Animals
All animal studies were performed according to ARRIVE (Animal Research: Reporting In Vivo Experiments) guidelines published in 2010 (https://arriveguidelines.org). Adult female Sprague-Dawley rats (n = 24) (Envigo RMS, Inc., Indianapolis, IN) were pair-housed in ventilated polycarbonate rat cages and maintained in a temperature (21 ± 1°C) and light (0700 h to 1900 h) controlled vivarium with ad libitum food and water. The rats were allowed to acclimate to the facility for one week before undergoing experimental procedures. After the acclimatization period, the rats were randomly assigned to the following groups: CCI + LMNSC008 (n = 8), CCI + VEH (n = 8). Control groups include SHAM + LMNSC008 (n = 4), and SHAM + VEH (n = 4) to assess experimental differences as compared with shame surgery groups +/- LMNSC008 cells [“LMNSC008” is shortened to “NSC” throughout this paper]. All experimental manipulations were conducted during the lights-on phase. All procedures were conducted in accordance with the Guide for the Care and Use of Laboratory Animals and were reviewed and approved by the University of Pittsburgh Institutional Animal Care and Use Committee (IACUC). Mindful effort was made to minimize animal pain, suffering, or discomfort, and to limit the number of rats used.
Surgery
Anesthesia was induced with 4% isoflurane in 2:1 N2O:O2, which was followed by endotracheal intubation, placement on a stereotaxic frame, and mechanical ventilation. Surgical anesthesia was maintained with 2% isoflurane and the same volume of carrier gases. Core temperature was monitored and maintained at 37 ± 0.5°C with a rectal thermistor and heating pad, respectively. Utilizing aseptic procedures, a controlled cortical impact (CCI) injury was produced as previously described.[26, 27] Specifically, a midline scalp incision was made, the skin and fascia were opened, and a craniectomy was made in the right hemisphere with a high-speed dental drill. The bone flap was removed, and the craniectomy was enlarged further to fit the impact tip (6 mm, flat), which was lowered through the craniectomy until it touched the dura mater and then advanced farther to produce a brain injury of moderate severity (2.8 mm tissue deformation at 4 m/s). Sham rats were not subjected to the impact but did receive all other surgical manipulations to control for the potential effects of the anesthesia and craniectomy. After the injury procedures, the anesthesia was discontinued, the incision was promptly sutured closed, and the rats were extubated and assessed for acute neurological outcomes.
Cyclosporin A, NSCs, and VEH administration
To enhance the engraftment of LMNSC008 cells, an immunosuppressive regimen of cyclosporin A (CsA; 10 mg/kg; s.c.) was provided to all rats beginning two days before the first IN administration of NSCs or VEH and continuing once per day until the brains were harvested.
Human LMNSC008 cells from our Master Cell Bank were genetically modified using lentivirus to express green fluorescent protein (eGFP) and firefly luciferase (FFluc) genes were prepared for IN administration according to established SOPs[12, 20, 28, 29]. Briefly, LMNSC008 cells were thawed, washed, and re-suspended in PBS (1x106 cells in 24 µL). Rats received IN injections (4 µL per drop and 3 drops per nare at 2 min intervals) for a total of 24 µL of LMNSC008 cells or the same volume of vehicle (VEH), which consisted of 2% HSA in PBS 20 min after disruption of the nasal epithelium with hyaluronidase. IN dosing occurred on days 7,9,11,13,15, and 17 after CCI or SHAM injury.
Euthanasia and brain harvesting
39 days after CCI or sham injury, the rats were deeply anesthetized with Fatal-Plus® (0.3 mL, i.p., Henry Schein Animal Health; Warrendale PA) and perfused transcardially with 300 mL of ice cold 0.1 M PBS and 600 mL of 4% paraformaldehyde (PFA). Brains were harvested and stored in PBS at 4°C until ready for the next experimental phase.
Brain clearing
Harvested brains were cleared using a modified CLARITY-PACT passive tissue clearing protocol[30]. Briefly, the brains were trimmed with a razor to remove the olfactory bulbs and cerebellum, and then 8–10 coronal sections (1 mm thick) were cut with a vibratome and labeled (S1-S7) with S1 and S7 being most anterior and posterior to the CCI site, respectively. Slices were stored at 4°C overnight in PBS until processed for clearing and staining as described below. PFA-fixed brain sections were transferred to individual 50 mL conical tubes and infused with ice-cold A4P0 hydrogel solution (40% wt/vol acrylamide, 10X PBS, 0.25% wt/vol thermo initiator, dH20) for 24 h at 4°C. Unused A4P0 was stored at -20°C, and aliquots were thawed overnight at 4°C as needed (always protected from light). Each conical tube was topped with a rubber stopper, and the next day oxygen was depleted from the tubes using a vacuum line and venting needle inserted through the rubber stopper for 10 min. The conical tubes were then placed in a 37°C water bath for 2 h or until the hydrogel solution had polymerized into a gel or thick liquid. Excess hydrogel was then peeled/poured off the tissue. Following transfer into new 50 mL conical tubes, each brain section was submerged in an 8% SDS clearing buffer (20% SDS, 1xPBS, 0.01% sodium azide) and incubated in a 37°C shaking incubator for 48 h or until cleared. Brain tissue was divided into 1 mm thick coronal brain sections and optical clearance utilizing the CLARITY-PACT protocol[31].
