of ATP (200 µM) was added, then changes in the fluorescence intensity of cells under the field of view were recorded after continuous shooting after pipetting and mixing [36, 37, 38].
Measurement of chloride channel activity TMEM16A with EYFP-H148Q/I152L
The ESCC cells were transfected with the pCDNA3.0-YFP-H148Q/I152L plasmid for 24 h and were plated into a 96-well blackboard transparent bottom plate at 1×104/well after digested and resuspended. EYFP-H148Q/I152L fluorescence was monitored in cells with fluorescence microscopy after 24 h. After discarding the culture medium, the cells were washed in PBS for three times, then 50 µl/well of isotonic NaI Krebs-HEPES solution was added. Fluorescence was continuously measured at a rate of 5 s/point for 200 s, the first 10 s as the baseline, and after 10 s, the hypotonic Krebs-HEPES solution containing 200 µM ATP was injected into the well at a rate of 150 µl/well/s and the determination was continued. The parameters were set with excitation wavelength 514 nm and emission wavelength 550 nm [39, 40].
In vivo assay
Animal experiments were approved by the Biomedical Ethical Committee of Peking University Cancer Hospital & Institute and performed along institutional animal welfare protocols concordant with the NIH guidelines. Six-week-old male SCID/Beige mice were purchased from Charles River (Beijing, China). For tumor metastasis model, mice were randomized into two groups, KYSE30lm3 cells (2×106) were injected into the tail vein of mice, which were subsequently killed 8 weeks later. For footpad tumor model, KYSE30lm3 cells (2×105) were injected into the right footpad of mice which were killed 4 weeks later. All mice were treated with mT16A#5 (10 mg/kg), Cetuximab (1 mg/kg) or mIgG (40 mg/kg) twice a week.
Cell proliferation assay
A Cell Counting Kit 8 (CCK-8; Dojindo Laboratories) was used to evaluate cell proliferation. At 24 h after transfection, the cells were seeded into 96-well plates with 1,000 cells per well and cultured for 24, 48, 72, 96, and 120 hours. Then, 10 µl of CCK-8 solution was added to each well and incubated for 1 h. Optical density was examined at the wavelength of 450 nm.
Statically analysis
The SPSS (version 26) software package (SPSS Inc, Chicago, IL) was used for statistical analysis. The data were expressed as the mean ± SD, and the data from specific experiments were compared by one-way ANOVA, Student’s t-test, or χ2 test. GraphPad Prism 6 software (GraphPad Software, San Diego, CA, USA) was used for statistical figure or chart display. Chi-square analysis was used for differential expression of TMEM16A and EGFR in ESCC tissue microarrays. All experiments were repeated at least three times with consistent results. P-value<0.05 was considered statistically significant.