2.10 Transfection of siRNA-Loaded Liposomes
To evaluate the knockdown efficiency of liposomes containing CD73 siRNA, 3×104 of 4T1 cells were seeded into 24 well plates in RPMI 1640 medium (10% FBS) without antibiotics, at 37°C for 24 h in a humidified incubator containing 5% CO2. After an overnight incubation, cells were divided into five groups including liposomal CD73 siRNA(25nM), CD73 siRNA/lipofectamine complex (25nM) (positive control), naked CD73 siRNA (25nM), and empty liposome (negative control). Cells were transfected with the optimized concentration of siRNA (25nM) in FBS and antibiotic-free OPTI-MEM medium at 40 to 60% confluency for 6 h. After this time, the medium was replaced with complete OPTI-MEM (10% FBS, 100 units/ml penicillin and100 µg/ml streptomycin) and cells were incubated at 37°C for another 48 h. After this final incubation time, cells were trypsynised and collected for evaluating the levels of CD73 mRNA and protein.
2.11 RNA Extraction and Quantitative Real-Time Reverse Transcription PCR (qRT-PCR)
Total RNA was extracted using RNA isolation kit (Qiagen, Germany) and cDNA was synthesized from extracted total RNA using QuantiTect Reverse Transcription kit (Qiagen) according to the protocol. RT-qPCR was carried out using a SYBR Green master mix (amplicon), cDNA template (50 ng, 2 µl), and primers (0.5 µl) in the final volume of 12 µl in a light cycler (Roche) real-time PCR system. The primer sequence for CD73 gene and GAPDH were: CD73 forward primer: 5′-TCCTGCAAGTGGGTGGAAT C- 3′, CD73 reverse primer: 5′- TAGATGGGCACTCGACACTTG-3′; GAPDH forward primer: AATGGATTTGGACGCATTGGT, GAPDH reverse primer: TTTGCACTGGTACGTGTTGAT. The thermocycler parameters were set according to the master mix (amplicon) protocol as follows: all samples were pre-incubated at 95˚C for 5 min and amplified 35 cycles at 95˚C for 15 sec and 58˚C for 30 sec (2 step amplification). All samples were run in duplicate. Melting curve analysis was performed to evaluate product quality and the rate of non-specific amplification. GAPDH was selected as the housekeeping gene and internal control. Relative CD73 gene expression was normalized against GAPDH and analyzed by the ΔΔCT method.
2.12 Flow Cytometry Analysis
To evaluate gene silencing by nanoliposomes containing CD73 siRNA, the expression of CD73 ectonucleotidase was evaluated by flow cytometry. After treatment time, 4T1 cells of each group including
Liposomal CD73 siRNA (25 nM), siRNA/lipofectamine complex (25 nM) (positive control), naked CD73 siRNA (25 nM), and empty liposome (negative control) were harvested and washed twice with the washing buffer (PBS containing 0.5% BSA and 0.1% NaN3). Then, cells were stained with PE rat anti-mouse CD73 and PE Rat IgG2b isotype control mAb in 50µl PBS washing buffer at 4°C for 30 min in the dark. After an additional three times wash, cells were suspended in 500 µl washing buffer and analyzed by flow cytometry (BD FACS Calibur™, BD Biosciences, San Jose, USA).
2.13 In Vivo Studies
2.13.1 Animal and Ethics Statement
Female BALB/c mice (4-6 weeks) were purchased from Royan Institute (Tehran, Iran) and kept under the appropriate conditions. All animal studies were carried out according to the rules of the Institutional Ethical Committee and Research Advisory Committee of Mashhad University of Medical Sciences. Moreover, This study was approved by the Institutional Ethical Committee and Research Advisory Committee of Mashhad University of Medical Sciences (Ethic No. IR.MUMS.fm.REC.1396.11) and complied with the ARRIVE guidelines (https://arriveguidelines.org).
2.13.2 Anti-tumor Study
The experiment was performed on 70 female BALB/c mice, which were previously inoculated with 4T1 cells. For tumor inoculation, mice were first anesthetized via intraperitoneal injection of ketamine-xylazine (K, 100 mg/kg; X, 10 mg/kg). In order to evaluate the anti-tumor effectiveness of prepared formulation in combination with Doxil, 4× 105 4T1 cells were injected into each mouse and after nine days, mice with palpable tumors were divided into seven different groups (10 mice in each group) including PBS, naked CD73 siRNA (5 µg/mice), liposomal negative control siRNA ( NC siRNA) (5 µg/mice), liposomal CD73 siRNA (5 µg/mice), GE11-liposomal CD73 siRNA (5 µg/mice), combination (Doxil (5 mg/kg) + GE11-liposomal CD73 siRNA (5 µg/mice)), and Doxil (5 mg/kg). The formulations containing CD73siRNA were injected intravenously twice per week and for four weeks, while a single dose of Doxil was injected into relevant groups. Bodyweight and tumor volume was measured during the time of the study. Time-to-event endpoints (TTE), median survival time (MST), tumor growth delay (%TGD), and increase in lifespan (%ILS) were also determined for each experimental group. From each group, five mice were sacrificed after the last injection at the fourth week and tumor tissues were removed to evaluate CD73 expression, tumor weight, and immune responses. The remaining mice (five mice in each group) were followed up to evaluate the survival rate.
