Osteoblastogenesis Alters Small RNA Profiles in EVs Derived from Bone Marrow Stem Cells (BMSCs) and Adipose Stem Cells (ASCs)
Abstract
:1. Introduction
2. Experimental Section
2.1. Cell Culture and Osteoblastic Differentiation
2.2. EV Purification
2.3. Nanoparticle Tracking Analysis (NTA) of EVs
2.4. Western Blotting of EVs
2.5. RNA Extraction
2.6. Small RNA Library Preparation and Sequencing
2.7. Raw Data Processing
3. Results
3.1. Characterization of EVs from BMSCs and ASCs
3.2. Small RNA Profiles of MSCs and MSC-EVs
3.3. Osteoblastic Differentiation Alters miRNA Expression in MSCs and MSC-EVs
3.4. Differential tsRNA Expression
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sample | miRNA Name | BaseMean | Log2Fold Change | Sample | miRNA Name | BaseMean | Log2Fold Change |
---|---|---|---|---|---|---|---|
ASC cells | hsa-let-7i-3p | 479 | −1.6 | BMSC cells | hsa-let-7i-3p | 427 | −1.0 |
hsa-miR-146b-5p | 20821 | 2.1 | hsa-miR-146b-5p | 3630 | −1.1 | ||
hsa-miR-1908-5p | 39 | 1.5 | hsa-miR-1908-5p | 31 | 1.7 | ||
hsa-miR-210-3p | 1191 | −2.8 | hsa-miR-210-3p | 1236 | −1.7 | ||
hsa-miR-210-5p | 89 | −2.9 | hsa-miR-210-5p | 104 | −1.5 | ||
hsa-miR-222-5p | 151 | −1.5 | hsa-miR-222-5p | 443 | 1.0 | ||
hsa-miR-335-3p | 1681 | −4.0 | hsa-miR-335-3p | 3536 | −2.6 | ||
hsa-miR-335-5p | 1248 | −3.5 | hsa-miR-335-5p | 2835 | −1.7 | ||
hsa-miR-6842-3p | 281 | 2.2 | hsa-miR-6842-3p | 65 | 3.8 | ||
hsa-miR-95-3p | 172 | 6.2 | hsa-miR-95-3p | 21 | 5.0 | ||
ASC cells | hsa-miR-125b-2-3p | 808 | 1.1 | ASC-EVs | hsa-miR-425-5p | 15 | −4.8 |
hsa-miR-425-5p | 1440 | 1.1 | hsa-miR-125b-2-3p | 29 | 4.7 | ||
BMSC cells | hsa-miR-133a-3p | 120 | 1.3 | BMSC-EVs | hsa-miR-133a-3p | 15 | 7.1 |
hsa-miR-146a-5p | 86 | −1.1 | hsa-miR-146a-5p | 26 | −3.9 | ||
hsa-miR-146b-5p | 3630 | −1.1 | hsa-miR-146b-5p | 1450 | −2.2 | ||
hsa-miR-155-5p | 871 | −1.4 | hsa-miR-155-5p | 183 | −1.1 | ||
hsa-miR-378a-3p | 2747 | −1.4 | hsa-miR-378a-3p | 1026 | −1.9 | ||
hsa-miR-483-5p | 168 | 8.5 | hsa-miR-483-5p | 20 | 7.5 |
miRNA Name | BaseMean | Log2FoldChange |
---|---|---|
hsa-miR-10b-5p | 172,238 | −1.1 |
hsa-miR-10a-5p | 71,894 | −2.0 |
hsa-miR-22-3p | 44,127 | 1.3 |
hsa-miR-191-5p | 30,963 | −1.4 |
hsa-miR-486-5p | 22,431 | −1.2 |
hsa-miR-100-5p | 20,117 | −1.1 |
hsa-miR-146b-5p | 1450 | −2.2 |
hsa-miR-378a-3p | 1026 | −1.9 |
hsa-let-7d-5p | 908 | 1.2 |
hsa-miR-30c-5p | 370 | 1.3 |
