2.1 Ethics Statement
All animal experiments were approved by the Animal Ethics Committee of Nanjing First Hospital (protocol number: DWSY-2104386) and were carried out according to the National Institutes of Health “Guidelines for Care and Use of the Laboratory Animals”. Do everything possible to minimize animal suffering.
2.2 VaD animal model and corresponding treatment
Healthy adult male SD rats (8 weeks old; weight 280–300 g) were provided by the Model Animal Research Center of Nanjing University (Nanjing, China) and raised under the a 12-h dark/light cycle, appropriate temperature, suitable humidity and ad libitum feed. 4% isoflurane anesthetized the rats at 48 h before surgery. TMAO was administered and 2VO model was established following our previous research protocol [11]. In brief, The rats were anesthetized and bilateral common carotid arteries were isolated and ligated gently. The sham operation group performed the same procedure, but did not include the ligating step. The 2VO rats were continuously administered TMAO before and after surgery, while the rats were instilled with sterile water in the sham group.
TMAO (catalog number: 317594, purity: 95%, CAS: 1184-78-7) was purchased from Sigma-Aldrich. The lentivirus vectors (LV-sh-Fendrr, agomir-145-5p, antagomir-145-5p, and LV-sh-PXN ) and lentiviral vector negative control were supplied by GenePharma (Shanghai, China). As previously reported [16], lentivirus vectors were injected into the CA1 area of hippocampus 7 days before 2VO surgery. First, the stereotaxic devicefixed the anesthetized rats (RWD LifeScience, CA, USA ). Injection axes was as flows with reference to bregma: mediolateral, ± 3.2 mm; anteroposterior, − 4.52 mm; dorsoventral − 3.16 mm using coordinates under the surface of skull. Two microliters of lentiviral vector were injected into the hippocampal CA1 region using a 10 µL syringe (Hamilton). After the injection is over, the needle was held in place for a moment and then removed extremely slowly to prevent he solution from flowing back. After removal of the needle, the drill holes were closed with bone wax and the incisions were sutured to rehabilitate the rats.
2.3 LncRNA Sequencing
The Gene Denovo Biotechnology Co., Ltd (Guangzhou, China) provided the RNA-sequencing analysis. Total RNA was extracted from rat hippocampal tissue using the Trizol kit (Life Technologies, CA, USA) and the sample RNA quality was evaluated by a 2100 Bioanalyzer (Agilent Technologies, CA, USA). After removing the ribosomal RNA, the total RNA obtained was reverse-transcribed to cDNA and then quantified as well as pooled using the ABI StepOnePlus Real-Time PCR System (Life Technologies). Finally, we performed up-sequencing according to the PE150 mode of Illumina novaseq 6000. Raw reads containing splice or low-quality bases were filtered by fastp (version 0.18.0). Ribosomal RNA (rRNA) was removed using the comparison tool bowtie2, and clean reads of paired ends were compared to a reference genome (Rattus norvegicus Ensembl_release106) using HISAT2 (version 2.1.0). StringTie software was used to perform quantitative analysis of lncRNA. Genes differential expression analysis was performed by DESeq2 software. Parameter |log2(Foldchange)| ≥ 1 and P-value < 0.05 were defined as significantly differentially expressed lncRNAs. The sequencing database is archived in GenBank (GSE249873).
2.4 Functional enrichment analysis
The predicted differentially expressed mRNAs were analyzed by Gene Ontology (GO) analyses and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis using the R package clusterProfiler. The p-value of < 0.05 was deemed significant for statistical analysis.
2.5 Open Field Test (OFT)
The rats were placed in the center of a square black box and were allowed to move freely. The camera connected to an Any-maze® tracker recorded and calculated (New Soft Information Technology Co., Ltd.™., Shanghai, China) the time spent by the rats and the total travel distance into the center. After each trial, the chamber was washed with 75% ethanol and left to dry to avoid olfactory cues.
2.6 Morris Water Maze Test (MWM)
The water maze device, which is equally divided into four quadrants was employed and a transparent circular stage was under the water surface. Every rat was exposed to four training trials on 5 successive days. The rats were randomly put in the water from four quadrants each day until they found the stage and stayed for 15 s out of 60 s. When the stage was not found less than 60 s, the rats were brought into the stage. On the second day of the last trial, the path length of the rats to reach the stage was recorded by the video tracker (Noldus Information Technology B.V.™, Wageningen, Netherlands) after moving out of the stage, and the means of the four trials were determined.
2.7 Nissl Staining
Nissl staining was used to detect Nissl bodies in neurons. The paraffin-embedded brain tissues of rats were cut into 5 µm-thick sections, which were stained with Nissl staining solution for 1 h at 56 ℃ (Solarbio, Beijing, China) after dewaxing and rehydration. Next, the sections were dried with gradient concentrations of ethanol, rinsed with xylene, and sealed with neutral gum. The sections were carefully observed and photographed with an Olympus microscope (Olympus™, Tokyo, Japan).
