Materials and reagents
Calcium nitrate tetrahydrate, trisodium phosphate, sodium selenite, linoleic acid, octadecylamine, anhydrous ethanol, nitrate acid, PAMAM-G3, anti-TLR9 rabbit polyclonal antibody, fluorescein isothiocyanate isomer I (FITC), 4′,6-diamidine-2′-phenylindole dihydrochloride (DAPI), brain-heart infusion broth (BHI), agar, hemin and menadione, cell counting kit-8 (CCK-8), and PMA were purchased from Sigma-Aldrich (St. Louis, MO, U.S.A.). Poly(I:C) (tlrl-picw), ultrapure LPS (tlrl-peklps), ORN06/LyoVec (tlrl-orn6), ODN BW006 (tlrl-bw006), ODN 2395, and QUANTI-Blue medium were purchased from InvivoGen (San Diego, CA, U.S.A). A bicinchoninic acid (BCA) protein assay kit, H&E staining kit, defibrinated sheep blood, and Schaedler broth were purchased from Solarbio (Beijing, China). Paraformaldehyde (4%) was purchased from Servicebio (Wuhan, Hubei, China). A TRAP/ALP staining kit was purchased from FUJIFILM Wako Chemicals (Osaka, Japan). Anti-iNOS (D6B6S) rabbit monoclonal antibody (cat. #13120), anti-arginase-1 (D4E3M) XP rabbit monoclonal antibody (cat. #93668), and PathScan Sandwich ELISA Lysis Buffer were purchased from Cell Signaling Technology (Danvers, Massachusetts, U.S.A). Alexa Fluor 594-conjugated goat anti-rabbit IgG (H+L) (cat. #ZF-0516) was purchased from ZSGB-BIO (Beijing, China). Anti-CD11c (N418) Armenian hamster monoclonal antibody (cat. #14-0114-82), anti-F4/80 (BM8) rat monoclonal antibody (cat. #14-4801-82), human anti-CD80 antibody (cat. #46-0809-41), human anti-CD83 antibody (cat. #17-0839-4), human anti-CD86 antibody (cat. #12-0869-41), human anti-CD209 antibody (cat. #25-2099-41), human anti-CD14 antibody (cat. #12-0149-41), human anti-CD68 antibody (cat. #25-0689-41), and human anti-CD197 antibody (cat. #17-1979-41) were purchased from eBioscience (San Diego, CA, U.S.A). An anti-rabbit HRP-DAB IHC Detection Kit (cat. #CTS005) was purchased from Novus (Minneapolis, MN, U.S.A). Human anti-CD14 antibody (cat. #325603) was purchased from BioLegend (San Diego, California, U.S.A). Human anti-CD36 antibody (cat. #555454) was purchased from BD Biosciences. Alexa Fluor 647-conjugated goat anti-Armenian hamster IgG antibody (cat. #ab173004) and anti-CD3 rabbit polyclonal antibody (cat. #ab5690) were purchased from Abcam (Cambridge, UK). Dylight 488-conjugated AffiniPure goat anti-rat IgG (H+L) (cat. #E032240) was purchased from EARTHOX (San Francisco, CA, U.S.A). ProLong Gold Antifade Mountant (P36930), UltraPure salmon sperm DNA, a Quant-iT PicoGreen dsDNA assay kit, LysoTracker Red DND-99, a Mitochondria Isolation Kit, ELISA kits for human and mouse TNF-α, human and mouse IL-6, human IL-10, human TGF-β, and BMP-2, a TaqMan Advanced miRNA cDNA Synthesis Kit, and a RevertAid First Strand cDNA Synthesis Kit were purchased from Thermo Scientific (Waltham, Massachusetts, U.S.A). An iScript One-Step RT-PCR Kit with SYBR Green was purchased from Bio-Rad (Hercules, CA, U.S.A.). A 2’3’-cGAMP ELISA kit was purchased from Cayman Chemical (Ann Arbor, MI, U.S.A.). Dulbecco's modified Eagle's medium (DMEM), RPMI-1640 medium, fetal bovine serum (FBS), and 0.25% trypsin-EDTA were purchased from Gibco (Carlsbad, CA, U.S.A.). A dermal cell basal medium and keratinocyte growth kit were purchased from the American Type Culture Collection (ATCC, Manassas, VA, U.S.A.). An RNApure Total RNA Fast Extraction Kit (cat. #RP1202) was purchased from Bioteke Corporation (Wuxi, Jiangsu, China). Cy5.5-labeled CpG 1826 and primers were synthesized and purchased from Integrated DNA Technologies (IDT, Coralville, IA, U.S.A.). All other reagents were commercially available and were used as received (Table S2).
