Patient tissues
This study was approved by the Ethics Committee of Fudan University Shanghai Cancer Center, and written informed consent was obtained from all patients. Human normal skin tissue (n = 39), nevus (n = 32), basal cell carcinoma (n = 32) and malignant melanoma tissues (n = 213) were collected during surgical resection of malignant melanoma at Fudan University Shanghai Cancer Center between 2014 and 2017. Seven of the normal skin tissues were obtained from malignant melanoma patients. The specimens were immediately frozen in liquid nitrogen after surgery. Patient features were seen in Supplementary Table 1.
Immunohistochemistry (IHC) assay
The tissue sections were stained with hematoxylineosin and by IHC using indirect immunoperoxidase technique. The antibody of human PARVB (sc-374581) was purchased from Santa Cruz (USA). The IHC stains were assessed independently by three observers who had no knowledge about the specimen characteristics.
Quantitative real-time PCR (qRT-PCR)
Total RNAs were extracted with Trizol regent (Invitrogen, USA). Then, first-strand cDNA was generated by Prime Script™ RT Master Mix(Takara, Japan). Gene transcripts were quantitated on 7900HT Fast Real-Time PCR System (Life Technologies Corporation, USA) using SYBR® Premix Ex Taq™ II (Takara, Japan) and normalized with GAPDH. The primers were listed in Supplementary Table 2.
Western Blot
Total protein was resolved on SDS-PAGE gel. Western blot assays for human and mouse PARVB were performed using the antibodies described in IHC staining (sc-374581). Human and mouse β-actin proteins were determined using the specific antibody (sc-8432, Santa) as a loading control.
Cell lines
Human melanoma cell line A375 and mouse melanoma cell line B16 were purchased from the Cell Bank of the Type Culture Collection Committee of the Chinese Academy of Science (Shanghai, China). Human melanoma cell line SK-MEL-28 were purchased from the American Type Culture Collection (ATCC, USA). A375 was cultured in DMEM (Invitrogen, USA) supplemented with 10% FBS (Invitrogen). SK-MEL-28 and B16 were cultured in RPMI 1640 medium (Invitrogen) supplemented with 10% FBS (Invitrogen). All cells were cultured at 37 °C in a humidified atmosphere with 5% CO2.
Plasmids construction and cell transfection
The code sequence of human HIF-1α, HIF-2α and PARVB were synthesized (Genewiz Co., Suzhou, china) and inserted into pcDNA3.1 vector (Invitrogen, USA). The shRNA plasmids of PARVB and control plasmids were purchased from Genomeditech Co. (Shanghai, China). GV248 was used as the plasmid vector. Sh-PARVB-2 plasmid and the control plasmid were packaged into lentivirus (Genomeditech Co.).
The possible promoter region (-1706bp ~ 264 bp from transcription initiation site) of PARVB containing the potential HRE sites (5’-G/ACGTG-3’) were synthesized (Genewiz Co.) and inserted into pGL3-reporter Luciferase Reporter Vector (Promega, USA). The fragments containing partial potential HRE sites (b: -1109bp ~ 264 bp; c: -593bp ~ 264 bp; d: -116bp ~ 264 bp; e: 48bp ~ 264 bp from transcription initiation site) were obtained through PCR methods (primers seen in Supplementary Table 2) and cloned into pGL3-reporter Luciferase Reporter Vector using a Quick-Fusion cloning kit (Bimake, USA) according to the manufacturer's protocol. VEGF promoter (-1080bp~-874 bp from transcription initiation site) luciferase reporter vector was obtained as reported previously [17]. The mutant HRE site 7 and 8 promoter plasmids were constructed based on PARVB promoter plasmid (a: -1706bp ~ 264 bp) using a MutanBEST Kit (Takara) following the manufacturer’s instructions.
Plasmids were transiently transfected into cells with DNA Transfection Reagent (Bimake) when they grew to 50 ~ 70% confluence according to the manufacturer’s instructions.
Cell Counting Kit 8 (CCK8) assay
Cells were seeded in 96-well plates at a density of 5 × 103 and cultured for 72 h and analyzed with the Cell Counting Kit 8 (Bimake, USA). Results were measured by absorbance at 450 nm using an ELx800 microplate reader (BioTek Instruments Inc., USA).
Cell cycle assay
Cycle distribution was analyzed by flow cytometry. Briefly, Cells were collected and fixed with ice-cold 70% ethanol, washed with PBS, and resuspended in 0.5 mL PBS containing propidium iodide and RNase A. After final incubation at 37 °C for 30 min, cells were analyzed using a FACSCalibur flow cytometer (Becton-Dickinson, USA). Data were analyzed using FlowJo software (Tree Star, USA).