2.8 Luciferase report assay
The wild-type (wt) or mutant-type (mut) 3′-UTRs of Fendrr or PXN were cloned into the pmirGLO vector (Promega, USA). HEK-293 T cells were seeded in 24-well plates. When the fusion reached 70% − 80%, cells were co-transfected with wt or mut 3′-UTRs of Fendrr or PXN luciferase reporter plasmids, together with agomir-NC or agomir-145-5p by Lipofectamine 2000. The cells were harvested 24 h after transfection, and assayed for luciferase activity.
2.9 Fluorescence in Situ Hybridization (FISH)
FISH was applied to assay the localization of Fendrr, miR-145-5p and PXN expression in the sections of hippocampal tissue of 2VO rats with the FISH kit in accordance with the instructions of the manufacturer. In brief, the sections of paraffin-embedded hippocampus were soaked in xylene I (Guoyao, Shanghai, China) for 15 min, in xylene II for 15 min, and subsequently in pure ethanol (Guoyao, Shanghai, China) for 5 min. Then, the sections were digested with proteinase K (20 µg/mL, Servicebio, Wuhan, China) solution at 37°C for 25 min. For each section was added with the pre-hybridization solution (Riobo biotech, Guangzhou, China) for 1 h at 37°C. Hybridization buffer (Riobo biotech, Guangzhou, China) with 50 nM biotin-labeled lncFendrr (Gene Pharma, Shanghai, China) or miR-145-5p (Gene Pharma, Shanghai, China) was heated to 65 ℃ for 5 min and added dropwise to the sections, which were then allowed to hybridize at 37 ℃ overnight with or without anti-PXN (1:1000; #50195; CST; Boston, MA, USA). After washes and blocking, sections were incubated with DAPI (Servicebio, Wuhan, China) to stain the cell nuclei. The sections were observed with a Nikon upright fluorescence microscope (Nikon, Tokyo, Japan) and photographed. The sequence of the Fendrr probe was as follows: ATGTTCTAAATGTTTCTTGATTCTG; The sequence of the mir-145-5p probe was as follows: AGGGATTCCTGGGAAAACTGGAC.
2.10 RNA immunoprecipitation (RIP) assay
Ago2-RIP assays were carried out using an EZ-Magna RIP RNA kit (#17–704, Millipore, MA, USA). Hippocampal tissue was lysed in RIP lysis buffer and incubated with negative control IgG (Millipore, MA) or anti-Ago2 (#ab32381, Abcam) conjugated magnetic beads. Immunoprecipitated RNA was isolated by Proteinase K buffer and analyzed by RT-qPCR.
2.11 Reverse transcription-quantitative polymerase chain reaction (RT-qPCR)
Total RNA of rat hippocampal tissues was isolated using Trizol reagent (Invitrogen, CA, USA). The obtained total RNA was reverse-transcribed to cDNA using the cDNA Synthesis Supermix kit (Takara, Japan). Then, the target genes were quantified with SYBR® Premix Ex TaqTM II (Takara, Japan) on the ABI 7500 fast real-time PCR system (Applied Biosystems, USA). The expression of target genes was analyzed by the 2−ΔΔCT method using U6 and β-actin as internal references for miRNA and mRNA, respectively. Primer sequences are listed in Supplemental Table S1.
2.12 Western Blot Analysis
Rat hippocampal tissues were homogenized with RIPA lysate buffer and the protein concentration was quantified with a BCA Protein Assay Kit (Thermo Fisher Scientific, Inc.™, Carlsbad, CA, USA). Equal amounts of samples were used to perform sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The total protein was transferred to a polyvinylidene fluoride (PVDF) membrane (Millipore), which is blocked with 5% skimmed milk for 2 hours. PVDF membrane was incubated with anti-PXN (1:1000; #50195; CST; Boston, MA, USA) or β-actin (1:1000, #4970; CST, Boston, MA, USA), overnight at 4 ◦C, and anti-rabbit IgG HRP (1:4000; CST, Boston, MA, USA) for 2h at room temperature. The bands were finally visualized with the ECL kit (Millipore™, Merck, Darmstadt, Germany) and using the Image J to quantify the protein band density. All data were standardized to β-actin.
2.13 Enzyme-linked immunosorbent assay (ELISA)
TNF-α, IL-1β and IL-6 ELISA kits (Abcam, MA, USA) were used in accordance with the manufacturer’s instructions aimed to evaluate the inflammatory cytokine levels in the hippocampus. The levels of these cytokines were measured by absorbance using a micro enzyme-linked immunosorbent assay reader (Tecan, USA).
2.14 Statistical analysis
The experiments data were represented as the mean ± SD and analyzed by Prism 8 software (GraphPad™, San Diego, CA, USA). Comparison between the two groups weas made using the t-test, and comparison among multiple groups was adopted using one-way or two-way analysis of variance (ANOVA) followed by Tukey’s post-test. Each experiment was repeated at least 3 times. Data were deemed to be statistically significant when P < 0.05.