Introduction
Deep vein thrombosis (DVT), attributed to changes in venous homeostasis, presents a common reason of cardiovascular mortality [
1]. DVT usually occurs in the lower extremities but can also occur in other sites [
2]. In spite of anticoagulant therapy, many DVT patients may suffer from post-thrombotic syndrome [
3]. Interaction of platelets with monocytes and neutrophils can induce DVT [
4]. Moreover, DVT is related to the predominance of inflammatory cells [
5]. It is clear that inflammation has a key role in the pathophysiology of DVT [
6,
7]. Therefore, seeking novel targets for managing inflammation in DVT is required.
It is noteworthy that the transcriptome high-throughput sequencing performed in the current study predicted the long non-coding RNA (lncRNA) colorectal neoplasia differentially expressed (Crnde) as a pivotal gene in DVT. Crnde, a type of 1910-nt lncRNA encoded on human chromosome 16, is implicated in multiple cancers [
8]. Upregulation of Crnde was found in injured rat carotid artery as well as vascular smooth muscle cells induced by platelet-derived growth factor-BB [
9]. Crnde as a potential biomarker induced inflammation in alcoholic liver disease [
10].
Prenylcysteine oxidase 1 (Pcyox1) is a type of enzyme responsible for prenylated protein degradation and release of hydrogen peroxide, cysteine and isoprenoid aldehyde [
11]. Pcyox1 can be expressed in vascular and blood cells, and the lack of Pcyox1 brought about platelet hypo-reactivity as well as impaired arterial thrombosis [
12].
Of note, our bioinformatics analysis screened microRNA (miR)-181a-5p as the differentially expressed one in DVT which could bind to both Crnde and Pcyox1l (the paralogous gene of Pcyox1. Strikingly, a previous study demonstrated that Crnde sponged miR-181a-5p, thereby leading to aggravation of inflammation underlying sepsis [
13]. Moreover, upregulation of miR-181 could diminish the luciferase activity in cells with FXI-3’UTR and might serve as a novel therapeutic target for prevention of thrombosis [
14]. Interestingly, it was previously unfolded that miR-181a-5p in cooperation with miR-181a-3p could repress vascular inflammation as well as atherosclerosis [
15]. Moreover, miR-181a-5p alleviated inflammatory response in pulmonary arterial hypertension induced by monocrotaline, which was achieved by targeting endocan [
16]. In view of the aforementioned reports, we thus proposed a hypothesis in the current study that lncRNA Crnde might affect vascular inflammation injury in DVT by regulating the miR-181a-5p/Pcyox1l axis.
Materials and methods
Ethical approval
This study was performed under the approval of the Ethics Committee of Xiangya Hospital, Central South University. All animal experiments were conducted strictly following the Guide for the Care and Use of Laboratory Animals.
Establishment of mouse DVT model
Fifty-four BALB/C mice aged 4–6 weeks old (18–22 g) (Hunan SJA Laboratory Animal Co., Ltd., Changsha, China) were housed for 2 weeks in a specific-pathogen-free environment at a constant room temperature of 20–25℃ with constant 60–65% humidity. Mice were acclimatized to the pre-experimental environment with free access to food and water under 12-h dark/light cycles.
The mouse DVT model was constructed by inferior vena cava stenosis under sevoflurane inhalation anesthesia. Mice were fixed in a supine position on the operating table and their abdomen was shaved and sterilized with a 0.5% povidone-iodine solution. The medial skin of the thigh was cut longitudinally, and the femoral veins were exposed at 2 cm depth, with a mosquito clamp holding three different veins. The mouse model was established after the suture incision. Sham-operated mice underwent a longitudinal suture incision of the medial skin of the thigh [
17,
18]. Mice were given normal feeding after they regained consciousness.