2.13.3 Tumor CD73 Expression
In order to evaluate the effect of formulations containing CD73 siRNA on downregulation of CD73, in the fourth week of the experiment, two mice from each group were sacrificed, tumors were isolated and RNA was immediately extracted from the tumor tissues using RNA extraction kit. Then, cDNA was synthesized and real-time PCR was performed according to the protocol mentioned in the in vitro study section.
2.13.4 Isolation of Tumor-infiltrated Lymphocytes
In order to isolate tumor-infiltrated lymphocytes (TILs), three mice in each group were sacrificed through injection of 100 µl of ketamine-xylazine solution. Tumors were immediately removed and washed twice with cold PBS, under sterile condition, and cut into tiny pieces with a sterile scalpel in a warm (37°C) collagenase type I solution (2 mg/ml in PBS). In the next step, the digest was quenched by adding RPMI-1640 medium supplemented with 10% FBS. Subsequently, cells were harvested with the cell strainer and washed excessively with cold PBS. In addition, erythrocytes were lysed with ACK lysing buffer (0.15 M NH4Cl, 1.0 M KHCO3, 0.1 mM Na2EDTA). The remaining cells were re-suspended in RPMI-1640 medium supplemented with 10% FBS.
2.13.5 Flow Cytometry Analysis of Isolated Cells
Flow cytometry (FCM) analysis of TILs was performed using the FACS Caliber flow cytometer (BD FACS Caliber™, BD Biosciences, San Jose, USA). Approximately 1.0 × 105 cells were seeded and cultured in a 24 well plate containing 1 ml of RPMI-1640 10% FBS per well. Afterward, cells were stimulated with 2 ml/ml of PMA/ionomycin plus Brefeldin-A cocktail (BioLegend, San Diego, CA) for 6 h at 37 ⁰C. Then, cells were harvested by centrifugation at 250×g for 5 min, washed twice with PBS (containing FBS 2%), and stained according to the supplier’s instructions (Cytofix/Cytoperm TM Plus Fixation/Permeabilization, BD Biosciences, California, USA). Briefly, the cell suspension was stained with cell surface marker antibodies (2 ml/tube), i.e. mouse anti CD73, mouse anti- CD8a-PE-cy5, mouse anti-CD3-APC, mouse anti- CD25-FITC, and mouse anti-CD4-PE-cy5 antibodies, for 20 min in the dark at 4 ºC. Cellular suspensions were then washed with PBS (containing FBS 2%) using centrifugation (250 g for 5 min). Then, they were fixed and permeabilized with Cytofix/Cytoperm buffer solution (BD Bioscience) for 20 min. Next, cells were stained with fluorescent-labeled specific antibodies against intracellular cytokine (2 ml/tube) in Perm/Wash buffer (BD Bioscience) for 30 min at 4 ⁰C. Antibodies included mouse anti-IFN-g-FITC, mouse anti-IL-4-PE, and mouse anti-Foxp3-PE. Cells were washed with Perm/Wash buffer and re-suspended in PBS (containing 2% FBS). Finally, the frequency of cells producing specific surface and intracellular markers were determined using BD FACS Caliber (BD Bioscience) flow cytometry.
2.13.6 CD73 Level in Tumor Tissue
CD73 levels in tumor cell suspensions was measured by staining with anti-mouse CD73 antibody. Considering that CD73 is a peripheral ectonucleotidase and is located on the surface of tumor cells, the process of staining was carried out the same as the previously described tumor-infiltrated lymphocytes staining approach.
2.14 Statistical Analysis
Statistical analysis was carried out using Graph Pad Prism version 6 (Graph Pad Software, USA). Independent samples t-test and post-hoc test for one-way ANOVA were used. Tukey's multiple comparisons were used to evaluate the differences among groups. A P value< 0.05 was considered statistically significant. Data are presented as Mean ± SD. Survival studies were analyzed by log-rank test in Graph Pad Prism software.