Background
Methods
Exosome isolation and collection from ASCs
Animal model and surgical procedures
Intravenous administration of exosomes and CM
XenoLight DiR for in vivo and ex vivo biodistribution imaging procedures
Behavioral testing
Elevated body swing test (EBST)
Forelimb akinesia
Paw grasp
Brain and organ harvesting, fixation, and sectioning
Measurement of impact and peri-impact area: Nissl staining analysis
RNA sequencing: RNA quality control
Library preparation
Sequencing
Alignment to genome
ncRNA counting and annotation
Fold change calculations
Hierarchical clustering
Real-time qPCR using SYBR green
Results
Exosome treatment improves motor impairment and reduces lesion volume in a MALAT1-dependent manner
Imaging of exosomes in vivo shows distribution primarily to the abdomen and head regions
Imaging of exosomes ex vivo in organs shows localization primarily to the spleen and brain
RNA sequencing transcriptome analysis identifies cellular processes crucial to recovery that are specifically mediated by MALAT1
RNA Seq of the brain and spleen transcriptome identifies genes affected by TBI and treatment with exosomes
Gene expression patterns following treatment with hASC exosomes
Brain | |
Pattern 1 | |
Pancreatic adenocarcinoma signaling | |
Role of CHK proteins in cell cycle checkpoint control | |
T helper cell differentiation | |
Cyclins and cell cycle regulation | |
Th1 pathway | |
Bladder cancer signaling | |
Inhibition of angiogenesis by TSP1 | |
Dopamine receptor signaling | |
ILK signaling | |
B cell development | |
Cell cycle regulation by BTG family proteins | |
Inhibition of matrix metalloproteases | |
Thyroid cancer signaling | |
HIF1α signaling | |
Crosstalk between dendritic cells and natural killer cells | |
Th1 and Th2 activation pathway | |
Role of JAK family kinases in IL-6-type cytokine signaling | |
Role of JAK1 and JAK3 in γc cytokine signaling | |
Role of Oct4 in mammalian embryonic stem cell pluripotency | |
Autoimmune thyroid disease signaling | |
Spleen | |
Pattern 1 | Pattern − 1 |
Heme biosynthesis II | cAMP-mediated signaling |
Mitotic roles of polo-like kinase | G-Protein coupled receptor signaling |
Heme biosynthesis from uroporphyrinogen-III I | Serine biosynthesis |
Tetrapyrrole biosynthesis II | Superpathway of serine and glycine biosynthesis I |
Estrogen-mediated S-phase entry | LPS/IL-1-mediated inhibition of RXR function |
GADD45 signaling | Protein kinase A signaling |
Cell cycle: G2/M DNA damage checkpoint regulation | Cardiac hypertrophy signaling |
Cyclins and cell cycle regulation | Fatty acid activation |
dTMP de novo biosynthesis | nNOS signaling in skeletal muscle cells |
Cell cycle control of chromosomal replication | Corticotropin releasing hormone signaling |