Synthesis of SeHANs
SeHANs were synthesized using a modified liquid-solid-solution (LSS) method. Briefly, 1.18 g calcium nitrate tetrahydrate was dissolved in 25 mL deionized water and then mixed with an organic solution composed of 1.5 g octadecylamine, 12 mL linoleic acid, and 48 mL anhydrous ethanol. Thereafter, 461.25 mg trisodium phosphate and 48.65 mg sodium selenite were dissolved in 20 mL deionized water and added dropwise to the above mixture. After stirring at room temperature for 10 min, the suspension was transferred into a hydrothermal reactor and allowed to react for 12 h at 110 °C. The resulting precipitates were washed with anhydrous ethanol and deionized water at least six times and collected by centrifugation, and were stored in anhydrous ethanol at 4 °C.
Synthesis of [email protected]
To decorate SeHANs with PAMAM-G3 (G3), SeHANs (1 mg) were mixed with G3 (10 mg) in PBS (pH 7.4, 0.2 mL), and the mixture was incubated for 12 h at room temperature with shaking. G3-coated SeHANs ([email protected]) were centrifuged at 3000 rpm for 5 min to remove unbound G3 and were washed three times with PBS. The size and zeta potential of [email protected] were measured with a Zetasizer (Nano ZS90, Malvern Panalytical).
Characterization of SeHANs and [email protected]
X-ray diffraction (XRD, PANalytical B.V., Holland) and FTIR (Vertex 70, Bruker, Germany) analyses were performed to investigate the phase composition and functional structure of SeHANs and [email protected] Morphology studies were performed using field emission scanning electron microscopy (FSEM, FEI, Holland) and field emission transmission electron microscopy (FTEM, FEI, Holland). Elemental mapping was performed using FTEM. The valence state of selenium in nanoparticles and PAMAM-G3 grafting on the surface of SeHANs were determined by XPS (Kratos, Japan). PAMAM-G3 content was detected by thermogravimetric analysis (TGA, PerkinElmer, U.S.A.) in an N2 atmosphere. Specific surface area was measured by BET analysis (Micromeritics, U.S.A.).
Selenium content in SeHANs and [email protected]
The amount of selenium in synthesized nanoparticles was quantified using an inductively coupled plasma optical emission spectrometer (ICP-OES, Prodigy Plus, Leeman Labs, U.S.A.). Nanoparticles (2.5 mg) were dissolved in 1 mL of 70 wt% nitric acid and diluted to 10 mL with 1 wt% nitric acid before ICP-OES analysis.
Patient sample collection
Saliva and serum samples from 11 patients with periodontitis and 14 healthy volunteers were obtained from West China Hospital of Stomatology, Sichuan University. Sample collection was performed with the approval of the Ethics Committee of West China Hospital of Stomatology, Sichuan University. Periodontitis was confirmed by periodontal pockets that showed bleeding upon probing (with ≥5.0 mm probing depth), ≥3.0 mm of clinical attachment loss, and radiographic evidence of alveolar bone loss on at least two teeth per quadrant.50 Periodontal tissue from healthy volunteers showed no redness, no bleeding on probing, and no clinical attachment loss, and radiographs showed periodontal areas without bone loss.
Biodegradation and selenium release by SeHANs and [email protected]
Selenium release by SeHANs and [email protected], which represented their biodegradation, was detected by ICP-OES in three different solutions: PBS pH 7.4, saliva from healthy donors, and saliva from periodontitis patients. Saliva was collected and sterilized with a 0.22-μm filter (Millipore), then nanoparticles were prepared as a suspension at 2.5 mg/mL with these three solutions in 1.5-mL tubes. Thereafter, the tubes were placed in a water bath shaker at 37 °C. At each time point, the tubes were centrifuged at 12,000 rpm for 15 min to collect 1 mL of supernatant, and 1 mL of fresh buffer solution was added to restore the volume. The collected supernatant was digested with 1 mL of 70 wt% nitric acid and diluted to 10 mL with 1 wt% nitric acid before ICP-OES analysis.
