Characterization of nanoparticles
All nanoparticles used in this study were characterized as a part of previous work [16, 21, 41], and detailed information, including dynamic light scattering (DLS), inductively coupled plasma-mass spectrometry (ICP-MS), and zeta-potential analysis for these materials is presented elsewhere [41]. Briefly, spherical AgNPs in sizes 10, 20, 75, and 110 nm were obtained from NanoComposix (San Diego, CA) in BioPure formations. AgNPs were suspended in a 2 mM sodium citrate solution. Nanoparticles were checked for sterility, endotoxin contamination, and protein corona formation as previously described [21]
Procurement of excised intestinal samples
This study was conducted under the approved protocol for obtaining intestinal tissue samples (terminal ileum) from the Cooperative Human Tissue Network (CHTN) located at the University of Alabama at Birmingham. The CHTN coordinates with other centers to provide high-quality tissue specimens to researchers. The use of these tissue samples was approved by US Food and Drug Administration’s RIHSC (Research Involving Human Subject Committee). All specimens were human terminal ileum taken from subjects as a part of routine surgical procedures. All tissue culture items were procured from ThermoFisher Scientific, Waltham, MA. Samples were shipped overnight on ice in nutritive transport media (RPMI 1690 with GlutaMAX, supplemented with pen/strep) from the coordinating Center to the National Center for Toxicological Research in Jefferson, AR. All specimens used in this study were found to be normal tissue by post-surgical pathological examination. All patient information was protected and the only information available for each sample was age, race, and sex.
Treatment of samples
Once received, all patient specimens were processed according to strict handling procedures. For each set of experiments, a positive control (tissue exposed to silver acetate; AgOAC) and a negative control (tissue without nanoparticle) were maintained separately as described below. Ileal tissue specimens were removed from transport media and washed with RPMI media, then placed onto dental wax and cut using a 6-mm biopsy punch (ThermoFisher Scientific, Waltham, MA). Individual tissue biopsy punches were placed into 6-mm polyester transwell inserts (Corning, Corning, NY), one biopsy punch per transwell, with the mucosal side facing up. Culture media, composed of RPMI 1690 with GlutaMAX, supplemented with 10% FBS, pen/strep, and fungizone, was then added to the apical and basal transwell compartments. Finally, AgNPs or a positive control (AgOAC) were added to the apical compartments of each transwell at final concentrations of 20 µg/mL. The same volume of media alone was used as the negative control. Tissue punches treated with nanoparticles or controls were incubated with 5% CO2 at 37 °C for 2 and 24 hours. Samples were collected for electron microscopy, extraction of protein or mRNA as described below.
Examination of tissues by electron microscopy
To determine if the ileal samples maintained their integrity during sample transport, some ileal specimens (obtained during the initiation of this study) were processed and treated as previously described for evaluation by SEM and TEM. The biopsy punches were placed in 24-well plates and treated as described earlier. At the designated time point, individual biopsy punches were transferred to 1 mL 3% glutaraldehyde (Electron Microscopy Sciences, Hatfield, PA). Samples were then processed in the NanoCore facility at the National Center for Toxicological Research for evaluation by SEM and TEM as described earlier with FE-SEM (Zeiss Merlin) and JEM-2100 200 keV (JEOL USA, Inc., Peabody, MA) instruments [42].
Extraction of protein and RNA from ileal tissue
At the designated time point, tissue punches were removed from transwell plates and processed to extract RNA and protein using the mirVana PARIS RNA and Protein Purification Kit (ThermoFisher Scientific, Waltham, MA). Briefly, tissue punches were minced into 1-mm segments using a sterile scalpel and then segments were placed into ice-cold Dissociation Buffer and homogenized using a pellet pestle motor and a Micro Tissue Homogenizer set (ThermoFisher Scientific). The remainder of the protein extraction was then performed according to the manufacturer’s instructions. RNA extraction from the samples was completed as described earlier [43]. Protein and RNA samples were stored at -80 °C until further use.
Measurement of cytokine levels in tissue samples
Cytokine levels in ileal tissue samples were measured using the Bio-Plex Multiplex Immunoassay System (Bio-Rad, Hercules, CA), which uses a bead-based multiplex system to quantify specific target proteins. Protein extracts were thawed on ice and protein concentration was measured using Bradford reagent (Bio-Rad). Samples were adjusted to 500 µg/mL total protein and plates were prepared for analysis using protein extracts (2 replicates per sample), reagents, and instructions from two different Bio-Plex Pro Human Cytokine kits: an 8-plex assay for the measurement of the cytokines IL-1b, IL-2, IL-4, IL-6, IL-8, IL-10, GM-CSF, IFN-γ, and TNF-α and a custom-created assay designed for the measurement of the cytokines IL-12 (p70), Basic FGF, IP-10, RANTES, and VEGF. The 8-plex assay was chosen as a general panel of cytokines involved in the intestinal immune response, including cytokines involved in pro- and anti-inflammatory responses and T-cell signaling. Additional cytokines specifically related to conditions of chronic intestinal inflammation were custom designed. Plates were read on a Bioplex 200 instrument using Bio-Plex Manager software (Bio-Rad). Raw data was exported and analyzed using the Bio-Plex Data Pro Software (Bio-Rad). Statistical analysis was performed using a paired t-test, with each nanoparticle-treated explant paired to its untreated control. Significance was designated as a p-value < 0.05.
Gene expression analysis
Quantity and quality of RNA extracted from ileal tissue samples at the 24-hour time point were analyzed using a NanoDrop® ND-1000 spectrophotometer (NanoDrop, Wilmington, DE). The Turbo DNA-free kit (Life Technologies, Carlsbad, CA) was used to remove contaminating DNA. Treated RNA was re-quantified and reverse transcribed using the Two-Step Reverse Transcription TaqMan kit (Applied Biosystems, Foster City, CA) to produce cDNA. Sample cDNA was run on a RT2 Profiler PCR Array Human Cell Junction Pathway Finder (Qiagen, Valencia, CA). Eighty-four unique genes related to cell junctions and intestinal permeability were examined including adherens junctions, focal adhesions, tight junctions, gap junctions, desmosomes, and hemidesmosomes. Plates were analyzed using an ABI 7500 Real-Time PCR system (Life Technologies). Data was analyzed in the Qiagen Data Analysis Center using glyceraldehyde-3 phosphate dehydrogenase (GAPDH) as the housekeeping gene for normalization. The qPCR data was analyzed statistically using a student’s t-test. Significance was designated as a p-value < 0.05.