Data processing
Ninety BCa tissues were collected from patients that underwent either TURBT or radical cystectomy in Shanghai Tenth People’s Hospital (STPH) between November 2019 and September 2020. Informed consent was prior obtained from patients. The protocol of total RNA extraction, paired-end libraries synthetization and RNA-sequence were available in our previous methods. The mRNA (RNA-sequencing) Fragments Per Kilobase of transcripts per Million mapped reads (FPKM) standardized values of genes were calculated and selected for further analyses. Monthly telephone follow-up was done to obtain the disease-free survival (DFS) of these patients. This study was reviewed and approved by the Ethics Committee of Shanghai Tenth People’s Hospital.
The FPKM standardized mRNA expression data and clinical information of BLCA patients were downloaded from TCGA (https://gdc-portal.nci.nih. gov/). The processed gene expression data of GSE13507, GSE48277, GSE32894 and GSE31684 with the prognostic information of BLCA patients were downloaded from the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/). The processed gene expression data and clinical information of IMvigor210 trial that included patients with metastatic urothelial cancer treated with atezolizumab (PD-L1 inhibitor) were obtained from the website http://research‐pub.gene.com/IMvigor210CoreBiologies.
Meta-analysis
Meta-analysis was performed to investigate the prognostic value of in SULF2 using ‘meta’ R package v4.16 and ‘metafor’ R package v2.4. Univariate Cox analysis was used to calculate the hazard ratio (HR) and 95% confidence interval (CI) of SULF2 in each data set. Then, the HR and 95% CI from each data set were selected to calculate the combined value. The χ2 -based Q test and I2 statistical test were used to investigate the heterogeneity. When P<0.05 or I2>50%, the random effects model was used to calculate the combined value; otherwise, the fixed effects model (P>0.05 or I2<50%) was used. Egger’s funnel plot was used to evaluate the publication bias. P>0.05 was considered as no publication bias.
Gene Set Enrichment Analysis (GSEA)
In STPH, BCa patients were divided into high and low expression groups based on the median expression of SULF2. GSEA (http://www.broadinstitute.org/gsea/index.jsp) was performed to investigate the BLCA-related signaling pathways affected by high expression of SULF2. A nominal P<0.05 and a false discovery rate (FDR)<0.25 were considered significant.
Cell lines and Reagents
Human BCa cell lines T24(Cat.SCSP-536), UMUC3(Cat.CRL-1749), 5637(Cat.TCHu 1), RT4(Cat.TCHu226) and J82(Cat.TCHu218), normal urothelial cell line SV-HUC-1(Cat.TCHu169), mouse BCa cell MB49(Cat.AC-340699), and human acute monocyte THP-1 leukemia cells(Cat.TCHu 57) were purchased from the Chinese Academy of Sciences, Institute of Chemistry and Cell Biology (Shanghai, China). The above cells are all in DMEM or RPMI-1640 medium with 10% fetal bovine serum (Gibco)and 1% penicillin/streptomycin (Hyclone; GE Healthcare Life Sciences, Logan, UT). McCoy's 5A medium containing 10% FBS and 1% penicillin/streptomycin used for RT4. All cells were cultured in a 37°C incubator with 5% CO2.
In order to obtain macrophage-like differentiated THP-1 cells, THP-1 cells were seeded at a density of 3×106 cells/flask and exposed to 100 ng/ml phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich) 48 hours. After that, replace the medium containing PMA with fresh medium to obtain the resting state of macrophages (M0), and then add 20 ng/ml IFNγ and 1 mg/ml LPS (Sigma-Aldrich) to differentiate into M1 Phenotype, or adding 20 ng/ml IL-4 to differentiate into M2 phenotype.
Cell proliferation assay
The effect of SULF2 on cell proliferation was tested by CCK-8 assay and 5-Ethynyl-20-Deoxyuridine (EDU) incorporation experiment. For the EDU assay, the experiment was carried out according to the manufacturer’s instructions of the kit (Beyotime Biotechnology, Shanghai, China). For CCK 8 determination, Cells were seeded into 96-well plates at a density of 2×10 3 cells/well, each well added 10μl CCK-8 reagent (Yeasen Biotechnology, Shanghai, China) and the cells were Maintained at 37°C for 1.5 hours. The absorbance at 450 nm was measured using a microplate spectrophotometer (BioTek, Winooski, VT). The experiment was repeated three times.
RNA extraction and real-time polymerase chain reaction (qPCR)
According to the manufacturer's instructions, Trizol reagent (Invitrogen, Carlsbad, CA) was used to extract total RNA from human tissues or cells, and then a reverse transcription system kit (Vazyme Biotech Co., Ltd, China) was used to generate the first strand cDNA. Use ChamQ universal SYBR qPCR master mix (Vazyme Biotechnology Co., Ltd, China) and ABI Prism 7500 sequence detection system (Applied Biosystems, CA) for qRT-PCR. The qPCR parameters are as follows: 40 cycles of 30 seconds at 95°C, then 10 seconds at 95°C and 30 seconds at 60°C. GAPDH was used as an endogenous control(Supplementary Table3). The relative fold change is analyzed by the 2-ΔΔC(t) method. Repeat the measurement 3 times.
