Cells and patient samples
ESCC cells lines KYSE150, KYSE520, TE1, KYSE180, KYSE450, KYSE410 and the immortalized esophageal epithelial cell line NE1 were maintained in Dulbecco’ s modified Eagle’ s medium (DMEM, Gibco, NY, USA) and RPMI 1640 supplemented with 10% fetal bovine serum (FBS, Gibco) with 5% CO2 in 37℃. This study included 140 randomly selected patients with primary ESCC who underwent radical esophageal resection at the First Affiliated Hospital of Shantou University Medical College and Sun Yat-sen University Cancer Center from 2010 to 2017. None of the patients received preoperative radiotherapy or chemotherapy. 106/140(75%) were male and 34/140 (25%) were female. The median age was 57.8 years (range, 37-75 years). This study was approved by the ethical review committees of the Sun Yat-sen University Cancer Center. All participants involved in our study provided written informed consent.
Pooled CRISPR/Cas9 sgRNA screen and establishment of MAP2K3 knockout (KO) cell lines
A pooled lentivirus-based plasmid library, encompassing 2925 different sgRNAs against 976 human kinase genes (3 sgRNAs per gene), was obtained from EdiGene (Beijing, China). The list of genes was obtained from the KinBase database (http://kinase.com/human/kinome/).The library was co-transfected, with a lentivirus expression system, using Fugene HD (Promega, WI, USA). Lentivirus was packaged and concentrated by using a three-plasmid system (pCMVR8.74, pcmv-vsv-g & cas9-2a-mchy-bsd) to obtain the high-titer lentivirus wrapped in cas9-2a-mchy-bsd. Forty-eight hours after transfection, lentivirus-containing supernatants were collected and clarified by centrifugation. After selection with puromycin for 7 days, ~2×108 cells were infected (MOI of 0.3) and then incubated for 2-3 weeks with or without drug treatment. Genomic DNA was extracted from transfected or control cells, and sgRNA sequences were amplified, and subjected to next generation sequencing using an Illumina HiSeq 2500 platform.
The stable knockout (KO) cell lines which were negative for all isoforms of MAP2K3 were established from KYSE520 cells using the CRISPR/Cas9 system. Briefly, sgRNA targeting the MAP2K3 gene were designed using the CRISPR Design Online Tool (https://www.genscript.com/gRNA-design-tool.html). After transfection, the puromycin-resistant cells were selected and expanded. Westernblot and Sanger sequencing were performed to confirm the knockout.
Nuclear and cytoplasmic extraction and western blot analysis
NE-PERTM nuclear and cytoplasmic extraction reagents (Thermo Scientific, MA, USA) were used to separate and prepare cytoplasmic and nuclear extracts from ESCC cells. Western blotting was performed as described previously [11]. Antibodies against human β-actin, MAP2K3, p-MAP2K3, EGFR, p-EGFR, STAT1, p-STAT1, STAT3, p-STAT3, caspase 3, cleaved(cl-) caspase 3, GFP, Ki67, Flag, Ub, HA, MDM5, cleaved(cl-) PARP were purchased from Cell Signaling Technology (MA, USA).
Immunohistochemistry (IHC)
IHC staining was performed using the EnVision System using peroxidase labeling (Dako, Carpinteria, CA) as described previously[11]. IHC staining was examined by two pathologists who were blinded to the clinical outcome. Expression of MAP2K3, STAT3 or indicated protein was analyzed by an individual labeling score considering the proportion of positively stained tumor cells and the intensity of staining. Intensity of stained cells was graded into four levels: 0: negative staining; 1: weak staining; 2: mild staining; and 3: strong staining. The area of staining was evaluated and recorded as a percentage: 0: no staining; 1: positive staining in 1-25% of tumor cells; 2: 26% to 50%; 3: 51% to 75%; 4: >76% of tumor cells. Intensity and fraction of positive cell scores were multiplied, and in this scoring system, low expression was defined as having scores of 0-6, and high expression was defined when the score was 8-12.
Chemicals, plasmids transfection and stable cell lines established
Cycloheximide (CHX), 5-aza-2’-deoxycytidine (5-aza) were purchased from MCE (NJ, USA). All drugs were dissolved in dimethyl sulfoxide (DMSO; Sigma, St. Louis, MO, USA). The Flag-wild-type (wt) MAP2K3 plasmid, dominant-negative MAP2K3 (S-A), constituted activated MAP2K3(S-E) constructed by replacing Ser-189 and Thr-193 with Ala or Glu residues, Flag-MDM, MDMC464A, GFP-STAT3 wt, STAT3 (Y705A), STAT3 (S727A), MIR19B transcriptional activity reporter plasmids and three mutant type plasmids (mt1: -1462/-1452; mt2: -1295/-1285; mt3: both mutant) were purchased from Vigene (Guangzhou, China). Transfection of plasmids was performed using Lipofectamine 3000 reagent (Invitrogen, NY, USA) according to the manufacturer’s instructions.
In addition, the miR-19b-3p mimic or miR-19b-3p inhibitor, and MAP2K3 siRNA were purchased from GenePharma (Jiangsu, China). Transfection of siRNA or miRNA mimics or inhibitors was performed using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer’s instructions. Lentivirus encoding a miR-19b-3p mimic or miR-NC was packaged in human embryonic kidney 293T cells and the virus was collected according to the manufacturer's instructions. Stable cell lines were established by infecting ESCC cells with lentivirus, followed by puromycin selection.