DNA-binding efficiency of SeHANs and [email protected]
Bare SeHANs or [email protected] (200 mg) were mixed with salmon sperm DNA (2–30 mg in 1 mL Tris-EDTA buffer) and incubated for 3 h at room temperature with shaking. The mixture was centrifuged at 3000 rpm for 5 min, and the supernatant containing unbound DNA was collected and analyzed with a Quant-iT PicoGreen dsDNA assay to determine the amount of DNA bound to the nanoparticles.
Porphyromonas gingivalis and Fusobacterium nucleatum strains were provided by the State Key Laboratory of Oral Diseases, the West China School of Stomatology, Sichuan University. Porphyromonas gingivalis and were stored in glycerol broth at –80 °C. The bacteria were cultured in brain heart infusion (BHI) or 5% defibrinated sheep blood agar, both supplemented with 5 mg/mL hemin-menadione. Fusobacterium nucleatum was cultured in Schaedler broth. Bacteria were incubated in an anaerobic environment (90% N, 5% CO, 5% H2) at 37 °C.
DAMP and MAMP isolation
HGF-1 and primary gingival keratinocytes (PGKs) (ATCC) were maintained according to ATCC protocols and were harvested for DAMP collection. Mitochondria were collected from HGFs with a mitochondrion isolation kit and were used for DAMP isolation. Bacteria (Porphyromonas gingivalis and Fusobacterium nucleatum) were used for MAMP isolation. Cells and bacteria were collected in 1.5-mL tubes and ultrasonicated for 10 min. The concentration of DNA was measured. For DNA measurements, mixtures were centrifuged at 10,000 rpm for 5 min, and supernatants were collected for DNA quantification. Isolated DAMPs and MAMPs were stored at -80 °C until further use.
In vitro cytotoxicity assay
RAW 264.7 cells were seeded into 96-well culture plates at a density of 2×104 cells/well and cultured until the cells were fully attached. Then the cells were treated with different concentrations of NABNs or soluble PAMAM-G3 for 24 h and were counted with a cell counting kit-8 (CCK-8).
Extraction and quantification of cfDNA
Extraction of cfDNA from saliva or serum was performed with a DNeasy Blood & Tissue Kit (QIAGEN, Germany). Concentrations of cfDNA in saliva, serum, DAMPs, and MAMPs were measured with a Quant-iT PicoGreen double-stranded DNA Assay Kit.
In vitro TLR3, TLR4, TLR8, and TLR9 activation assay
Stable hTLR3-, 4-, 8-, and 9-overexpressing HEK-Blue cells were purchased from InvivoGen (San Diego, CA, U.S.A.) and were initially propagated in DMEM with 10% (v/v) FBS and maintained in growth medium supplemented with selective antibiotics. Before treatment, certain numbers of HEK-Blue hTLR cells (5×104 cells/well hTLR3, 2.5×104 cells/well hTLR4, 4×104 cells/well hTLR8, and 8×104 cells/well hTLR9 cells) were seeded and cultured in basal DMEM overnight in 96-well plates, then stimulated with the appropriate agonists (1 μg/mL low molecular weight poly(I:C) for hTLR3, 10 ng/mL ultrapure LPS for hTLR4, 0.5 μg/mL ORN06/LyoVec for hTLR8, and 1 μg/mL ODN BW006 for hTLR9). In the scavenger-treated groups, PAMAM-G3 (2 µg/mL), SeHANs (10 µg/mL), or [email protected] (10 µg/mL) were added 30 min prior to adding the agonist. After 24 h, the activation of reporter cells was determined with QUANTI-Blue medium. One microliter of human saliva, 5 μL of human serum, DAMPs from PGKs (cfDNA concentration: 1 µg/mL), DAMPs from HGFs (cfDNA concentration: 1 µg/mL), DAMPs from mitochondria (cfDNA concentration: 500 ng/mL), MAMPs from Porphyromonas gingivalis (cfDNA concentration: 1 µg/mL), and MAMPs from and Fusobacterium nucleatum (cfDNA concentration: 1 µg/mL) were also prepared as agonists to test the function of cationic scavengers. Briefly, 50 μL supernatant from each well of the cell culture plate was transferred to 150 μL QUANTI-blue medium to test the corresponding embryonic alkaline phosphatase (SEAP) activity, which was first loaded into the empty well and incubated at 37 °C for the reaction, and OD620 was measured.