Transcriptome high-throughput sequencing and data processing
Inferior vena cava tissue samples from DVT mice (lesion area of the thrombus) and control mice (n = 3) were collected to a vacuuming tube containing 3.8% sodium citrate, and after blood sampling, full transcriptome sequencing of six samples was completed on the high-throughput sequencing platform Illumina. Trimmomatic tool was used for quality pretreatment of raw data: (1) removal of the adaptor; (2) removal of low-quality reads; (3) removal of low-quality bases from the 3′ and 5′ ends; (4) counting original sequencing amount, effective sequencing amount, Q30 and GC content, and summarizing the number of reads in the whole quality control process. Sequence alignment was performed between the filtered high-quality reads and the mouse genome using hisat2 software.
Differential gene expression analysis and enrichment analysis
Differential expression analysis of lncRNAs and mRNAs was performed using the R language “edgeR” package based on the read counts of the lncRNAs and mRNAs, with |log2FC| > 1 and p < 0.05 set as the criteria. Subsequently, six differentially expressed lncRNAs and six differentially expressed mRNAs were selected for RT-qPCR to verify whether the transcriptome data were reliable.
The volcano plots were then drawn using the “ggplot2” package in R language and the differential gene expression heatmaps using the R software “heatmap” package. GO and KEGG enrichment analyses of mRNAs were performed by the R language “clusterProfiler” package.
Lentiviral vectors
Lentiviral vectors expressing short hairpin RNA (sh)-negative control (NC), sh-Crnde, agomir NC, miR-181a-5p agomir, sh-NC + overexpression (oe)-NC, sh-Crnde + oe-NC and sh-Crnde + oe-Pcyox1l were injected into the mice via the tail vein 1 day before model construction [
19]. These lentiviruses (150 µL for each group) were all purchased from GenePharma (Shanghai, China). The nucleotide sequence of Crnde was obtained by NCBI, and the Crnde interference sequences were designed by the ThermoFisher database (Table
S1).
Mouse DVT model was constructed five days after lentivirus injection. Mice were sham-operated (n = 6), or modeled as DVT mice without treatment (n = 6), or treated with sh-NC (n = 6), sh-Crnde (n = 6), agomir NC (n = 6), miR-181a-5p agomir (n = 6), sh-NC + oe-NC (n = 6), sh-Crnde + oe-NC (n = 6) or sh-Crnde + oe-Pcyox1l (n = 6).
Measurement of weight and length of thrombus
Seven days after molding, mice were anesthetized with intraperitoneal injection of 3% pentobarbital sodium and were euthanized by cervical dislocation. Afterwards, the mice were fixed to the operating table in a supine position. The skin of the medial thigh was cut vertically, the femoral vein was exposed to a 2 cm incision, and the femoral vein was cut. The thrombus was removed from the inferior vena cava to observe the thrombus characteristics and ablation. The weight (mg) and the length of the thrombus (mm) were measured.
ELISA for serum levels of inflammatory factors
Mouse serum levels of IL-1β, IL-6, and IL-8 were determined using the ELISA kit for IL-1β (ab100704, Abcam, Cambridge, UK), IL-6 (ab100712, Abcam), and IL-8 (SEKM-0046, Solarbio, Beijing, China), referring to the kit instructions [
20]. Absorbance was obtained at 450 nm using a microplate reader (800TS, BioTek, Winooski, VT) and analyzed using the Origin 9.5 software.
HE staining
Inferior vena cava tissues from mice were fixed with 10% neutral formaldehyde for more than 24 h, embedded in paraffin, and sliced into serial Sect. (5 μm). Hematoxylin (H8070-5 g, Solarbio) was used to stain the sections for 4 min, followed by eosin solution (PT001, Shanghai Bogoo Biological Technology Co., Ltd., Shanghai, China) staining for 2 min [
21]. The morphology was observed under an optical microscope (Olympus BX51, Olympus, Tokyo, Japan).
