Cell culture
Human umbilical vein endothelial cells (HUVECs), endothelial colony-forming cells (ECFC), human microvascular endothelial cells (HMVECs), and human alveolar epithelium cells (HAECs) were cultured in endothelial cell growth basal medium-2 (Lonza) supplemented with 2% fetal bovine serum, human FGF-β, vascular endothelial growth factor, R3-insulin growth factor-1, human endothelial growth factor, hydrocortisone, ascorbic acid, heparin, gentamicin, and amphotericin-B (Lonza). HMVECs were cultured in microvascular endothelial cell growth medium BulletKit (Lonza).
Reagents and antibodies
Antibodies recognizing pRb, phospho-pRb, cleaved PARP, phospho-SRC (Y416), p21, p16, mTOR, phospho-mTOR (S2448), phospho-mTOR (S2481), phospho-ERK1/2, phospho-AKT (T308), phospho-AKT (S473), phospho-NDRG1 (Thr346), phospho-p70S6K (Thr389), and phospho-SIN1 (Thr86) were from Cell Signaling Technology (Danvers, MA, USA). Antibodies recognizing flotillin-1, cyclin D1, cyclin A, CDK2, CDK4, AKT, phospho-PKCα (Ser657), integrin β1, integrin β3, and integrin β5 were from Santa Cruz (Dallas, TX, USA). Antibodies recognizing clathrin and caveolin-1 were purchased from Biosciences (San Diego, CA, USA). Antibodies recognizing p53, actin, and CD31 antibodies were from Leica Biosystems (Wetzlar, Germany), Abcam (Richmond, BC, Canada), and Thermo Fisher Scientific (Waltham, MA, USA), respectively. Antibodies recognizing integrin β4, integrin α6, Raptor, Rictor, and FLRT2 were from Abcam (Cambridge, UK), while an antibody recognizing phospho-integrin β4 (Y1510) was from Assay Biotechnology (Sunnyvale, CA, USA). The anti-integrin β4 antibody (clone ASC-8) for blocking integrin β4 activity was purchased from Millipore (Charlottesville, VA, USA). Rapamycin, LY294002, and PD098059 were purchased from Millipore. Torin was purchased from Selleckchem (Houston, TX, USA).
SA-β-Gal staining
Cells were washed with 1X phosphate-buffered saline (PBS), fixed in 3.7% formaldehyde for 5 min, and washed with PBS. The fixed cells were then incubated with a solution containing 1 mg/mL of 5-bromo-4-chloro-3-indolyl B-D-galactoside (X-Gal), 40 mM citric acid/sodium phosphate (pH 6.0), 5 mM potassium ferrocyanide, 5 mM potassium ferricyanide, 150 mM NaCl, and 2 mM MgCl2 for 16 h at 37°C. The cells were then washed and imaged using a microscope (Olympus CKX41; Olympus Shinjuku, Tokyo, Japan).
Human arterial tissue samples
Human vascular tissue sections of the splenic arteries were obtained from atherosclerosis patients at Yeungnam University Hospital (Daegu, Republic of Korea) aged 1–90 years (grouped in 10-year age intervals; n = 20 for each group) consenting to surgical excision from 1995 to 2012 with Internal Review Board approval (YUMC 2015-01-017).
Immunoblotting analysis
The cells were lysed using radioimmunoprecipitation assay (RIPA) lysis buffer containing protease inhibitors (Roche, Basel, Switzerland) and phosphatase inhibitors (Sigma-Aldrich, St Louis, MO, USA). Equal amounts of proteins were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The resolved proteins were transferred to a nitrocellulose membrane, which was then blocked with 3% non-fat dried milk or 3% bovine serum albumin (BSA) and incubated with the primary antibodies at 4°C overnight. Next, the membrane was incubated with horseradish peroxidase-conjugated secondary antibodies for 1 h. The protein bands were developed using an enhanced chemiluminescence reagent (Thermo Fisher Scientific) and visualized after exposure to X-ray film (Agfa Gevaert NV, Mortsel, Antwerp, Belgium).
Immunoprecipitation
The cell lysates were prepared using a 1% NP-40 lysis buffer (25 mM Tris-HCl (pH 7.5), 150 mM NaCl, and 1% NP-40) containing protease inhibitors (Roche) and phosphatase inhibitors (Sigma-Aldrich). The lysates were precleared with Sepharose beads coupled with Protein G or A (Sigma-Aldrich), the indicated antibodies added, and tumbled with Sepharose beads coupled with Protein G or A. The immune complexes were then subjected to SDS-PAGE, followed by immunoblotting.
