Cell culture and animals
Human adult RPE cells (APRE-19; American Type Culture Collection, Manassas, VA, USA) were cultured in Dulbecco`s modified Eagle’s/Ham’s F12 (Invitrogen, Grand Island, NY, USA) with 10% fetal bovine serum (Invitrogen), 100 μg/mL streptomycin, and 100 U/mL penicillin at 37°C under 5% CO2 and 95% humidified air.
Adult C57BL/6 mice (aged between 6-8 weeks old, weighed 20 ± 1 g) were used in this study. All animals were treated according to the guidelines of the ARVO statement for the Use of Animals in Ophthalmic and Vision Research. The experimental procedures were approved by the Institutional Animal Care and Use Committee of Shanghai Jiao Tong University (Shanghai, China). The mice were housed and maintained in the animal care services facility and subjected to a 12-hour light/dark cycle with constant access to nourishments. Chrysin (Sigma-Aldrich, C801052) was dissolved in dimethyl sulfoxide (DMSO); a final use concentration of DMSO was <0.5%.
A2E formation and treatment
A2E was synthesized as described previously.[27] RPE cells were incubated with A2E in culture medium for 24h and washed three times to remove extracellular A2E. After A2E loading, RPE cells were exposed to 460 ± 20 nm wavelength light (4000lx; Osram, Augsburg, Germany) for 20 min, as described previously [27] .
Laser-induced Mouse CNV model
C57BL/6J male mice aged between 6 and 8 weeks and approximately 20 g were included. After application of tropicamide (Santen, Osaka, Japan) for pupil dilatation, animals were anesthetized with intraperitoneal injection of 1% pentobarbital sodium (0.1 mL/10 g body weight) (Guge Biotech, Wuhan, China). Covered with loxacin eye ointment (Xing Qi Pharmaceutical Companies, Shenyang, China), and four laser spots were distributed around the optic nerve head with an argon laser (110 mW, 100ms, 50μm, OcuLight Infrared Laser System 810 nm, Iridex Corp., Mountain View, CA, USA). Appearance of a gray bubble indicative of the rupture of Bruch`s membrane were included. If retinal bleeding occurred, the animal was eliminated. Eyes were enucleated at different time points.
Perfusion fixation
Mice were perfused transcardially with cold 4% paraformaldehyde. In brief, mice were administered with an over dose (0.2mL) of 1% sodium pentobarbital and monitored until the point when the animal fails to respond to pinching of the foot. Incisions in the abdomen and diaphragm were made to expose the heart and perfusion needle was placed into ascending aorta. Cold 4% paraformaldehyde was poured into left ventricle of mouse through a peristaltic perfusion pump (Cole-Parmer Masterflex, NewYork, USA). Twitching of muscles suggests that the perfusion is proceeding properly. After the effluent runs clear, pump was stopped, eyes were harvested, post-fixed for two hours and then placed in PBS to make choroidal flatmounts or put into 30% sucrose solutions to make frozen sections.
Choroidal flatmount and immunofluorescence staining
After perfusion fixation and post-fixation, choroidal flatmounts were made under an operating microscope (Olympus, Tokyo, Japan). The cornea, lens and vitreous of a mouse eye were removed and the retina was separated from the choroid. Then the remaining RPE-choroid cup was cut four to six radial incisions to be flattened. Then the RPE-choroid complexes were blocked in 5% goat serum albumin with 0.3% Triton X-100 for one hour at room temperature, and were incubated with FITC-labeled isolectin-B4 (IB4) (FL-1201, Vector Laboratories, Burlingame, CA) and primary Abs FITC-labeled isolectin-B4 (IB4) (FL-1201, Vector Laboratories), γ-H2AX(1:100 dilution, #2577, CST),anti-RPE65 (78036, Abcam), ) at 4℃ overnight. The next day, RPE-choroid complexes were washed and incubated in appropriate secondary antibodies at room temperature for one hour. Secondary antibodies used were Alexa Fluor 488 and Alexa Fluor 594 (SA00003-11 and SA00006-4, Proteintech, Chicago, USA). At the end of the process, 4,6-diamidino-2-phenylindole (DAPI) (Vector Laboratories, Bu rlingame, CA) was used to counterstain the nucleus. Images were taken with a fluorescence microscope (Olympus, Tokyo, Japan) or a Leica TCS SP8 confocal laser scanning microscope (Leica TCS NT, Wetzlar, Germany).