Western blot and immunohistochemistry
Protein in the inferior vena cava tissue was extracted with an extraction kit (EX2410, Solarbio) and determined using the BCA Protein Assay kit (Pierce; Thermo Fisher Scientific, Rockford, IL). Proteins (20 µg per lane) were subjected to 10–12% SDS-PAGE and transferred to a polyvinylidene difluoride membrane. The membrane was then blocked with 5% BSA for 2 h, and incubated overnight at 4℃ with the primary anti-Pcyox1l antibody (0.5 mg/mL, PA5-57955, 0.4 µg/mL, Thermo Fisher Scientific). After washing, the membrane was incubated with a goat anti-rabbit horseradish peroxidase-conjugated secondary antibody (2 mg/mL, ab6721, 1 : 2000, Abcam) for 2 h at room temperature and developed using an enhanced chemiluminescence system (Pierce; Thermo Fisher Scientific). Anti-GAPDH antibody (2 mg/mL, ab8245, 1 : 500-1 : 10,000, Abcam) was used as an internal reference.
For antigen retrieval, the sections of mouse thrombus and inferior vena cava tissues were treated with 0.3% H2O2 methanol treatment for 10 min, washed with distilled water, immersed into 0.01 M citrate buffer solution (PH6.0), and radiated with microwave in a microwave oven for 10 min. After the retrieval solution was cooled down to room temperature, the sections were dripped with normal goat serum and incubated at 4℃ overnight with the following antibodies: anti-Pcyox1l antibody (0.5 mg/mL, PA5-57955, 1 : 500-1 : 1000, Thermo Fisher Scientific), F4/80 monoclonal antibody (0.5 mg/mL, ab300421, 1 : 5000, Abcam), myeloperoxidase polyclonal antibody (0.5 mg/mL, ab208670, 1 : 1000, Abcam). Next, the sections were further incubated with secondary antibody goat anti-rabbit IgG (2 mg/mL, ab6721, 1 : 2000, Abcam) at 37℃ for 20 min. Horseradish peroxidase-labeled streptavidin was used to incubate the sections at 37℃ for 20 min, followed by DAB (ST033, Whiga, Guangzhou, China) color development. Hematoxylin (PT001, Shanghai Bogoo Biological Technology Co., Ltd.) was used for counterstaining the sections, and Images were observed and photographed under a microscope.
RT-qPCR
Total RNA was extracted from the inferior vena cava tissue [
22]. For RNA, First Strand cDNA Synthesis Kit (K1622, Fermentas, Hanover, MD) was used for reverse transcription of 1 µg of total RNA into cDNA. For miRNA, PolyA Tailing Kit (B532451, Sangon, Shanghai, China) was used for reverse transcription into cDNA. The synthesized cDNA was detected by RT-qPCR with the Fast SYBR Green PCR kit (Applied Biosystems) and the ABI PRISM 7500 RT-PCR system (Applied Biosystems), with three replicates set for each well. The 2
−ΔΔCt method was utilized to analyze the relative gene expression as normalized to GAPDH and U6. The sequences of the primers used for the experiments are shown in Table
S2. The materials used in the above test steps were purchased from Servicebio, Wuhan, China.
Isolation, culture and identification of mouse primary vascular endothelial cells
We isolated and purified mouse primary vascular endothelial cells as previously described [
23]. In brief, a 6-well plate was put on ice, and 1 mL of matrix was applied on one well of the plate without introducing any bubbles. The plate was incubated in an incubator at 37℃ for 20 min to solidify the substrate. The tissue was implanted into the coagulation matrix using sterile microanatomy forceps. The lumen was placed on the matrix downward without touching the endothelium, and 3–4 tissue blocks were placed on the matrix close to each other. Next, cells were cultured with 200 µL of endothelial cell growth medium (C0065C, Gibco, Carlsbad, CA) at 37℃ with 5% CO
2 for 4–6 h, followed by addition of medium to reach 1 mL. On the 4th day, the medium and tissue blocks were removed, and 2 mL of new endothelial cell growth medium was added for allowing the endothelial cells to further proliferate on the matrix for 2–3 days. Subsequently, the primary endothelial cells were transferred to a T12.5 flask covered with 0.1% gelatin (#07903, STEMCELL Technologies, Shanghai, China), further cultured with 4 mL of endothelial cell growth medium and stably passaged 3 times.