Cell viability
Cells were seeded in 60-mm dishes, cultured for 24 h, and treated with conditioned media (CM) as indicated in the figures for 3 days. Next, the cells were trypsinized and harvested. Cell viability was measured using the trypan blue exclusion assay; cell suspensions were diluted (1:1) with 0.4% trypan blue (GIBCO, Grand Island, NY, USA) and counted using a hemocytometer under a microscope (Olympus CKX41; Olympus).
Cell cycle analysis
Cells were harvested by trypsinization, fixed in 95% ethanol, washed with PBS, resuspended in 1 mL PBS containing 1 mg/mL RNase and 50 mg/mL propidium iodide (Sigma-Aldrich), and incubated in the dark for 30 min. The distribution across cell cycle compartments was analyzed using a fluorescence-activated cell sorting (FACS) Calibur flow cytometer (BD Biosciences, San Diego, CA, USA).
BrdU incorporation assay
Cell proliferation was measured using a BrdU cell proliferation assay kit (Roche Applied Science) following the manufacturer’s instructions. BrdU incorporation was determined by measuring the absorbance at 450 nm using a spectrophotometer.
RNA interference
Cells were transfected with siRNA duplexes using RNAiMAX (Invitrogen, Karlsruhe, Germany). The sequences of the siRNAs (Bioneer Inc., Daejeon, Korea) were as follows:
Con Si: 5′-CCUACGCCACCAAUUUCGUdTdT-3′
FLRT2 Si: 5′-GAGCUUGGUAAAUGUCACUdTdT-3′
FLRT2 Si #2: 5′-CACUCUACACUAUACAGUAdTdT-3′
FLRT2 Si #3: 5′-GCAUUUCUAAAGGCCAUUUdTdT-3′
Mouse FLRT2 Si: 5′-[Cyanine5]CACUCUACACUAUACAGUAdTdT-3′
p53 Si: 5′-CACUACAACUACAUGUGUAdTdT-3′
p21 Si: 5′-CUGUACUGUUCUGUGUCCUdTdT-3′
FGFR Si: 5′-CUCACUGUGGAGUAUCCAUdTdT-3′
SRC Si: 5′-GGCUGAGGAGUGGUAUUUUdTdT-3′
AKT Si: 5′-GACAACCGCCAUCCAGACUdTdT-3′
Raptor Si: 5′-CACCTCACTTTATTTCCATdTdT-3′
Rictor Si: 5′-ACUUGUGAAGAAUCGUAUCdTdT-3′
EPS8L2 Si: 5′-GAGCUUUCUCUGGCCAAGUdTdT-3′
PLVAP Si: 5′-GUGACAACACACACCAUGAdTdT-3′
GPC1 Si: 5′-GUGCUUUGCCUGGCUACAUdTdT-3′
SDC1 Si: 5′-GACUUGGAAGACUCCAUGAdTdT-3′
CACNG6 Si: 5′-CGGCUCUCCCUCUUUCAUAdTdT-3′
EPHB6 Si: 5′-GGUGAAUGUAAGACGCUGUUdTdT-3′
PLCD3 Si: 5′-CCUGGAGAAGACAGUAGAAdTdT-3′
ITGB1 Si: 5′-CAGACAUCAUUCCAAUUGUdTdT-3′
ITGB3 Si: 5′-CAGAUGUCAUUCCAUAUCAdTdT-3′
ITGB4 Si: 5′-GACUUCGUGUGCGGACAGUdTdT-3′
ITGB5 Si: 5′-CUGUUGAAGGUACAUCGUUdTdT-3′
Plasmid transfection
Plasmids were transfected using Lipofectamine 2000 reagent (Invitrogen, Karlsruhe, Germany), following the manufacturer’s instructions. The plasmids expressing pRK5 beta4 and pRK5 beta4 1355 T (ΔCYT) were purchased from Addgene (Cambridge, MA, USA). The plasmids expressing FLRT2 (NM_013231) Human Tagged ORF Clone and FLRT2 (NM_201518) Mouse Tagged ORF Clone were purchased from OriGene (Rockville, MD, USA).
RT-qPCR: reverse transcription (RT) followed by real-time quantitative polymerase chain reaction (qPCR)
Total RNA was extracted using the TRIzol reagent (Invitrogen), following the manufacturer’s instructions and resuspended in diethyl pyrocarbonate-treated water. The RNA was subjected to reverse transcription (RT) using a complementary DNA (cDNA) synthesis kit (Bio-Medical Science Co. Ltd, Daejeon, Korea). The cDNA was then subjected to real-time quantitative (q)PCR analysis using pre-designed gene-specific primers purchased from Bioneer Co., Ltd. (Daejeon, Korea) and iQ™ SYBR® Green Supermix (Bio-Rad Laboratories, Hercules, CA, USA) in a CFX Connect™ Real-Time PCR Detection System (Bio-Rad Laboratories).