Immunofluorescent staining
Brain tissue was stained with human specific antibodies Stem121 (Y40410, 1:500, Takara Bio) and anti-nestin SP103 (ab105389, 1:100, Abcam) antibodies to locate and visualize IN administered LMNSC008 cells, as well as native tissue structure using NeuN (ab177487, 1:200, Abcam), GFAP (ab7260, 1:500, Abcam), and Tuj1 (ab18207, 1:750, Abcam) to mark mature neurons and glial cells. NeuN and Tuj1 were used as markers of mature and maturing neurons, and GFAP for reactive astrocytes. Tissue sections were placed in a 12-well plate and underwent three washes with TBST (1x TBS, 0.1% Triton X-100) for 10–15 min shaking at room temperature (RT). Sections were blocked (1xTBS, 5% BSA, 1% Triton X-100) for 1 h of shaking at RT, then incubated in primary antibody at RT, and covered from light for 24 h. After three 10-min washes in TBST, secondary antibody was added (ab150063, ab150062, ab150131, ab150106, 1:1000, Abcam), and the tissues were incubated for another 24 h at RT on a covered shaker. When applicable, a third set of washes was followed by 1 h of incubation in DAPI and a final fourth set of washes with TBS to prepare for mounting. Cleared, stained, and washed brain sections were mounted with RIMS solution (40g of Histodenz was diluted in 30 ml of 0.02M phosphate buffer, Sigma Aldrich), on glass slides with an attached 3-mm deep border. Slides were kept at RT and protected from light until ready for imaging, which was within one week of staining to prevent signal degradation.
Imaging and quantification
Mounted slides were visualized and imaged using a ZEISS LSM900 confocal laser scanning microscope, and Zen (Blue) was used to set and capture these images. First, a large cross-sectional tile image of the brain section was created at 10X magnification to create a “map” of the subsequent z-stack images taken over the hippocampal and TBI regions of TBI and SHAM control brains. Boundaries were set, and 16 focus points were distributed, adjusted, and focused in a single light channel. Depending on the immunostaining used, the tile was set to capture each channel with appropriate exposure times in widefield by using the “set exposure” option. Signals for green fluorescence, AF647, AF555, and DAPI stains were captured using the 488nm, 640nm, 561nm, and 405nm lasers, respectively. Individual confocal Z-stacks at 10X magnification were taken along the areas of TBI and hippocampus when visible, as well as the uninjured contralateral hemisphere near the hippocampus (dentate gyrus) and cortical edges. The image size of a 2-dimensional section was 1024 pixels; scan speed was set to 8, bi-lateral direction, 2x averaging. All light channels were set to 1 Airy Unit and individually adjusted for master gain and diode laser intensity (%) as appropriate to maximize image output clarity Z-stack range was from 200–350 µm thick with a 7 µm interval depth. All other parameters were left at default settings.
Following imaging, Zen files were converted and uploaded to IMARIS, where the 3D sections were processed using the Spot tool following background subtraction in all color channels to correct for any autofluorescence in the tissue or background staining. The Spots tool, which uses an approximated average user-input average diameter to identify and count points of greatest light intensity in a single-color channel, was used to calculate the average stained cell count. A 2 µm range of cell sizes in 0.25 µm increments was used to get a distribution of the average count across a range of input diameters for GFAP-stained reactive astrocytes and NeuN-stained maturing neurons in coronal sections. Measurements were done in the two hippocampal dentate gyrus regions in both the right-TBI and left-normal hemispheres, as well as the TBI damage site in the right hemisphere and intact coronal areas of the respective contralateral hemisphere.