Identification of primary endothelial cells: a 6-well plate was paved with 0.1% gelatin, and then 3 × 10
5 cells were seeded in each well. After 24 h of culture at 37℃ with 5% CO
2, the cell morphology and adherence were observed under a light microscope. Cells were taken out from the culture plate and fixed with 1 mL of 10% formaldehyde at room temperature for 30 min. Next, 1 mL of PBS was used to suspend the cells, followed by incubation with anti-CD31 (0.5 mg/mL, ab222783, 1:100, Abcam) and anti-VE-Cadherin (0.2 mg/mL, ab205336, 1:1000, Abcam) on ice in darkness for 1 h. The cells were incubated with the secondary antibody against IgG (1.7 mg/mL, ab172730, 1:100, Abcam) on ice in darkness for 1 h and then with 1 ug/mL DAPI in dark for 10 min. Finally, the fluorescence intensity and distribution were observed under a fluorescence microscope to identify the purity of endothelial cells. Figure
S1A shows that the primary endothelial cells had good spindle-shaped and pebble-shaped morphology. Figure
S1B shows that about 95% of primary endothelial cells expressed endothelial marker proteins CD31 and VE-Cadherin, suggesting successful isolation of primary endothelial cells with high purity.
FISH assay
The FISH technique was used to determine the localization of Crnde with miR-181a-5p in the cells. Crnde was labeled by a Cy5 probe and fam probe was used to label miR-181a-5p. The probes were designed and synthesized by GenePharma and a FISH kit (GenePharma) was utilized to detect the signal of the probes according to the manufacturer’s instructions. Images were taken with a Lei TCS SP8 laser scanning confocal microscope (Leica Microsystems, Mannheim, Germany). The cell experiments were independently repeated three times.
Dual luciferase reporter gene assay
Cells were transfected with the luciferase reporter plasmid containing Pcyox1l with the wild-type or a mutated version of the binding site and mimic-NC or miR-181a-5p mimic with Lipofectamine 2000 (Invitrogen). After 48 h of transfection, the cells were collected to detect luciferase activity using the Dual-Luciferase reporter assay system (Promega) as normalized to Renilla luciferase activity [
24]. The cell experiments were independently repeated three times.
RNA pull-down assay
A Biotin-labeled Crnde probe (Crnde probe) and a NC probe were purchased from Sangon. The Crnde or NC probe was incubated with magnetic beads at 4℃. An equal number of cells were seeded in two 10-cm culture dishes, respectively. After 24 h, the cells on the two culture dishes were collected for lysis, and 50 µL of cell lysates were frozen at -80℃ as Input. Cell lysates were then incubated for 1 h at room temperature with a magnetic bead mixture. After purification, the enrichment of RNA was determined by RT-qPCR. Data of the Input of the two groups of samples were standardized, and then the relative expression of Crnde and miR-181a-5p in the pull-down NC probe and Crnde probe samples was calculated based on the Ct value of each input sample. The cell experiments were independently repeated three times.
RNA immunoprecipitation (RIP) assay
Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore, Burlington, MA) for RIP assay. Cells were cultured with NP-40 RIP lysate buffer containing DTT (1 mM), PMSF (1 mM), RNase inhibitor (200 U/mL) and 1% protease inhibitor. RIP buffer with magnetic beads conjugated with AGO2 antibody (0.5 mg/mL, ab186733, 1:30, Abcam) to the whole cell lysate (200 µL), with IgG antibody (2 mg/mL, ab205718, 1:50, Abcam) serving as the NC. The beads were rinsed with pre-cooled NT2 buffer and incubated with protease K (10 mg/mL) for 30 min to prevent non-specific binding. The immunoprecipitated RNA was purified and the levels of miR-181a-5p and Pcyox1l mRNA were detected by RT-qPCR. The cell experiments were independently repeated three times.
Statistical analysis
All data were processed using SPSS 21.0 statistical software (IBM Corp. Armonk, NY). Measurement data were represented in the form of mean ± standard deviation. Data comparisons between two groups were conducted by unpaired t test, and those among multiple groups by one-way ANOVA with Tukey’s post hoc tests. p < 0.05 indicated significant differences.
