Table 1
Demographic characteristic of GB patients.
Study cohort
(18 patients)
|
Demographic characteristic
|
# of patients
|
% of patients
|
Age
|
over 70
|
5
|
27.8
|
60-70
|
5
|
27.8
|
50-60
|
3
|
16.7
|
40-50
|
3
|
16.7
|
under 40
|
1
|
5.6
|
NA
|
1
|
5.6
|
Gender
|
Male
|
13
|
72.2
|
Female
|
5
|
27.8
|
WHO grade classes
|
IV
|
18
|
100
|
Tumor
|
Primary
|
14
|
77.8
|
Recurrent
|
4
|
22.2
|
Tumor location
|
Frontal
|
6
|
33.3
|
Occipital
|
2
|
11.1
|
Temporal
|
5
|
27.8
|
Parietal
|
1
|
5.6
|
Tempo-Parietal
|
1
|
5.6
|
NA
|
3
|
16.6
|
aNA: not available
Tissue preparation
Human tumor tissue obtained from surgical resection of patients with grade IV GBM were fixed in 4% paraformaldehyde in 0.1 M phosphate buffer pH 7.6 overnight at 4°C. Dehydration of tissue was through a series of 80%, 95% ethanol one hour each followed by 100% ethanol overnight. Two 100% xylene washes were done for 1 hour each and then 1 hour in 60°C Paraplast Plus (Tyco/Healthcare, Mansfield, MA). After a change of Paraplast Plus, tissue was incubated in a 60°C vacuum oven for 2 hours prior to placing in molds to cool and solidify. Sections, 3 μm thick, were cut and collected on the superfrost plus slides (Fisher).
Immunohistochemistry
Double-staining
The PT Link (Dako) was used to deparaffinize and rehydrate the sections and unmask antigen sites. Slides were immersed in 10 mM citrate buffer, pH 6.0, for 10 min at 97°C and then cooled and washed in TBS. Endogenous peroxidase activity was inhibited by incubating the slides with Peroxide Block (ScyTek Laboratories, Utah, USA) for 7 minutes. After washing in distilled water and then in TBS, sections were treated with Avidin-Biotin Kit (Biocare-Medical) to reduce background staining caused by endogenous biotin. After 3 washes in TBS, nonspecific binding was blocked by 10 minutes incubation with Background Punisher (Biocare-Medical). Sections were incubated over-night at 4°C with Goat Anti-Human Iba1 polyclonal antibody (Novus Biologicals) 1:250, washed extensively in TBS and subsequently incubated with Ultratek HRP kit (ScyTek Laboratories) and the reaction was revealed by incubation with 3,3’-diaminobenzidine (Biocare-Medical). The same slides were washed extensively in distilled water and TBS and blocked with Background Punisher (Biocare-Medical). The rabbit anti-PDIA3 antibody 1:500 was incubated over-night at 4°C and after 3 washes in TBS, slides were incubated with the MACH 2 Rabbit HRP-Polymer (Biocare-Medical). The PDIA3-associated signal was then revealed by incubation with Vina Green chromogen kit (Biocare-Medical).
Immunostaining Analysis
For quantitative analysis, two blinded examiners counted the number of PDIA3+, IBA1+, or both PDIA3+ and IBA1+ cells in a number of 50 cells total in three randomly different areas of the slides. In particular, two blinded examiners have examined three different areas of the same slides and have counted 50 cells that included the number of positive cells for each antibody, the number of positive cells for both antibodies and the number of negative cells [31]. In total, the average of six counts was reported as percentage.
Cell cultures
The human microglia cell line (CHME-5; RRID: CVCL_5J53) was kindly provided by professor Pierre Talbot [32]. CHME5 cells were grown in DMEM media containing 10% FCS and antibiotics; experimental conditions were reached with DMEM at low concentration of FCS (1%) and cells were splitted at the 80% of the confluence.
Glioblastoma cell line T98G [T98-G] (ATCC® CRL-1690™) was kindly provided by professor Grazia Graziani (Tor Vergata University- Rome). T98G cells were grown in DMEM containing 10% FCS and antibiotics. Experimental conditions were reached with DMEM containing 1% FCS and antibiotics. Cells were splitted at the 80% of the confluence. All the experiments received institutional approval. Conditioned media from activated glioma cells was generated following a protocol described before [28]. Briefly, Basal Conditioned Media (B-CM) was prepared with 4 hours incubation in plain medium, followed by 3 washes with phosphate buffered saline (PBS) and addition of fresh plain medium for 24 hours. After that, CM was collected, centrifuged to remove cellular debris and stored at -80°C. Prestimulated Conditioned Media (PS-CM) was prepared with 4 hours incubation with a mixture of cytokines (10 ng/ml TNFα, 10 ng/ml IL1β, 10 UI/ml hIFNγ called TII), followed by 3 washes with PBS and addition of fresh plain medium for 24 hours. After that, the CM was collected, centrifuged and stored at -80°C.
