Animals
All in vivo experiments were approved by Institution Animal Care and Use Committee (IACUC) of Nanjing Medical University and the Approval No. IACUC-1706013 & 1912041. 10 to 12-week-old C57BL/6J male mice weighing 30 ± 2 g were purchased from the Animal Resource Center of the Faculty of Medicine of Nanjing Medical University for experimental use. All the animals were bred in a standardized barrier environment, maintained on a regular 12-h light/dark cycle and housed with access to food and water ad libitum (temperature 25 ± 2 ℃, humidity 55 ± 10%). All the experimental animals were allowed to adapt to the new environment for 2 weeks and fasted for 12 h before the experiments. All the animals were allocated to experimental groups and processed with randomization and the investigator was blinded to the group allocation. All the animals will be humanely euthanized.
Generation of PAFR knockout mice
The heterozygous recombinant PAFR knockout mice (C57BL/6J) were created by Crispr/Cas9-mediated genome engineering. Inter-cross heterozygous targeted mice to generate homozygous targeted mice. The PAFR gene (NCBI Reference Sequence: NM_001081211; Ensembl: ENSMUSG00000056529) is located on Mouse chromosome 4. 2 exons are identified, with the ATG start codon in exon 2 and the TAA stop codon in exon 2 (Transcript: ENSMUST00000070690) and to be selected as target site. Cas9 and gRNA were co-injected into fertilized eggs for KO Mouse production. gRNA target sequences include:
gRNA1 (matching forward strand of gene): GCCTTGGAATTGTTGATATAAGG
gRNA2 (matching reverse strand of gene): TTTATCGCATCCCCGGGTTAAGG
gRNA3 (matching reverse strand of gene): TGGATGTTGGCGTCCTCTCTAGG
gRNA4 (matching reverse strand of gene): TTCCTTGCCATGAGGGACCGAGG
Genotype identification
The pups will be genotyped by Polymerase Chain Reaction (PCR) and followed by agarose gel electrophoresis. Homozygotes: one band with 440 bp; Heterozygotes: two bands with 440 bp and 457 bp; Wildtype allele: one band with 457 bp. The wildtype mice generated by inter-cross heterozygous targeted mice were as control of homozygous PAFR knockout mice. 3 ~ 4 litters for each group were used for experiments.
PCR Primers1 (Annealing Temperature 60.0 ºC):
F1: 5’-CACTCAGGTCTCTCCTTCTACTAC-3’
R1: 5’-AAAGTAAAGGTAGAAGGACGACTGG-3’
Product size: 440 bp
PCR Primers2 (Annealing Temperature 60.0 ºC):
F1: 5’-CACTCAGGTCTCTCCTTCTACTAC-3’
R2: 5’-AAGTTAGCAAAGACCCATAGCACA-3’
Product size: 457 bp
Establishment of cerebral ischemia stroke model
The normal 10 to 12-week-old C57BL/6J male mice and homozygous PAFR knockout mice were used for focal cerebral ischemia/reperfusion experiments. A transient middle cerebral artery occlusion (tMCAO) model was established. Briefly, animals were anesthetized with isoflurane, and then the right external and internal carotid artery were exposed. Along the internal carotid artery into the middle cerebral artery, a nylon monofilament coated with silicon resin (Doccol) was introduced through a small incision and advanced to the carotid bifurcation. The monofilament was withdrawn to restore blood flow 1 h after the occlusion. Focal cerebral ischemia was assessed by Laser Doppler flowmetry. Neurological function was evaluated using a 4-point scale neurological score method (0, no observable deficit; 1, forelimb flexion; 2, decreased resistance to lateral push and immediate circling; 3, severe rotation progressing into loss of walking or righting reflex; 4, not walking spontaneously and some degree of consciousness). Animals dead in the model were excluded. The identification of ischemic core zones and penumbra field is performed as previously described.
Quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR)
Real-time qRT-PCR was carried out using the 2× SYBR Green qPCR Master Mix (bimake, B21203) in a QuantStudio 5 system (Thermo Fisher Scientific, USA). The Total RNA was extracted from tissues and cells by using a RNAiso Plus reagent (TaKaRa, 9109) and prepared for quantitative reverse transcriptase PCR by using MasterMix (abm, Cat. No. G592). A reverse transcription reaction was performed in a thermal cycler as follows: 37°C for 15 min, 65°C for 10 min, and held at 4°C forever. The relative expression of target genes was determined using the 2-ΔΔct method. The cycling conditions were as follows: denaturation at 95 ℃ for 15 s, followed by 40 cycles of DNA anneal and extension at 60 ℃ for 60 s and 72 ℃ for 30 s, and one cycle of 95 ℃ for 15 s, 60 ℃ for 60 s and 95 ℃ for 15 s. The primers are as follows.