DNA damage-induced 14-3-3σ signaling | |
Rapoport-Luebering glycolytic shunt | |
Pyrimidine deoxyribonucleotides de novo biosynthesis I | |
ATM signaling | |
Antiproliferative role of TOB in T cell signaling | |
Role of CHK proteins in cell cycle checkpoint control | |
Cell cycle: G1/S checkpoint regulation | |
Cell cycle regulation by BTG family proteins | |
Asparagine biosynthesis I | |
γ-Glutamyl cycle |
Brain mRNA changes
Spleen mRNA expression
Validation of RNA Seq results of gene expression
Noncoding RNA levels change with injury and exosome treatment in a MALAT1-dependent manner
Brain + 1 | Spleen + 1 | ||||||||
C vs T | C vs TE | C vs TEdM | C vs T | C vs TE | C vs TEdM | ||||
rno-miR-429 | 346.52 | 26.50 | 208.76 | rno-miR-451-3p | 3.70 | − 1.15 | 4.82 | ||
rno-miR-200b-5p | 99.01 | 7.42 | 127.07 | rno-miR-1949 | 1.78 | − 1.05 | 1.45 | ||
rno-miR-183-5p | 59.14 | 6.56 | 122.37 | rno-miR-6216 | 1.38 | − 1.22 | 1.30 | ||
rno-miR-182 | 56.38 | 1.00 | 43.57 | rno-miR-17-5p | 1.51 | − 1.13 | 1.52 | ||
rno-miR-96-5p | 48.13 | 1.00 | 61.72 | rno-miR-144-5p | 3.85 | 2.01 | 4.19 | ||
rno-miR-6216 | 2.67 | − 1.04 | 2.82 | rno-miR-484 | 1.52 | − 1.10 | 1.88 | ||
rno-miR-1193-3p | 1.34 | 1.03 | 1.20 | rno-miR-132-3p | 2.07 | 1.01 | 1.83 | ||
rno-miR-218a-2-3p | 1.24 | 1.07 | 1.30 | rno-miR-702-3p | 4.89 | 2.44 | 3.59 | ||
rno-miR-409a-5p | 1.85 | 1.04 | 1.84 | ||||||
rno-miR-92a-3p | 1.33 | − 1.08 | 1.29 | ||||||
rno-miR-339-5p | 1.39 | − 1.07 | 1.30 | ||||||
rno-miR-93-5p | 1.53 | 1.07 | 1.74 | ||||||
rno-miR-361-5p | 1.30 | − 1.01 | 1.50 | ||||||
rno-miR-31a-5p | 1.18 | − 1.13 | 1.30 | ||||||
rno-miR-21-3p | 1.29 | − 1.07 | 1.31 | ||||||
rno-miR-423-5p | 1.19 | − 1.10 | 1.26 | ||||||
rno-miR-210-3p | 1.35 | 1.11 | 1.45 | ||||||
rno-miR-532-3p | 1.25 | 1.11 | 1.26 | ||||||
rno-miR-103-3p | 1.18 | − 1.01 | 1.24 | ||||||
rno-miR-6319 | 1.39 | 1.12 | 1.27 | ||||||
rno-miR-378a-5p | 1.10 | 1.05 | 1.17 | ||||||
rno-miR-342-3p | 1.06 | − 1.05 | 1.09 | ||||||
Brain −1 | Spleen −1 | ||||||||
rno-miR-154-5p | − 1.48 | −1.17 | − 1.32 | rno-miR-708-3p | − 10.9 | 1.69 | − 1.39 | ||
rno-miR-7b | − 1.65 | −1.04 | − 1.80 | rno-miR-6329 | − 3.33 | − 1.07 | − 1.57 | ||
rno-miR-665 | − 2.57 | −1.11 | − 1.69 | rno-miR-148b-5p | − 1.22 | 1.14 | − 1.10 | ||
rno-miR-487b-3p | − 1.38 | 1.32 | − 1.54 | rno-miR-212-5p | − 1.44 | − 1.09 | − 2.17 | ||
rno-miR-672-3p | − 1.77 | 1.09 | − 1.41 | rno-miR-181a-1-3p | − 1.55 | 1.23 | − 1.16 | ||
rno-miR-10a-5p | − 1.47 | 1.29 | − 1.29 | rno-miR-1843b-5p | − 1.79 | 1.07 | − 1.37 | ||
rno-miR-770-5p | − 1.53 | 1.12 | − 1.60 | rno-miR-10a-5p | − 1.49 | 1.16 | − 1.22 | ||
rno-miR-666-5p | − 1.29 | 1.24 | − 1.32 | rno-miR-379-5p | − 1.92 | − 1.01 | − 1.32 | ||
rno-miR-29c-3p | − 1.52 | 1.07 | − 1.22 | rno-miR-411-5p | − 1.66 | − 1.12 | − 2.09 | ||