RNA interference (siRNA)
siRNA for PDIA3 was kindly provided by professor Fabio Altieri (University of Rome – La Sapienza) and Lipofectamine™ 2000 was purchased from Invitrogen. The day before transfection, 5 × 105 cells per well were seeded in a 6-well plate and were grown in normal conditions. The transfection was carried out according to the manufacturer’s instructions and the siRNA was used at 1 µg per milliliter final concentration. Cell lines were incubated 6 hours with the transfection complex under their normal conditions and after 48 hours incubation the selection with puromycin at 1µg/ml was conducted. Cells were grown with puromycin for at least two weeks and then PDIA3 gene and protein expression were carried out.
Nitrite assay
iNOS activity was assessed indirectly by measuring nitrite accumulation in the incubation media. Briefly, an aliquot of the cell culture media (80 μL) was mixed with 40 μL Griess Reagent (Sigma-Aldrich, St Louis, MO, USA) and the absorbance measured at 550 nm in a spectrophotometric microplate reader (PerkinElmer Inc. Waltham, MA, USA). A standard curve was generated during each assay in the range of concentrations 0–100 μM using NaNO2 (Sigma-Aldrich) as standard. In this range, standard detection resulted linear and the minimum detectable concentration of NaNO2 was ‡ 3.12 μM. In the absence of stimuli, basal levels of nitrites were below the detection limit of the assay at all the time points studied. The levels of NO were normalized with the protein content determined by Bradford's method (Bio-Rad, Hercules, CA, USA) using BSA as standard.
Urea assay
Urea levels in CHME5 and T98G cells were detected by the QuantiChrom Urea Assay kit (BIOassay System, Hayward, CA, USA), used according to the manufacturer's instructions. Briefly after 48h of incubation with the B-CM and PS-CM, an aliquot of cell culture media (50 µl) was mixed with 200 µL Urea Reagent (Bioassay system) and the absorbance measured at 430 nm in a spectrophotometric microplate reader (PerkinElmer Inc., MA, USA). A standard curve was generated during each assay in the range of concentrations 0-100 µg/ml using Urea as standard. In this range, standard detection resulted linear and the minimum detectable concentration of Urea was 3.12 µg/ml. The protein content in each sample was determined by Bradford’s method (Biorad, Hercules, CA, USA) using bovine serum albumin as standard.
Cytometer analysis
For intracellular analysis, cells were fixed and permeabilized with Fix/Perm buffer (ThermoFisher Scientific, MA, USA) and then incubated with primary monoclonal antibody anti-ARG1 (C-2) (Santa Cruz Biotechnology, Inc, TX, USA). Secondary monoclonal Antibody Goat anti-Mouse Alexa Fluor®-488 (ThermoFisher Scientific, MA, USA) was used. The purity of cell preparations was assessed by cytofluorimetric staining. Unstained cells were used as a negative control.
Cell Viability and Toxicity
In order to discriminate viable, non-viable cells and apoptosis detection in flow cytometry, cells were incubated with Propidium Iodide and Annexin V-FITC (Novus Biological - NBP2-29373). The assay was conducted following the manufacturer’s instructions. Compensation control cells were provided and unstained cells were used as negative control. Flow cytometry analysis was conducted with FC 500 (Beckman Coulter, Brea, CA) and the data were analyzed with Kaluza software (Beckman Coulter, Brea, CA). At least 50,000 events were acquired.
The cell viability was also measured using a specific luminescence kit: CellTiter-Glo® Luminescent Cell Viability Assay (Promega, WI, USA). Cell mortality was detected using a specific fluorescence kit: RealTime-Glo™ MT Cell Viability Assay (Promega, WI, USA). The assays were carried out according to the manufacturer's instructions.
ROS assay
Detection of intracellular reactive oxygen species (ROS) were reached using H2DCF-DA [2,7-dichlorodihydrofluorescein diacetate (10mM)] as probe. Briefly, cells were treated for 48h and after that, the incubation medium was replaced by Balanced Salt Solution (BSS - NaCl 124 mM, KCl 5.8 mM, dextrose 10 mM, Hepes 20 mM, CaCl2(H2O)2 0.3 mM) and cells were incubated for 30 minutes at 37°C. At the end of the incubation time H2DCF-DA 20 μM were added and cells were incubated for 45 minutes at 37°C.The fluorescence signal was quantified using a microplate fluorescence reader (VictorXTM4 microplate reader, PerkinElmer Inc, Waltham, Ma, USA), using 485 nm as excitation and 535 nm as emission wavelength.