Western Blot
Use RIPA buffer to extract total protein from cells or tissues. After quantifying the lysate by the bicinchoninic acid protein assay (Beyotime, China), 30μg protein sample was subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and then transferred to nitrocellulose membrane (Sigma-Aldrich; Merck KGaA) The blot was blocked with 5% skim milk at room temperature for 1 hour, and immunoblotting was performed with primary antibody at 4°C overnight. Subsequently, the blot was incubated with the appropriate HRP-labeled secondary antibody. Use Super ECL Detection (Yeasen Biotech Co. Ltd, China) to visualized and quantified the immunoreactive bands. GAPDH was used as an internal reference. Supplementary Table 1 lists the antibody companies and product number used
The mouse orthotopic bladder cancer model and in vivo growth assays
C57 female mice were used for in situ injection of BCa cells --MB49, and 1×106 treated cells were injected into the bladder through the urethra, 5 in each group. Four weeks later, the mice were sacrificed and the tumors in situ were taken out and immunized by flow cytometry Cell infiltration situation. For subcutaneous transplanted tumors, 1×106 treated T24 cells were injected subcutaneously into the right armpit of 4-week-old female BALB/c nude mice, 5 in each group. The mice were sacrificed four weeks later, and the subcutaneous tumors were removed. Monitor the mouse body weight, tumor diameter, and tumor volume every three days according to the formula (tumor volume = π/6 × length × width 2). In order to establish a metastasis model, 1×106 overexpressing or knocking down SULF2 cell lines were injected into the tail vein of 4-week-old nude mice, with 3 mice in each group. The in vivo imaging system (IVIS) was used every week to observe the tumor metastasis after 3 weeks.
Flow cytometry
In order to analyze the immune cells infiltrating the mouse orthotopic bladder cancer model, the mice were sacrificed at the 4th week after MB49 was injected into the C57 mice bladder, and the tumor tissue was cut and combined with collagenase (100 μg/ml) Incubate at 37°C for 30 minutes. The separated tumor cells were filtered with a 70um mesh, red blood cells were removed using red blood cell lysis buffer, the cells were resuspended in PBS, and then incubate with flow cytometry antibodies. After 30 minutes, the cells were washed 3 times with PBS and resuspended in 500ul of PBS buffer for flow cytometry analysis. For the cell cycle, cells were collected, trypsinized to form a cell suspension, and then fixed with 75% ethanol at 4°C overnight. On the second day, the cells were washed three times with PBS, and then RNase containing iodide (PI, 40%, Sigma- Aldrich) incubated for 30 minutes, washed the cells with PBS three times, and then used flow cytometry (BD Biosciences, USA). The experiment was repeated three times. The results are analyzed using Flowjo.
Co-cultivation system
In order to co-culture BCa cells and macrophages, we used a 0.4um Transwell chamber (Corning, Lowell, MA), the lower chamber is a THP1 cell line, and the upper chamber is a BCa cell lines that overexpresses or knocks down SULF2, as shown in Fig. 6A. The co-cultivation time is 48h. Collect the required cells for the next experiment.
Colony formation
For colony formation analysis, the SULF2 overexpression or knockdown cell line was seeded into a six-well plate at 1 × 10 3 /well, and cultured in an incubator for 14 days. After that, it was washed 3 times with cold PBS, fixed with 75% ethanol, and stained with 0.1% crystal violet. The image of the stained tumor cell colony was recorded with a digital camera and statistically analyzed.
Cell migration and invasion
Use Transwell chamber (Corning, Lowell, MA) to detect cell migration ability. Mix 5×10 4 cells in 200ul of FBS-free RPMI-1640 medium and add them to the upper chamber of the transwell chamber, and add 600 μl of cell culture medium containing 10% FBS to the lower chamber. Incubate in a 37°C incubator for 16 hours. Wash 3 times with cold PBS after 16 hours. Carefully wipe the cells that have not passed through the upper chamber with a wet cotton swab, fix with 75% ethanol for 30 minutes, and then stain with 0.1% crystal violet for 10 minutes. Observe cell migration under a microscope (Olympus Corporation). For tumor cell invasion experiments, Transwell filters are pre-coated with Matrigel (BD Biosciences, Franklin Lakes, NJ), and cells are allowed to invade for 24 hours. The rest of the experiment process is the same as the tumor cell migration experiment. Each experiment was performed in triplicate.
Immunohistochemistry (IHC)
Fix the tissue (human BCa tissue or mouse bladder tissue) in cold 4% paraformaldehyde. The fixed tissue samples were embedded in paraffin and sectioned. After hydration, antigen retrieval, and blocking procedures, incubate with the desired antibody overnight at 4°C. Next, the sections were incubated with biotinylated goat anti-rabbit antibody IgG for 20 minutes at room temperature, and then incubated with streptavidin-horseradish peroxidase for 30 minutes. Subsequently, diaminobenzidine-H2O2 was used as a substrate for peroxidase. When the cytoplasm of the cancer cells was stained yellow, two pathologists read the pathological sections and confirmed a positive result.
Statistical analysis
SPSS (version 22; SPSS, Inc., Chicago, IL) and R statistical software (version 3.6.1 R, https://www.r-project.org/) were used to analyze the data. The Kaplan-Meier (log-rank tests) was used to compare the OS (Overall survival) and DFS of the BCa patients between low and high expression groups. The differences between two groups were evaluated using Student's t-test, the chi-square test, or the Mann–Whitney U test, as appropriate. One-way ANOVA followed by Bonferroni’ test was used to compare multiple group comparisons. P-value <0.05 were considered statistically significant difference