Discussion
DVT, a coagulation disorder, is related to inflammation and causes morbidity and mortality [
29]. Our study intended to reveal the possible molecular mechanism of the Crnde/miR-181a-5p/Pcyox1l ceRNA regulatory network in DVT, which found that Crnde could promote thrombus formation through the /miR-181a-5p/Pcyox1l axis.
Initially, our high-throughput transcriptome sequencing analysis identified that Crnde was involved in DVT. We further validated that silencing of Crnde ameliorated vascular inflammatory injury, thereby curtailing DVT. Accumulating evidence has indicated the implication of lncRNAs in DVT. For instance, repression of lncRNA 1123 was unveiled to constrain lower extremity DVT by regulating miR-125a-3p to target interleukin 1 receptor type 1 [
19]. Additionally, lncRNA MALAT1 affected the vascular endothelial cell physiology in DVT via the miR-383-5p/BCL2L11 axis [
30]. It should be noted that the role of Crnde in DVT has been rarely reported. Nevertheless, the association of Crnde with inflammation has been increasingly revealed. Knockdown of Crnde contributed to amelioration of inflammation injury induced by LPS in WI-38 cells by mediating FOXM1 [
31]. Crnde induced inflammation in HK-2 cells via activation of the TLR4/NF-κB axis [
32]. Interestingly, Crnde was found to be upregulated in injured rat carotid artery as well as vascular smooth muscle cells [
9].
Further bioinformatics analysis predicted that the Crnde/miR-181a-5p/Pcyox1l ceRNA regulatory network might participate in DVT. In addition, overexpression of miR-181a-5p was revealed to attenuate vascular inflammatory injury, thereby curtailing DVT. miR-181 was previously suggested to be a promising therapeutic target for curtailing thrombosis [
14]. Vascular miR-181b could control tissue factor-dependent thrombogenicity as well as inflammation in type 2 diabetes [
33]. Besides, miR-181a-5p modulated the angiogenesis of human umbilical vein endothelial cells by targeting PDGFRA [
34]. Moreover, miR-181a-5p alleviated inflammatory response in pulmonary arterial hypertension induced by monocrotaline, which was achieved by targeting endocan [
16]. These reports can support our finding regarding the alleviatory role of miR-181a-5p in vascular inflammatory injury in DVT.
Mechanistically, we found in this study that Crnde could upregulate Pcyox1l expression by competitively binding to miR-181a-5p. The loss of Pcyox1 could cause platelet hypo-reactivity or impairment of arterial thrombosis, and Pcyox1 might be developed as an antithrombotic drug [
12]. Notably, deficiency in Pcyox1 in an ApoE mouse model inhibited atheroprogression, which was achieved partly by reducing inflammation and regulating platelet adhesion [
35]. Pcyox1l is rarely researched, though a previous study investigated the potential prognostic potential of the lncRNA transcript lnc-Pcyox1l in clear cell renal cell carcinoma but failed to find its differential expression in the malignancy [
36]. LncRNAs can modulate biological functions at epigenetic, transcriptional or post-transcriptional levels and miRs can affect physiological and pathological processes by mediating target mRNA translation or degradation [
37]. LncRNA transcripts serve as ceRNAs or natural miR sponges and competitively bind to shared miRs to co-regulate each other [
38]. To our knowledge, previous studies have indicated the interaction between Crnde and miR-181a-5p under different situations. Crnde could sponge miR-181a-5p, contributing to aggravation of sepsis-related inflammation [
13]. Moreover, Crnde downregulated the expression of miR-181a-5p to facilitate the proliferation and chemoresistance of colorectal cancer cells, with the involvement of Wnt/β-catenin signaling [
39]. It is worthy to note that there is scarcity of reports regarding the interaction between miR-181a-5p and Pcyox1l. In our study, the database-based bioinformatics analysis combined with dual luciferase reporter gene and RIP assays confirmed the targeting relationship between miR-181a-5p and Pcyox1l.
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