hsa-miR-155-5p | 183 | −1.1 |
hsa-let-7d-3p | 168 | 1.3 |
hsa-miR-12136 | 94 | −2.3 |
hsa-miR-1910-5p | 82 | 9.5 |
hsa-miR-4516 | 81 | −3.0 |
hsa-miR-877-5p | 42 | 2.0 |
hsa-miR-146a-5p | 26 | −3.9 |
hsa-miR-483-5p | 20 | 7.5 |
hsa-miR-133a-3p | 15 | 7.1 |
hsa-miR-3180-3p | 14 | −7.6 |
hsa-miR-34b-5p | 10 | 6.5 |
miRNA Name | BaseMean | Log2FoldChange |
---|---|---|
hsa-miR-769-5p | 20 | −3.7 |
hsa-miR-425-5p | 15 | −4.8 |
hsa-miR-125b-2-3p | 29 | 4.7 |
hsa-miR-145-5p | 97 | −5.9 |
Sample | tRNAs | Percentage of Total Reads Mapped to tRNAs | Sample | tRNAs | Percentage of Total Reads Mapped to tRNAs |
---|---|---|---|---|---|
ASCs | Gly-GCC | 34.59% | BMSCs | Gly-GCC | 26.99% |
Val-AAC | 15.97% | Val-CAC | 8.46% | ||
Val-CAC | 15.93% | Val-AAC | 7.41% | ||
ASC-Evs | Gly-GCC | 54.59% | BMSC-Evs | Val-CAC | 43.17% |
Glu-CTC | 16.14% | Val-AAC | 33.07% | ||
Gly-CCC | 16.09% | Gly-GCC | 13.07% |
Sample | tRNAs | BaseMean | Log2FoldChange | Note |
---|---|---|---|---|
BMSC-EVs | Ser-ACT | 15 | 5.4 | fragment |
Ser-GCT | 753 | 2.0 | fragment | |
Sup-TTA | 35 | 3.9 | fragment | |
Phe-GAA | 826 | 2.2 | fragment | |
Ile-AAT | 545 | 2.8 | fragment | |
Lys-TTT | 4439 | 1.4 | fragment | |
Gly-CCC | 236570 | −2.9 | halve | |
Leu-TAG | 393 | 1.9 | fragment | |
Gly-GCC | 804325 | −2.8 | halve | |
His-GTG | 22356 | −2.5 | halve | |
Thr-CGT | 234 | 2.1 | fragment | |
ASC-EVs | Arg-CCG | 204 | −3.5 | halve |
Phe-GAA | 826 | −3.0 | fragment | |
Asn-GTT | 147 | 2.8 | fragment | |
Ile-AAT | 545 | 2.6 | fragment | |
Ala-TGC | 1188 | 2.7 | fragment |
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Yan, Y.; Chang, C.; Su, J.; Venø, M.T.; Kjems, J. Osteoblastogenesis Alters Small RNA Profiles in EVs Derived from Bone Marrow Stem Cells (BMSCs) and Adipose Stem Cells (ASCs). Biomedicines 2020, 8, 387. https://doi.org/10.3390/biomedicines8100387
Yan Y, Chang C, Su J, Venø MT, Kjems J. Osteoblastogenesis Alters Small RNA Profiles in EVs Derived from Bone Marrow Stem Cells (BMSCs) and Adipose Stem Cells (ASCs). Biomedicines. 2020; 8(10):387. https://doi.org/10.3390/biomedicines8100387
Chicago/Turabian StyleYan, Yan, Clare Chang, Junyi Su, Morten T. Venø, and Jørgen Kjems. 2020. "Osteoblastogenesis Alters Small RNA Profiles in EVs Derived from Bone Marrow Stem Cells (BMSCs) and Adipose Stem Cells (ASCs)" Biomedicines 8, no. 10: 387. https://doi.org/10.3390/biomedicines8100387