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| Status |
Public on May 14, 2020 |
| Title |
Small RNA sequencing of human and macaque brain tissue and brain-derived extracellular vesicles separated by size exclusion chromatography |
| Organisms |
Macaca nemestrina; Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Extracellular vesicles (EVs) are involved in a wide range of physiological and pathological processes by shuttling material out of and between cells. Tissue EVs may thus lend insights into disease mechanisms and also betray disease when released into easily accessed biological fluids. Since brain-derived EVs (bdEVs) and their cargo may serve as biomarkers of neurodegenerative diseases, we evaluated modifications to a published, rigorous protocol for separation of EVs from brain tissue and studied effects of processing variables on quantitative and qualitative outcomes. To this end, size exclusion chromatography (SEC) and sucrose density gradient ultracentrifugation were compared as final separation steps in protocols involving stepped ultracentrifugation. bdEVs were separated from brain tissues of human, macaque. Effects of post-mortem interval (PMI) before final bdEV separation were probed. MISEV2018-compliant EV characterization was performed, and both small RNA and protein profiling were done. We conclude that the modified, SEC-employing protocol achieves EV separation efficiency roughly similar to a protocol using gradient density ultracentrifugation, while decreasing operator time and, potentially, variability. The protocol appears to yield bdEVs of higher purity for human tissues compared with macaque, suggesting opportunities for optimization. The interval between death/tissue storage/processing and final bdEV separation can also affect bdEV populations and composition and should thus be recorded for rigorous reporting. Different populations of EVs obtained through the modified method reported herein display characteristic RNA and protein content that hint at biomarker potential. To conclude, this study finds that the automatable and increasingly employed technique of SEC can be applied to tissue EV separation, and also reveals more about the importance of species-specific and technical considerations when working with tissue EVs. These results are expected to enhance the use of bdEVs in revealing and understanding brain disease.
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| Overall design |
Total RNA was extracted from brain tissue (BH), a minimally processed 10,000 x g centrifuge pellet (10K) following tissue extraction, and size exclusion chromatography-based separation of extracellular vesicles from 10K supernatant (EVs). Macaque brain tissues were also placed at room temperature for 2 hours and 6 hours before EV separation to assess the effect of time on EV separation.
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| Web link |
https://doi.org/10.1080/20013078.2020.1785746
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| Contributor(s) |
Huang Y, Witwer KW, Hill AF, Cheng L, Turchinovich A |
| Citation(s) |
32944174 |
| |
| Submission date |
May 13, 2020 |
| Last update date |
Sep 21, 2020 |
| Contact name |
Kenneth W. Witwer |
| E-mail(s) |
kwitwer1@jhmi.edu
|
| Phone |
4109559770
|
| Organization name |
Johns Hopkins University School of Medicine
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| Department |
Department of Molecular and Comparative Pathobiology
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| Street address |
733 N. Broadway
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platforms (2) |
| GPL23934 |
Ion Torrent S5 (Homo sapiens) |
| GPL28533 |
Ion Torrent S5 (Macaca nemestrina) |
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| Samples (29)
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| Relations |
| BioProject |
PRJNA632491 |
| SRA |
SRP261401 |
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