rno-miR-3594-3p | − 1.61 | − 1.04 | − 1.37 | rno-miR-192-5p | − 1.72 | 1.01 | − 1.80 | ||
rno-miR-485-3p | − 1.41 | − 1.13 | − 1.32 | rno-let-7f-5p | − 1.58 | 1.12 | − 1.20 | ||
rno-miR-139-3p | − 1.45 | 1.02 | − 1.27 | rno-miR-1b | − 1.53 | 1.14 | − 1.37 | ||
rno-miR-139-5p | − 1.54 | − 1.09 | − 1.41 | rno-miR-148a-3p | − 1.40 | − 1.10 | − 1.20 | ||
rno-miR-668 | − 1.19 | 1.12 | − 1.20 | rno-miR-126a-5p | − 1.46 | 1.09 | − 1.47 | ||
rno-miR-342-5p | − 1.15 | 1.10 | − 1.11 | rno-miR-28-5p | − 1.39 | 1.08 | − 1.30 | ||
rno-miR-344a-3p | − 1.18 | 1.01 | − 1.21 | rno-miR-204-5p | − 1.47 | 1.00 | − 1.20 | ||
rno-miR-330-3p | − 1.30 | − 1.05 | − 1.19 | rno-miR-181c-3p | − 1.67 | − 1.14 | − 1.42 | ||
rno-miR-1843a-3p | − 1.13 | 1.01 | − 1.16 | rno-miR-3068-3p | − 1.58 | − 1.08 | − 1.24 | ||
rno-miR-328a-3p | − 1.18 | − 1.08 | − 1.18 | rno-miR-30c-5p | − 1.41 | 1.03 | − 1.15 | ||
rno-miR-27a-3p | − 1.16 | 1.06 | − 1.21 | ||||||
rno-miR-139-5p | − 1.33 | − 1.07 | − 1.24 | ||||||
rno-miR-140-5p | − 1.30 | 1.06 | − 1.25 | ||||||
rno-miR-337-5p | − 1.42 | − 1.05 | − 1.34 | ||||||
rno-miR-30a-5p | − 1.16 | 1.03 | − 1.08 | ||||||
rno-miR-150-5p | − 1.29 | − 1.10 | − 1.16 | ||||||
rno-miR-147 | − 1.12 | 1.04 | − 1.09 | ||||||
rno-miR-30e-5p | − 1.24 | − 1.08 | − 1.14 | ||||||
ncRNA including snoRNA, snRNA | |||||||||
Brain + 1 | Brain − 1 | ||||||||
C vsT | C vs TE | C vs TEdM | C vsT | C vs TE | C vs TEdM | ||||
snRNA | U6 | 1.57 | 1.00 | 1.37 | snoRNA | SNORD42 | − 1.90 | − 1.24 | − 1.82 |
snoRNA | SNORD24 | 1.28 | 1.11 | 1.38 | lncRNA | PVT1 3 | − 1.98 | − 1.34 | − 2.18 |
snoRNA | SNORD60 | 1.25 | 1.00 | 1.22 | snoRNA | SNORA28 | − 1.29 | − 1.07 | − 1.97 |
snRNA | U6 | 1.09 | 1.00 | 1.06 | rRNA | Rnr2 | − 1.25 | − 1.07 | − 1.23 |
snoRNA | ACEA U3 | 1.64 | 1.05 | 1.59 | rRNA | Rnr2 | − 1.09 | − 1.10 | − 1.29 |
snoRNA | SNORA62 | 1.51 | − 1.04 | 1.27 | lncRNA | RMST 2 | − 1.19 | − 1.06 | − 1.13 |
snoRNA | SNORA73 | 1.39 | − 1.24 | 1.30 | |||||
snoRNA | SNORD62 | 1.76 | − 1.21 | 1.32 | |||||
snoRNA | SNORD15 | 3.17 | 1.38 | 3.12 | |||||
snoRNA | SNORA38 | 1.06 | − 1.00 | 1.06 | |||||
Spleen + 1 | Spleen − 1 | ||||||||
snoRNA | SNORD74 | 1.85 | − 1.39 | 1.52 | snoRNA | SNORA41 | − 3.84 | − 1.14 | − 1.85 |
snRNA | U6 | 1.67 | − 1.27 | 1.67 | snoRNA | SNORD33 | − 3.68 | − 1.64 | − 3.91 |
snoRNA | SNORD75 | 1.68 | − 1.03 | 1.50 | snoRNA | SNORA54 | − 3.49 | 1.06 | − 1.98 |
scRNA | 1.32 | − 1.23 | 1.14 | snoRNA | SNORD21 | − 3.48 | − 1.48 | − 3.88 | |
lncRNA | LOC100909539 | 1.37 | − 1.06 | 1.48 | snoRNA | SNORA71 | − 2.94 | − 1.55 | − 3.67 |
misc_RNA | 1.31 | 1.10 | 1.42 | vault_RNA | Vault | − 2.93 | − 1.49 | − 5.34 | |
lncRNA | Bc1 | 1.15 | 1.04 | 1.25 | snoRNA | SNORA11 | − 2.71 | − 1.08 | − 2.24 |