IHC staining and cell quantification of macrophages
Brain tissue was processed for immunohistochemical (IHC) staining for rat myeloid M1 and M2 cells and for hematoxylin & eosin (H&E) staining to determine the fate of these cells in TBI and SHAM controls. Coronal sections (n = 200 per rat) from each treatment group (CCI + NSC, CCI + VEH, SHAM + NSC, and SHAM + VEH) were cut and prepared for paraffin slides. Every twentieth slide was H&E stained. Areas demonstrating TBI damage were stained with CD68 (ab283654 for M1, Abcam) and CD163 (ab182422 for M2, Abcam) antibodies. QuPath was used for IHC quantification of CD68 and CD163, with files uploaded in their native NDPI format from the Hamamatsu scanner. Slides were scanned at 20x and produced as brightfield images. The brain area was manually outlined using fill and draw tools. Slides were then analyzed using default positive cell detection parameters for optical density sum, though for CD163 the intensity threshold was modified to 0.85 while CD68 remained at default. Artifacts and areas of darkness due to tissue folding were manually removed by two independent technicians to limit false positive cell counting. For each rat, the hemisphere containing CCI-induced damaged tissue was compared to the contralateral, undamaged side. The main outputs of analysis were highlighted area, total cell count, and total positive cell count.
Multiplex sandwich-based ELISA assays
Multiplexed ELISAs were performed on brains from each CCI group (CCI + VEH, CCI + NSC and SHAM + VEH). Quantibody® Rat Cytokine Array 67 Kit consisted of a combination of 2 non-overlapping arrays (QAR-CYT-3 and QAR-CYT-4, RayBiotech) to quantitatively measure the concentration of 67 rat cytokines and it is suitable for tissue lysate samples. A subset of snap frozen brains from each treatment group were dissected (Fig. S7), tissue lysates were prepared using Lysis Buffer (EL-lysis, RayBiotech) and Protease Inhibitor (AA-PI, RayBiotech) and a hand-held tissue homogenizer (PRO-PK-01200PMGXL, Pro Scientific). Tissues were lysed in 1X solution at the highest setting (level 3) for 2 minutes, then centrifuged to aid in the separation of particulate matter left over from cell debris and portions of analysis of tissue from pure lysate. These lysates were packaged and shipped to RayBiotech Services, where the Quantibody ELISAs were performed. The impact of TBI on cytokine expression was evaluated by comparing tissue samples from the impacted TBI site to the non-impacted contralateral site (Table 1). The proteins that were most affected due to TBI and due to the treatment with NSCs were assessed by the analysis listed in Fig. S4 and S5. The average protein concentration at each site was calculated as the average of both rats per cohort. From these average protein concentrations, the ratio of TBI to contralateral site as well as treated to non-treated rat was calculated. The cytokine concentration ratio of CCI site to contralateral site of the untreated rats (CCI + VEH-R vs CCI + VEH-L) was evaluated to quantify the impact of CCI on cytokine expression. The same methods were used to analyze SHAM + VEH (L) vs SHAM + VEH (R) and compared as controls. The cytokine expression ratio of CCI site in treated rats was compared to the CCI site in untreated rats (CCI + NSC-R vs CCI + VEH-R) to quantify the impact of NSC treatment on the cytokine expression. Mathematically, it was done as below:
$$Change in CCI related cytokines=\left[\frac{Average {cytokine concentration}_{CCI+VEH-R}}{{Average cytokine concentration}_{CCI+VEH-L}}-1\right]\times 100\%$$
1
$$Change in treatment related cytokines=\left[\frac{{Average cytokine concentration}_{CCI+NSC-R}}{{Average cytokine concentration}_{CCI+VEH-R}}-1\right]\times 100\%$$
2
Where the average cytokine concentration at a site is calculated as an average over all the rats in that comparison group. For comparison with controls a similar change in cytokine expression of SHAM + VEH/NSC-R to SHAM + VEH/NSC-L was quantified.
NanoString RNAseq sample preparation and data acquisition
Brain tissue was dissected, and RNA was isolated from snap frozen tissues according to a diagram in figure S7 and half was used for Nanostring analysis and half for protein ELISA assays. RNA expression in the ipsilateral and contralateral hemispheres of NSC and VEH-treated TBI brains was analyzed using the NanoString nCounter platform (NanoString Technologies) by digitally detecting and counting RNA expression in a single reaction without amplification. Each assay included six positive and eight negative RNA assay controls, plus ten mRNA housekeeping controls. RNA was hybridized with the Codeset from the gene panel at 65°C for 16 h. The post-hybridization probe-target mixture was quantified using the nCounter Digital Analyzer, and all data analyses were performed on nSolver (NanoString Technologies). All raw data were first normalized with internal positive and negative controls to eliminate variability unrelated to the samples, then normalized to the selected housekeeping genes using Geometric Means methods. Statistically significant (p < 0.05) and < 2-fold up- or down- regulated genes were analyzed and clustered as described below.
The datasets generated and analyzed during the current study are available in the [GSE242031] repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE242031.