mRNA analysis in real time PCR
Total cytoplasmic RNA from cell lines was extracted using the TRIzol reagent protocol and RNA from FFPE tissues was extracted using the Absolutely RNA FFPE Kit (Agilent, CA, USA) using the manufacturer’s instructions. RNA concentration was measured using the Qubit™ RNA HS Assay Kit (Thermo Fisher Scientific). Aliquots (1 µg) of RNA were converted to cDNA using random hexamer primers. Quantitative changes in mRNA levels were estimated by real time PCR using the following cycling conditions: 35 cycles of denaturation at 95 °C for 20 s; annealing and extension at 60 °C for 20 s; using the Brilliant III Ultra-Fast SYBR® Green QPCR Master Mix (Stratagene, CA, USA). PCR reactions were carried out in a 20-µL reaction volume in AriaMX real time PCR machine (Agilent, CA, USA). Genes’ expression was evaluated using the following primers: Human PDIA3 Forward: GCCACAGTCTTGTCCTCAAACTTG and reverse: TTCCTAAAAGCAGCCAGCAACTTG; human COX2 forward: TTGCTGGCAGGGTTGCTGGTGGTA and reverse CATCTGCCTGCTCTGGTCAATCGAA3; human IL 6 Forward: GGCTCATTCTGCCCTCGAGCC and Reverse: GGACCGAAGGCGCTTGTGGAG; human IL-1β Forward: AGCCATGGCAGAAGTACCGT and Reverse: TCCATGGCCACAACAACTGA; human GAPDH Forward: CCCTCGCCATGGTAAATACAT and Reverse: ACTGGATGGTACGCTTGGTCT. Relative mRNA concentrations were calculated from the take-off point of reactions (threshold cycle, Ct) using the comparative quantitation method provided by AriaMX software and based upon the -ΔΔCt method. Ct values for GAPDH expression served as a normalizing signal.
IL6 quantification and multiple cytokines analysis
IL6 levels in the incubation medium were detected using a specific enzyme-linked immunosorbent assay (ELISA - R&D System, MN, USA). The assay was carried out according to the manufacturer's instructions.
Levels of cytokines and chemokines from culture media were detected using the Proteome Profiler Human Cytokines XL kit (R&D System, MN, USA). The assay was conducted following the manufacturer’s instructions. 500µL of cell culture supernatant was run on each assay. Each spot was measured with image analysis software and the average pixel density of negative control spots was taken as background and subtracted. Then, each dataset was represented with GraphPad Software Prism and student t-test between B-CM and B-CM sh and PS-CM and PS-CM sh was conducted.
Western immunoblot
The cells were lysed in RIPA buffer (1 mM EDTA, 150 mM NaCl, 1% igepal, 0.1% sodium dodecyl sulfate, SDS, 0.5% sodium deoxycholate, 50 mM Tris–HCl, pH 8.0) (Sigma-Aldrich, MO, USA) containing protease inhibitor cocktail diluted 1:250 (Sigma–Aldrich, MO, USA). The protein content in each sample was determined by Bradford’s method (Biorad, CA, USA) using BSA as standard. A 100 µg aliquot of protein was mixed with 4X Bolt™ LDS Sample Buffer (Cat. No.: B0008 – Invitrogen, CA, USA) and 10x Bolt™ Sample Reducing Agent (Cat. No.: B0009 - Invitrogen, CA, USA), boiled for 5 min, and separated through 4-12% bis-tris plus gel (Invitrogen, CA, USA). Apparent molecular weights were estimated by comparison to colored molecular weight markers (Sigma-Aldrich, MO, USA). After electrophoresis, proteins were transferred to nitrocellulose membranes by iBlot™ 2 Gel Transfer Device (Invitrogen, CA, USA). The membranes were incubated in the presence of the primary and secondary antibody in the iBind™ Flex Western Device (Cat. No.: SLF2000 - Invitrogen™, CA, USA) for βactin and PDIA3. Primary antibody for IκBα, phospho-STAT3 and total STAT3 were incubated overnight with gentle shaking at 4°C. Each primary antibody diluition was 1:1000. Primary antibody was removed, membranes washed 3 times in Flex Solution, and further incubated for 1h at room temperature in the presence of specific secondary antibody diluted 1:15000 for anti-rabbit and 1:3000 for anti-mouse. Following three washes in Flex Solution, bands were visualized by incubation in ECL reagents (Thermo Scientific™) and exposure to Hyperfilm ECL (GE Healthcare NY, USA).
Statistical analyses
Data were described as median ± Standard Deviation (SD) or SEM as indicated in figure legends. Statistical analysis of the differences between pairs of groups was performed by Student’s t test. For multiple comparisons ANOVA analysis, followed by Sidak’s post-test, was used. Statistical significance was determined at α = 0.05 level. Differences were considered statistically significant when p < 0.05. Statistical analysis was performed with GraphPad software Prism version 7.04 (GraphPad Software, San Diego, CA, USA).