RNA sequencing data processing and analysis
Total RNA was isolated from HUVECs using TRIzol reagent, resuspended in RNase-free water, and used for RNA-seq analysis by Macrogen (Seoul, Korea). The expression level of each transcript was quantified as fragments per kilobase of transcripts per million mapped reads (FPKMs). The thresholds were set using the absolute value of twofold change to determine significant differences in gene expression. The DAVID gene annotation tool (version 6.8; http://david.ncifcrf.gov/) was used for gene ontology analysis of the genes of interest.
Tube formation assay
Matrigel (BD Biosciences) was polymerized (200 µL/well of a 48-well tissue culture plate) for 30 min at 37°C. Trypsinized HUVECs (4×104) were resuspended in 200 µL of CM and seeded into each well. The cells were cultured for 16 h and images of the tubes were captured using a microscope. The number of branch points and branches was counted, and the tube area was measured using the Fuji Multi Gauge V2.3 software (Fuji, Tokyo, Japan).
Immunofluorescence staining
The cells were fixed with 3.7% formaldehyde for 15 min, permeabilized with 0.1% Triton X-100 for 15 min, and blocked using 3% BSA in PBS for 1 h. Next, the cells were incubated with the primary and fluorescein-conjugated secondary antibodies for 1 h at room temperature. Immunofluorescence was examined using an LSM 510 META laser scanning microscope (ZEISS, Germany).
The Duolink Proximity Ligation Assay
To assess possible physical interaction between FLRT2 and ITGB4, HUVECs were subjected to Duo-link assay with anti-FLRT2 (Abcam) and anti-ITGB4 (Abcam) as primary antibodies, following the manufacturer’s instruction (Sigma-Aldrich). Fluorescent images of the cells were observed under an LSM 510 META laser scanning microscope.
Isolation and characterization of lipid rafts
HUVECs were lysed with 1 mL of lysis buffer (1% Triton X-100, 25 mM HEPES (pH 6.5), 150 mM NaCl, 1 mM EDTA, 1 mM phenylmethylsulfonyl fluoride, and protease inhibitor cocktail). Equal amounts of proteins were subjected to discontinuous sucrose gradient ultracentrifugation (40%, 30%, and 5%) using an SW41 Ti rotor (39,000 rpm) for 16 h at 4°C. The sucrose gradients were fractionated into 13 fractions, including the pellet. An opaque buoyant band corresponding to the lipid rafts was collected from the interface between the 30 and 5% sucrose gradients. Aliquots of fractions collected from the bottom of the gradient were analyzed using immunoblotting. The protein concentration was determined using the bicinchoninic acid method (Thermo Fisher Scientific), following the manufacturer’s instructions.
Immunohistochemistry
The tissues were cryosectioned into 20 µm-thick sections, fixed with 3.7% formaldehyde, and permeabilized with 0.01% Triton-X100 for 15 min. The samples were then blocked with 3% BSA for 1 h at room temperature and incubated with rat anti-CD31 (Thermo Fisher Scientific) and anti-FLRT2 (Abcam) diluted (1:50) in blocking solution overnight at 4°C. The sections were washed with PBS and incubated with Alexa Fluor 594 goat anti-hamster IgG (Jackson ImmunoResearch Laboratories, West Grove, PA, USA) and Alexa Fluor 488 goat anti-rabbit (Jackson ImmunoResearch Laboratories) diluted (1:50) in blocking solution for 1 h at room temperature. The sections were washed thrice with PBS and mounted on microscopy slides.
Animal experiments
Fifty µg of Cy5–tagged mouse FLRT2 Si or Flag-tagged FLRT2 plasmid were mixed with in vivo-jetPEI® (Polyplus transfection;Illkirch, France), following the manufacturer’s instructions. Cy5–tagged mouse FLRT2 Si was used to assess siRNA distribution in mouse aorta (thoracic) or vein (vena cava). The solution was vortexed gently and left for 15 min at room temperature. The mixture was injected into the tail veins of 8-week-old male mice four times over 14 days, and the treated mice were sacrificed for immunoblotting, SA-β-Gal staining, and immunofluorescence. All animal care and experimental procedures were approved by the INHA University-Institutional Animal Care and Use Committee (INHAIACUC) (Approval Number INHA-200917-722-1).
Statistical analysis
All data are expressed as mean ± standard deviation. The data were analyzed using one-way analysis of variance or Student’s t-test. The differences were considered significant at p < 0.05.