In vitro anti-inflammatory assays
RAW 264.7 cells were seeded and cultured in basal DMEM overnight at 2×104 cells per well in a 96-well plate. PAMAM-G3 (2 µg/mL) or [email protected] (10 µg/mL) were added in a final volume of 200 μL 30 min prior to addition of agonist. ODN BW006 (1 μg/mL), 1 µL of human saliva, 5 μL of human serum, DAMPs from PGKs (cfDNA concentration: 1 µg/mL), DAMPs from HGFs (cfDNA concentration: 1 µg/mL), DAMPs from mitochondria (cfDNA concentration: 500 ng/mL), MAMPs from Porphyromonas gingivalis (cfDNA concentration: 1 µg/mL), and MAMPs from Fusobacterium nucleatum (cfDNA concentration: 1 µg/mL) were then added into the well. After incubation for 24 h, the supernatants were collected and TNF-α and IL-6 levels were measured using ELISA kits.
THP-1 cells were purchased from ATCC and cultured in RPMI-1640 media supplemented with 10% FBS and selective antibiotics. Briefly, 8×104 cells were plated in 96-well plates in 200 µL RPMI media plus 25 ng/mL PMA for 48 h of treatment to induce differentiation to macrophages. For polarization, THP-1 macrophages were treated with PMA for 48 h, and periodontitis saliva was added during the final 18 h of treatment. PAMAM-G3 (2 µg/mL) or [email protected] (10 µg/mL) were added in a final volume of 200 μL 30 min prior to adding saliva. After incubation, supernatants were collected and TNF-α, IL-6, TGF-β, IL-10, and BMP-2 levels were measured with ELISA kits.
Animal model establishment and treatment
The design of the animal experiment was approved by the Ethics Committee of West China School of Stomatology (Chengdu, China). Male BALB/C mice (7-8 weeks old) were purchased from Dossy Experimental Animals Co., Ltd. (Chengdu, Sichuan, China) and maintained at the Experimental Animal Center of West China Second University Hospital (Chengdu, Sichuan, China). Animals were fed standard food and water ad libitum, and light was provided according to natural circadian rhythms.
The murine experimental model of periodontitis was established by placing a ligature (Coated VICRYL Suture, 5-0; Ethicon | J&J Medical Devices, Somerville, New Jersey, U.S.A.) around the cervix of the maxillary second molar.51 General anesthesia was administered by the intramuscular injection of Zoletil50 (50 mg/kg; Virbac, Carros, Grasse, France). The local administration of the materials (PAMAM-G3: 200 µg/mL; [email protected]: 1 mg/mL) or PBS (in the control group) was accomplished by microinjection using a microsyringe (25-µL syringe with a 32-gauge needle; Hamilton Company, Reno, Nevada, U.S.A.) into gingival tissue at six sites (5 µL/site) around the ligature, including the mesiobuccal gingiva, distobuccal gingiva, mesiopalatal gingiva, distopalatal gingiva, and mesial and distal gingival papilla. To reduce the amount of anesthesia and local damage to the gingival tissue, microinjections were performed every three days (on days 0, 3, 6, 9, and 12); on experimental days without injection, the materials and PBS were noninvasively smeared on the gingiva using disposable microapplicators (M6500-SF purple; TPC Advanced Technology, Inc., City of Industry, California, U.S.A.).
To further determine the effect of pathological DNA on periodontitis, local injection of CpG (ODN2395, 100 µg/mL; InvivoGen, San Diego, California, U.S.A.) was performed in addition to ligature placement. The injection of CpG was performed as described above 30 min after each injection of materials or PBS.
Animal body fluid and tissue sample collection
Saliva samples were collected before each injection after ligature placement and before sacrificing the animal, on days 3, 6, 9, 12, and 15. The saliva secreted by mice within 3 min after anesthesia was pipetted and collected. After centrifugation at 15,000 rpm for 10 min, the supernatant was collected and stored at -80 °C until further testing.