Invasion assay
Cell invasion ability was tested using transwell invasion assay. Briefly, 100 μl Matrigel (BD, USA) was firstly added onto the bottom of the transwell chamber (24 well insert; 8 mm pore size, Corning Costar Corp), then 1 × 105 cells in reduced serum medium (Opti-MEM, Gibco) were placed on the coated membrane in the chamber. Migrated cells on the permeable membrane were fixed and then stained with crystal violet.
Cell proliferation and apoptosis assay
The viability of ESCC cells was determined with a Cell Counting Kit 8 (CCK8, APExBio, Houston, TX, USA). 5×103 of ESCC cells were seeded in each well of a 96-well plate and allowed to adhere overnight. The change in cell number was determined every 24 hours. Cell density was determined by addition of CCK8 and measuring OD450 nm with a microplate reader.
Tumor cells were pretreated or transfected and collected by trypsinization to wash twice with ice-cold PBS. Then then cells were stained using an FITC Annexin/V Apoptosis Detection Kit (BD Pharmingen TM, USA) and quantified by flow cytometry (BD Biosciences, USA).
Colony formation assay
After transfection or drug treatment, cells were plated in six-well plates, at a density of 500 cells/well, and incubated for 10 days at 37oC. The cells were then fixed with 4% buffered formalin for 15 min and then stained with 1% crystal violet (Sigma Aldrich, China) for 30 min. The plates were gently washed with PBS and dried before microscopic evaluation. Cell clusters with >30 cells were considered as a colony.
Luciferase reporter assay
Transcriptional activity was measured with a Dual-Luciferase reporter assay system (Promega) according to the manufacturer’s instructions. Cells were co-transfected with the dual-luciferase reporter and indicated plasmids or miRNA mimic using Lipofectamine 3000 or RNAiMAX (Invitrogen). Each group was run in triplicate in 48-well plates. The luciferase activity was detected by Dual-Luciferase Reporter Assay System (Promega) after 48 h of transfection.
Immunocytochemistry
Cells (3×104 cells) grown on cover slips were fixed with 4% paraformaldehyde, permeabilized with 0.1% Triton X-100, blocked in 3% BSA, and incubated with primary antibodies overnight at 4oC. Then, the samples were incubated with an Alexa Fluor 488-conjugated anti-mouse IgG fragment (Invitrogen, 1:200) or an Alexa Fluor 555-conjugated anti-rabbit IgG fragment (Invitrogen, 1:200) at room temperature for 30 min in the dark, and were counterstained with 4’,6-diamidino-2-phenylindole (DAPI, Invitrogen, 1:300) to stain nuclei. Cells were observed and imaged using a laser-scanning confocal microscope (Leica Microsystems, Germany).
RNA extraction and quantitative RT-PCR
Using a RNeasy Mini Kit (Qiagen, Valencia, California), total cellular RNA was extracted from cells. Quantitative RT-PCR was performed according to previous published papers using the SYBR system (Takara, China) [18]. The mRNA levels in cell and tissue lysates were normalized against β-actin. The expression of indicated genes was normalized to an endogenous control by using the 2-DDCt method. Sequences of primers used for qRT-PCR in this study are listed in Supplemental Table 1.
Co-immunoprecipitation (Co-IP)
Co-IP was performed using special antibodies and protein G-conjugated Dynabeads (Invitrogen) according to the manufacturer's instructions. In brief, cell lysates were incubated with antibodies overnight at 4oC. The next day, Protein G-conjugated beads were added into the lysate at 4oC for 2 h. Then, the beads were washed extensively and boiled in SDS loading buffer. Western blotting was used to detect the immunoprecipitated proteins.
Chromatin immunoprecipitation (ChIP) assays
ChIP assays were essentially performed as protocol described with slight modifications: 5×106 cells were fixed with formaldehyde (1% final volume concentration, Sigma) for 10 min at room temperature. Fixation was stopped with the addition of 1/10 volume 1.25 M glycine and the samples were incubated for 5 min at room temperature. The sonication step was performed in a qsonica sonicator (5 min, 20 s on, 20 s off), and 200 µg of the protein-chromatin complex was used in each immunoprecipitation. Antibody-protein complexes were captured with preblocked dynabeads protein G (Invitrogen). ChIP DNA was analyzed by qPCR with SYBR Green (Biorad) on an ABI-7500 (Applied Biosystems) using the primers specified in Supplemental Table 1. The antibodies used are as followed: Anti-STAT3 and normal mouse IgG.
RNA sequence
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq 6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).
Animal studies
All animal experiments were undertaken in accordance with the NIH Guide for the Care and Use of Laboratory Animals, and with the approval of the institutional animal care and use committee at Sun Yat-sen University Cancer Center. For in vivo experiments, indicated treatment and control cells (1×107) were injected into the left and right oxter flank of 5-week-old BALB/C nude mice, respectively. Tumor formation was monitored over a 4-week period. Tumor volume was calculated by the formula: tumor volume = 0.5×length×width2. Tumor volume and body weight were measured every 3 days, and the tumor growth curve was plotted using the tumor volume on the vertical axis and day of measurement following tumor cell implantation on the horizontal axis.
Statistical analysis
Data are expressed as mean±SD of at least three separate experiments. The significance of differences between groups was estimated by Student’ s t-test or Wilcoxon test, as appropriate. Overall survival rates were calculated by the Kaplan-Meier method with the log-rank test applied for comparison. Survival data were evaluated using univariate and multivariate Cox proportional hazards models using statistical software (SPSS, IBM, USA). A p-value of ≤ 0.05 was considered significant.