Fluorescence angiography
FA was performed at day 7, after laser to observe the severity of CNV leakage. Firstly, mice were anesthetized with 1% sodium pentobarbital (Guge Biotech, Wuhan, China) i.p. at a volume of 5 μL·g-1 body weight. Secondly, each mouse was injected intraperitoneally with 0.05mL of 10% fluorescein sodium (Fluorescite; Alcon, Tokyo, Japan), and fundus angiogram photos were captured at the middle stage (2-3 minutes after dye injection) using a digital fundus camera (Heidelberg Retina Angiograph, Vista, CA).
SD-OCT
The preparation of mice was described in the section of laser-induced Mouse CNV model. The Bioptigen SDOIS (Bioptigen, Inc., Durham, NC) was used in this study, which is a noninvasive imaging Class Ⅰ, Type B, IPXO, continuous operation medical device. The SDOIS apparatus is comprised of a base system as well as an animal imaging mount and rodent alignment stage (AIM-RAS), which contains a SD-OCT hand held probe (HHP). After the HHP lens was situated close to the right eye of the animal, the InVivoVue Clinic application was activated and the scanning began- following setup of subject profile for image acquisition, we selected the rectangular scanning protocol consisting of a 3 mm by 3 mm perimeter with 1000 A-scans per B-scan with a total B-scan amount of 100. This a modification of the recommended parameters of 1.4 mm by 1.4 mm set by the company for performing rectangular scans.
Western blot
To obtain protein in choroids, mice were killed promptly by cervical vertebra dislocation, eyeballs were harvested instantly and put in cold PBS. Corneas, lenses, vitreouse and retina of mouse eyes were removed and the RPE-choroid tissues were put and chopped into homogenate using a tissue chopper (SONICS &MATERIALS INC.; NEWTOWN, USA) in radio-immunoprecipitation assay (RIPA) lysis buffer with Phenylmethanesulfonyl fluoride (Beyotime biotechnology, China).
Proteins were separated by SDS-polyacrylamide gel electrophoresis, transferred to polyvinylidene difluoride membrane, and probed with antibodies specific for γ-H2AX (1:1000 dilution, #2577, CST), for Phospho-NF-κB p65 (Ser536) (1:1000 dilution, #3033), for p65 (1:1000 dilution, #8242, CST), for VEGFA (46154,Abcam), for p-STAT3 (9145S, CST), for GAPDH (1:5000, dilution, 60004-1-Ig, Proteintech) antibodies were used to determine protein amounts as a loading control.
Cell viability assay
The Cell Titer 96 Aqueous One Solution cell proliferation assay (Promega, Madison, WI, USA) was performed. Briefly, RPE cells were seeded in 96-well flat-bottomed microliter plates in eight repeat cultures at a concentration of 1 × 104 cells/well. After treatment, each well was incubated with 20 μM MTS assay solution for 2 h at 37°C and the absorbance was measured using an enzyme-linked immunosorbent assay plate reader at 490 nm emission wavelength. Cell viability was expressed as the percentage of absorbance in cells with indicated treatments to that in cells with solvent control treatment.
Immunofluorescence
Slides were either fixed with MeOH at –20°C or with 4% formaldehyde at room temperature for 10 to 15 min, and were then incubated with blocking buffer (0.8× PBS, 50 mM NaCl, 0.5% Triton X100, 3% milk) for 1 h, followed overnight by incubation at 4°C with primary antibody to γ-H2AX (ab2893, 1/100, abcam) and mouse polyclonal antibody to TRF1 (ab10579, 1/100, abcam) in 0.8× PBS, 50 mM NaCl, 0.5% Triton X 100, and 3% milk. Cells were then washed three times for 10 min in 0.8× PBS, 50 mM NaCl, and 1.5% skimmed milk at RT. Incubation with donkey polyclonal anti-mouse ALEXA488 (A21202; Molecular Probes) and donkey polyclonal anti-rabbit ALEXA555 (A31752; Molecular Probes) antibodies was performed for 1 h at 37°C in the dark in 0.8× PBS, 50 mM NaCl, 0.5% Triton X 100, and 3% skimmed milk. All antibody incubations were performed in a moist chamber. Cells were then washed three times for 10 min in 0.8× PBS, 50 mM NaCl, and 0.5% Triton X 100. Slides were then rinsed in PBS, counterstained with DAPI, mounted in VECTASHIELD, and stored at 4°C in the dark.