Animals were sacrificed 15 days after ligature placement. Oral microbiome samples were collected using an ultrafine polystyrene swab (25-800 1PD 50; Puritan Medical Products, Guilford, Maine, U.S.A.) according to a published protocol,52 and were stored at -80 °C until further testing. Blood samples were collected by eyeball extirpation under general anesthesia, coagulated at room temperature for 30 min, then centrifuged at 3,000 rpm for 10 min to collect serum. Serum was stored at -80 °C until further testing.
After blood collection, animals were sacrificed by cervical dislocation. First, half of the maxilla on a random side was dissected and rinsed in cold PBS. The crown of the molars, maxillary bone, and buccal soft tissues were removed from samples, and only the gingival tissues and alveolar bone around the three molars were collected. The trimmed maxillary sample was temporarily placed on dry ice and stored at -80 °C for further testing. Then, the other side of the maxilla, heart, liver, spleen, lung, and kidney were dissected and fixed in 4% paraformaldehyde at 4 °C overnight. The fixed samples were rinsed with tap water for 6 h and were stored in 70% ethanol at 4 °C until further testing.
Micro-CT reconstruction and bone resorption quantitative analyses
Fixed maxillary samples were used first for micro-CT scanning (vivaCT80; SCANCO Medical, Brüttisellen, Switzerland). Scanning was performed at 145 mA and 55 kVp every 10 µm at high resolution. Further measurements of the vertical distance between the cementoenamel junction (CEJ) and alveolar bone crest (ABC) and three-dimensional reconstruction were performed with Mimics Research v19.0.0 (Materialise; Leuven, Belgium). The mesial and distal CEJ-ABC (µm) of the maxillary second molar were recorded as the mean of the numbers measured on five mesiodistal sectional planes. After three-dimensional reconstruction, a standard figure of the buccal and palatal aspect of the maxillary molars was obtained, on which the bone resorption area (mm2) was measured using Photoshop CC (Adobe; San Jose, California, USA). The bone resorption area was defined as the area enclosed by the continuous line of CEJ of the three molars and ABC.
After micro-CT scanning, maxillary samples were decalcified in 10% ethylene diamine tetra acetic acid-PBS solution at 4 °C for three weeks. Then, the decalcified maxilla and fixed organs were dehydrated, embedded in paraffin wax, and sectioned (4 µm). H&E staining and TRAP/ALP staining were performed using a staining kit.
For IF analysis, DCs were detected by an anti-CD11c Armenian hamster monoclonal antibody and Alexa Fluor 647-conjugated goat anti-Armenian hamster IgG antibody. Macrophages were detected by an anti-F4/80 rat monoclonal antibody and DyLight 488-conjugated AffiniPure goat anti-rat IgG (H+L). In addition, markers of macrophage subpopulations were co-stained to identify the macrophage composition. M1-type and M2-type macrophages were stained by an anti-iNOS and anti-arginase-1 rabbit monoclonal antibody, respectively. 4',6-diamidino-2-phenylindole (DAPI) was used to stain the cell nucleus. All IF-stained slices were mounted using ProLong Gold Antifade Mountant. Images were captured using an Upright Automated Fluorescence Microscope (BX63; Olympus, Tokyo, Japan), and relative quantitative analyses were performed by comparing the integral optical density (IOD) of the positive area using Image-Pro Plus v6.0.0 (Media Cybernetics; Rockville, Maryland, U.S.A.).
For immunohistochemistry (IHC) analysis, the expression and location of TLR9 was detected by an anti-TLR9 rabbit polyclonal antibody. T cells were detected by an anti-CD3 rabbit polyclonal antibody. IHC was performed using an Anti-Rabbit HRP-DAB IHC Detection Kit. Images were captured using an Aperio ScanScope slide scanner (Leica Biosystems, Wetzlar, Germany), and relative quantitative analyses were performed as described above.
Protein and RNA extraction from animal samples
Maxillary samples that were stored at -80 °C were homogenized using a high-speed tissue grinder (KZ-II; Servicebio, Wuhan, Hubei, China). Total RNA was extracted by using an RNApure Total RNA Fast Extraction Kit, and the quality and concentration of total RNA was assessed by a Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, U.S.A.). Then, reverse transcription was performed using a RevertAid First Strand cDNA Synthesis Kit, and complementary DNA was stored at -20 °C until further testing.