Mouse-GAPDH-Forward: AGGTCGGTGTGAACGGATTTG
Mouse-GAPDH-Reverse: GGGGTCGTTGATGGCAACA
Mouse-PAFR-Forward: TCTGAGTTTCGATACACGCTCT
Mouse-PAFR-Reverse: CATAGCCGTTGGCAACCAC
Mouse-Mfge8-Forward: CGGGCCAAGACAATGACATC
Mouse-Mfge8-Reverse: TCTCTCAGTCTCATTGCACACAAG
Western blotting
Tissue and cell samples were dissociated in 100 µL of RIPA consisting of 1% phenylmethanesulfonyl fluoride (PMSF) (KeyGEN, KGP610). The protein concentrations were determined with a BCA Protein Assay kit (KeyGEN, KGP903), and the proteins were denaturalized with 6× loading buffer. Total proteins (20 µg) were separated by sodium dodecyl sulfate – polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to Immobilon-P PVDF Membrane (Millipore, Cat# IPVH00010). Then, 5% skim milk in Tris-buffered saline–Tween-20 was used to block the membranes for 2 h at room temperature. The membranes were then incubated with the following primary antibodies at 4°C overnight: PAFR (abcam, Cat# ab104162, 1:200), Sp1 (active motif, Cat# 2793151, 1:500), α-tubulin (Proteintech, Cat# 10094-1-AP, 1:2000).
Nissl Staining
The paraffinized mice brain sections were treated with Nissl Staining Solution (KeyGEN, KGMP0185). The basic nervous structure of the brain displayed a bluish-purple color. Nissl bodies represented that the nerve cells had a high ability to synthesize proteins. When the nerve cells were damaged, the Nissl corpuscles decreased significantly. The number of stained cells was counted randomly and analyzed with Image-Pro Plus 6.0.
Immunofluorescence and confocal image acquisition
Mice were anesthetized with isofluorane and perfused with 4% paraformaldehyde (PFA). The brains were dehydrated using a graded series of alcohol, cleared in xylene, and embedded in paraffin. Then, paraffin sections (5 µm) were cut by a rotary microtome (LEICA, RM2245, Heidelberg, Germany). After deparaffinization, sections were incubated with 5% goat serum for 1 h and then stained with primary antibodies (IBA1, goat, abcam, Cat# ab5076, 1:500; IBA1, rabbit, WAKO, 019-19741, 1:500; NeuN, Millipore, MAB377, 1:400; PAFR, abcam, Cat# ab104162, 1:200; MFG-E8, Santa Cruz Biotechnology, sc-8029, 1:500) overnight at 4 ℃. The slices were incubated with Alexa Fluor donkey anti-mouse, anti-goat, and (or) anti-rabbit secondary antibodies (1:1000 dilution, Invitrogen Life Technologies, NY, USA) after washing with PBS. Images were captured by a confocal microscopy or two-photon Microscope (Zeiss LSM880 with NLO & Airyscan). 3D reconstructions were generated using ZEN software (blue/black edition).
Primary neuron and microglia cultures
Primary neuron and microglia cultures were prepared from cerebral cortices of embryonic day (E) 16 ~ 18 mice embryos. Cerebral cortices were dissected and digested with 0.125% trypsin (Life Technologies, 27250-018) and 0.025% DNase I (Biofroxx, 1121MG010) at 37 ℃ for 15 min. Dissociated cells were filtered with 80-µm cell strainer, collected by brief centrifugation and plated on 24-well plates (Corning, 3524) coated with 0.01 mg/mL Poly-D-Lysine (Sigma, P6407) and cultured in DMEM (Life Technologies, 11965-084) containing 10% Fetal Bovine Serum (Life Technologies, Australia, 10099-141), 50 U/mL penicillin-streptomycin (Life Technologies, 15140122). At 6 h after seeding, the medium was changed to Neurobasal medium (Life Technologies, 21103-049) supplemented with 2% B27 (Life Technologies, 17504044) and 50 U/mL penicillin-streptomycin. Neurons were maintained at 37 ℃ in an incubator and grown for 10 ~ 12 days with half of the media replaced every 2 days. Microglia were separated from the mixed primary culture by shaking off for 5 h at 100 rpm and then planked in plates with DMEM medium containing 10% FBS and 50 U/mL penicillin-streptomycin. Primary microglia were transfected in a 6/24-well plate with SiRNA, purchased from GenePharma (Shanghai, China) using siRNA-Mate (GenePharma, G04002), according to the manufacturer’s instructions. The sequences are as follows.
Mouse-Ptafr siRNA:
Forward: 5’-CCAACUUCCAUCAGGCUAUTT-3’
Reverse: 5’-AUAGCCUGAUGGAAGUUGGTT-3’
Negative control:
Forward: 5’-UUCUCCGAACGUGUCACGUTT-3’
Reverse: 5’-ACGUGACACGUUCGGAGAATT-3’
Primary neuron-microglia physical coculture
Cortical neurons (1×10^6 cells/mL) were cultured in 24-well plates and grown for 8 ~ 9 days replaced with Neurobasal medium without B27 supplement, which inhibits the growth of glial cells. Primary microglia (1×10^5 cells/mL) were seeded and cultures 1:10 with neurons.