Chromosome PNA-FISH
Briefly, cells were washed with PBS and 10 mL of fresh culture medium with 60 μL of colcemid (10 ng/mL) added and incubated at 37°C, after which the cells were collected. Cells were then centrifuged at 300 × g. The supernatant was then aspirated. Next, 25 mL of KCl were added and mixed by inverting. A total of 100 μL of fresh fixative (methanol/acetic acid = 3/1) was added and mixed. Incubated the tubes in a 37°C for 15 min and centrifuged at 300 × g at 4°C. Then, added 30 mL of fresh fixative and incubated overnight. Centrifuged the fixed cells and aspirated the fixative, leaving 2 mL in the tube. Precooled slides were placed in the humidity chamber and the resuspended cells were added to a slide. We then allowed the slides to dry overnight.
Next, slides were fixed in 4% formaldehyde for 2 min, followed by washing three times. Prewarmed 50 mL of 0.01 M HCl to 37°C and added 50 μL/10 mL of pepsin stock (100 μg/μL, Sigma) to it. Slides were then put in the solution and incubated at 37°C, after which the slides were fixed in 4% formaldehyde. Next, slides were dehydrated by 50, 75, and 100% ethanol. Once dry, applied 120 μL of PNA probe in blocking buffer (70% deionized formamide, 100 mM Tris, pH 7.2, 1% blocking reagent). The slide was denatured at 80°C for 3 min and incubated for 2 h at 37°C. Then, the slide washed twice in washing buffer I (70% deionized formamide, 10 mM Tris, pH 7.2) and three times in washing buffer II (0.05% Tween-20, 50 mM Tris, pH 7.4, 150 mM NaCl). Stained the slides in 4',6-diamidino-2-phenylindole (DAPI) and washed the slides in PBS. The slides were stored at 4°C.
Microscopy
PNA-FISH assays were recorded on an AxioPlan microscope from ZEISS, equipped with a Plan-Apochrom at 63×, NA 1.4, oil immersion lens, and a cooled CCD camera (CoolSNAP HQ, Photometrics). Image acquisition, processing, and analysis software were from MetaMorph (Molecular Devices). Images of immunofluorescence were recorded using a confocal microscope from Leica.
SA-β-gal staining
The senescence-associated beta-galactosidase (SA-β-gal) staining assay was performed using an SA-β-gal staining kit (Beyotime, China) and performed as the manufacturer`s instructions.
RNA analyses
Total RNA samples were isolated using TRlzol (#15596-018, Invitrogen) and then reverse transcribed into cDNAs using a kit from Takara (#RR047A).
RNA-seq and bioinformatics analyses
RNA-seq was performed according to the manufacturer’s guidelines and previous protocols (C-10365, Life Technologies) [28]. RNA deep-sequencing analyses were performed at BGI-Tech (Shanghai, China). For bioinformatics analyses, transcript structure and abundance were estimated using Cufflinks software and differential expression analysis was performed using Cuffdiff software. [29] The cutoff value of differential expression gene was: | log2 (fold change) | > 1, p-value < 0.05. Gene ontology (GO) enrichment analysis was performed using DAVID ver. 6.7 (Database for Annotation, Visualization and Integrated Discovery), which is a web-based application (https://david.ncifcrf.gov/)
Real-time PCR (RT PCR) validation
RT-PCR primer sequences were designed using Primer3 web software (version 4.0.0). The primer sequences used are provided in Additional file 2. The GAPDH gene was used to calculate the relative fold-differences based on comparative cycle threshold (2–ΔΔCt) values. The RT-PCR procedure was as follows: 1 μL of cDNA in H2O was added to 5 μL of 2× SYBR Green buffer, 0.1 μM each primer, and H2O to a final volume of 10 μL. Differences between the two samples were calculated using Student’s t-test at a significance level of 0.05 in Graphpad Prism 6.0 software. All expression analysis was performed for three biological repeats and the average values of three repeats values were shown in the figures.
Statistical analysis
Based on the univariate test, continuous normal variables were expressed as the mean value ± SD. Parametric variables of normal distribution were analyzed either by the two-tailed t-test or the F test of ANVOA, followed by the Duncan test for each two group comparison. Results were considered significant at p < 0.05. Statistical analysis was performed with Graphpad Prism 6.0 software.