Total protein used for ELISA was extracted using PathScan Sandwich ELISA Lysis Buffer. The concentration of total protein was measured by the BCA method. The total protein sample was stored at -80 °C until further testing.
Cytokine concentration analysis
TNF-α and IL-6 levels in culture supernatants of RAW 264.7 cells and concentrations of TNF-α, IL-6, TGF-β, IL-10, and BMP-2 in culture supernatants of THP-1 cells were determined using ELISA kits.
Quantitative real-time polymerase chain reaction assay
TRIzol reagent was used to extract total RNA, and 1 μg of total RNA was reverse-transcribed using an iScript One-Step RT-PCR Kit with SYBR Green. Quantitative polymerase chain reaction (PCR) was then performed using SYBR Green. Amplified transcripts were quantified using the comparative Ct method.
Biochemical parameter analysis
Alanine transaminase (ALT), aspartate transaminase (AST), blood urea nitrogen (BUN), total bilirubin (TBIL), phosphocreatine kinase (CK), and creatinine (CRE) were measured on a chemistry analyzer (Chemray-800, Rayto) with reagents and settings recommended by the manufacturer.
Fluorescent labeling of cationic scavengers and the intracellular uptake of [email protected]
FITC (150 mg) dissolved in DMSO (50 mL) was slowly added to PAMAM-G3 (3 mg) dispersed in sodium bicarbonate buffer (50 mM, pH 9.0, 0.4 mL) with vigorous stirring. The mixture was incubated for 12 h at 4 °C. FITC-labeled PAMAM-G3 (FITC-G3) was purified using an Amicon Ultra0.5 mL 10K filter (Merck Millipore, Germany). FITC-G3 was used to coat SeHANs for further confocal laser scanning microscopy (CLSM) imaging.
RAW 264.7 cells were seeded onto a cover glass at a density of 10,000 cells/cm2. After 12 h, Cy5.5-labeled CpG (1 mg/mL) was added to cells with FITC-G3 (2 mg/mL) or [email protected] (10 mg/mL) and incubated for 12 h. After 4 h, 8 h, and 12 h of treatment, the cells were washed with PBS, stained with LysoTracker Red DND-99 and DAPI, and mounted for CLSM.
Flow cytometry analysis
THP-1 cells were treated with the method described in the in vitro anti-inflammatory assay section. Then, the cells were collected for flow cytometry analysis. Cells were washed with fluorescence-activated cell sorting (FACS) buffer (1x PBS plus 0.5% FBS) and blocked with Human TruStain FcX (Fc Receptor Blocking Solution). To identify DCs and monocytes, cells were stained with antibodies against human CD14, CD80, CD83, CD86 and CD209 for 30 min at 4 °C. To identify macrophages and monocytes, cells were stained with antibodies against human CD14, CD36, CD68, and CD197. After staining, cells were washed and then resuspended in 1x DAPI in FACS buffer. Flow cytometry data were collected on an LSRFortessa or LSR II (BD Biosciences) and analyzed using FlowJo software (BD Biosciences).
16S RNA analysis
Genomic DNA from oral microbiome samples from mice was isolated and prepared for 16S rRNA gene amplification (V1-V3 region) and sequencing at Majorbio (Shanghai, China) with a MiSeq 300 PE (Illumina MiSeq System) using primers (338F 5’-ACTCCTACGGGAGGCAGCAG-3’; 806R 5’-GGACTACHVGGGTWTCTAAT-3’). The experiment was independently repeated four times. A total of four samples in each group were prepared (n=4). Bioinformatics was performed with mothur and QIIME 2.0. Operational taxonomic unit (OTU) clustering was performed using USEARCH. Sequences were aligned and taxonomically assigned with the Silva database. To avoid biases due to different sequencing depths, OTU tables were rarefied to the lowest number of sequences per sample. Analyses were performed on the I-Sanger Cloud Platform (http://www.i-sanger.com). For alpha diversity, the Shannon index, Chao index, Simpson index, and Ace index at the OTU level were calculated. For beta diversity, PCA at the OTU level was performed, and analysis of similarities (ANOSIM) based on the Bray-Curtis distance was used to examine community differences. Average relative abundances of species are shown with Cicros plots and bar plots.