PARVB knockout B16 cell line construction
CRISPR-Cas9 target sites were designed (Supplementary Table 2), synthesized (Genewiz Co.) and cloned into pCas9/gRNA3 plasmid (Inovogen Tech. Co., Beijing, China) using a Quick-Fusion cloning kit (Bimake). B16 cells were transfected with the constructed plasmids and selected with Ampicillin. Selected cells were cloned using limiting dilution and the targeted sequence was confirmed by DNA sequencing.
Xenograft mouse models
Eight-week-old female BALB/c nude mice were purchased from JRDun Biotechnology (Shanghai, China), and were maintained under specific pathogen-free, 12-h light–dark cycle (room temperature 22.5 ± 0.2 °C, humidity 40–60%) conditions and the animals had free access to feedstuff and water. Mice were euthanized by injecting excessive dose of Pentobarbital Sodium at the end of the experiments to ameliorate the suffering of mice. Animal care and experiments were performed in accordance with the Provision and General Recommendation of Chinese Experimental Animals Administration Legislation and were approved by the Ethics Committee of Fudan University Shanghai Cancer Center.
For human melanoma animal models, fourteen mice were equally randomized into a normal control group and a shRNA group. After transfection with control lentivirus or sh-PARVB-2 lentivirus. A375 cells were injected subcutaneously to the right upper flank of the nude mice. Tumor volumes were counted every 4 days in accordance with the equation: 0.5 × length × width2. 28 days after tumor cell injection, all mice were dislocated to death and the excised tumor tissues were weighed. Ki-67 staining were performed to detect tumor cell proliferation.
For mouse melanoma animal models, ten mice were equally randomized into a normal control group and a knockout group. Wild type or PARVB knockout B16 cells were injected subcutaneously to the right upper flank of the nude mice. Tumor volumes were counted every 5 days. 30 days after tumor cell injection, all mice were dislocated to death and the excised tumor tissues were weighed.
Wound healing assay
Cells were cultured in 12-well plates, transfected as indicated, and cultured to confluency. Cells were scraped with a 200 µl pipette tip (time 0 h), washed twice with PBS, and cultured in serum-free medium. Cell migration progress was photographed at 0 h, 24 h and 48 h following injury.
Transwell assay
The invasion capability of melanoma cells was measured 24-well-cell permeable supports 8 µm pore size transwell chamber with matrigel (354480, Corning, USA). 1 × 105 cells in serum-free medium were seeded in the upper chamber, and 500 µl medium supplemented with 10% FBS was added to cover the bottom chamber as chemoattractant. After 24-h incubation, cotton swabs were used to gently remove cells remaining on the upper membrane. Cells on the bottom surface were then fixed with 4% paraformaldehyde and stained with 1% crystal violet for 15 min. Cell invasion was assessed by counting stained cells under a microscope on five random fields.
Chromatin immunoprecipitation (ChIP) assays
ChIP assays were performed by using a ChIP assay kit (Millipore, USA) following the manufacturer’s instructions. Briefly, cells cultured under the hypoxic or normaxic conditions were subjected to ChIP assays with anti-HIF-1α or anti-HIF-2α antibody. Normal IgG was used as a control for nonspecific binding of genomic DNA. DNA fragments pulled down by the antibodies were then recovered and subjected to qRT-PCR with PCR primer sets (Supplementary Table 2).
Luciferase reporter assay
HIF-1α or HIF-2α overexpression vector and the constructed luciferase reporter plasmids were co-transfected into A375 cells by DNA Transfection Reagent (Bimake). The luciferase activity was measured by using the Dual Luciferase assay kit (Promega) and normalized with the internal standard.
Statistical analysis
Statistical analysis was conducted by SPSS 21.0 software (IBM, USA). Data are presented as Mean ± Standard Deviation (SD). Chi-square test or Fisher’s exact test (two-tailed) was used for the comparison of count data. Independent Student t-test (two-tailed) was used for the comparison of measurement data. The Kaplan-Meier method was used to establish survival curves, and log-rank test was applied for comparative analysis of differences in patient survival. Factors measuring p ≤ 0.1 from log‑rank tests were subjected to the cox proportional hazard analysis and calculation of the hazard ratio and 95% confidence interval. P ≤ 0.05 was considered statistically significant. All experiments were repeated at least three times.