Oxygen and glucose deprivation and reoxygenation (OGD-R)
OGD experiments were performed using an incubator (Thermo Fisher Scientific, Waltham, USA) with premixed gas (95% N2 and 5% CO2) kept at 37 ℃. To initiate OGD, cells culture medium was replaced with deoxygenated, glucose-free DMEM (Life Technologies, 11966-025). After OGD, the cells were then transferred to a normoxic incubator (95% air and 5% CO2) replaced with normal medium. While, the time of OGD challenge and reoxygenation could be adapted according to different cells and culture system.
The detection of microglial phagocytosis
The experiment is followed according to the pHrodo™ Red zymosan bioparticles conjugate for phagocytosis (Life Technologies, P35364) procedure. Microglia were labeled with Cell Tracker™ Green. After twice washed with PBS, microglia were incubated with PBS containing 10 µL/ml of pHrodo Red zymosan bioparticles at 37°C for 15 min (if microglia were treated with OGD, incubated when reoxygenation). The treated microglia were examined every 30 min by a fluorescence microscope (Zeiss, Heidelberg, Germany).
Drug treatment
In vitro BV2 cells were treated with IL-4 (PeproTech, 20 ng/ml) to induced phagocytosis and Sp1 inhibitor Plicamycin (100 nM). Apafant (MCE, HY-108634) and Ginkgolide B (MCE, HY-N0784) applied in vitro experiments were 1 µM. Apafant (cayman, 14532) given in vivo was resolved in 10% DMSO and 90% saline with the concentration of 10 mg/ml. Ginkgolide B (MCE) administrated in vivo was resolved in 10% DMSO and 90% (20% SBE-β-CD (MCE, HY-17031) in saline) with the concentration of 10 mg/ml. The administration doses of mice with Apafant and Ginkgolide B after ischemic stroke were 14 mg/kg.
Coimmunoprecipitation (CO-IP) assay
For immunoprecipitation, BV2 cell lysates were incubated in RIPA lysis buffer for 30 min at 4°C, with agitation three times every 10 min, followed by centrifugation at 12,000 × g for 10 min at 4°C. Five hundred microliters of supernatant solution were incubated with specific antibodies overnight at 4°C with constant swirling; 40 µL of 50% protein A/G agarose beads (Santa Cruz, 15596026) were then added with incubation for 3 h. The beads were collected by centrifugation at 12,000 × g for 1 min at 4°C and washed three times using the lysis buffer. The precipitated proteins were eluted by suspending the beads in 6× loading buffer and then heated at 95°C for 5 min. The eluate was analyzed by immunoblotting.
Chromatin immunoprecipitation (ChIP)
ChIP assays were performed using a ChIP Assay Kit (Millipore, 17–295). 275 µL of 37% formaldehyde were added to each 10 mL of medium with swirling for 10 min. One milliliter of 10 × glycine buffer (1.25 M) was then added, and the mixture was swirled for 10 min to inactivate excess formaldehyde. The medium was then removed, and the cells were washed with ice-cold phosphate-buffered saline (PBS) twice and collected into a microfuge tube with 1 mL PBS and a mixture of proteinase inhibitors, followed by centrifugation at 1000 × g at 4°C for 5 min. Then 200 µL of lysis buffer plus proteinase inhibitors were added to suspend the cells, which were sonicated 20 times for 20 s each, with a 40 s rest each time at 40% setting, followed by centrifugation at 13,000 × g for 15 min. Supernatant solutions were diluted in dilution buffer, 60 µL of protein G agarose were added, and the mixture was rotated at 4°C for 1 h. The agarose was then removed by centrifuging at 2,000 × g for 1 min, and 4 µL of supernatant solution were saved at 4°C as “input.” Immunoprecipitation was performed overnight at 4°C with 1 µg normal rabbit IgG (CST, Cat# 2729) or anti-PAFR. Protein G agarose was then added, and the mixture was rotated for another hour. The complex was washed in sequence with low-salt, high-salt, LiCl, and Tris EDTA (TE) buffers (twice). Protein–DNA complexes were then eluted with TE elution buffer at 65°C for 5 h to reverse the cross-links. The samples were then treated with RNase A and proteinase K and then DNA was extracted and purified. The PCR primer of MFG-E8 promoter are as follows.
A: 5’-AGCCCAGACTAGTCTGGAACTC-3’
B: 5’-ACTCCTGGATTATTTTATTTTATTT-3’
C: 5’-AGCCCTCCCTCTTCCCAC-3’
D: 5’-GGCCAGTGGGCGGAGCT-3’
E: 5’-GGAGCGGACGCAGGAACT-3’
Z: 5’-GAGGCGCAGAGTAGCATG-3’
Statistical analysis
Data was analyzed in a blinded way. Statistical analyses were performed using Graphpad Prism7. Multiple comparisons were conducted using one/two-way ANOVA and Tukey’s multiple comparisons test or Kruskal-Wallis nonparametric test followed by Dunn multiple comparisons test. The means of the two treatment groups were analyzed using unpaired or paired Student’s t-tests. Data are expressed as means ± standard error of measurements (SEMs). A value of p < 0.05 indicates that the difference was statistically significant.