Abstract
Poor reproducibility within and across studies arising from lack of knowledge regarding the performance of extracellular RNA (exRNA) isolation methods has hindered progress in the exRNA field. A systematic comparison of 10 exRNA isolation methods across 5 biofluids revealed marked differences in the complexity and reproducibility of the resulting small RNA-seq profiles. The relative efficiency with which each method accessed different exRNA carrier subclasses was determined by estimating the proportions of extracellular vesicle (EV)-, ribonucleoprotein (RNP)-, and high-density lipoprotein (HDL)-specific miRNA signatures in each profile. An interactive web-based application (miRDaR) was developed to help investigators select the optimal exRNA isolation method for their studies. miRDar provides comparative statistics for all expressed miRNAs or a selected subset of miRNAs in the desired biofluid for each exRNA isolation method and returns a ranked list of exRNA isolation methods prioritized by complexity, expression level, and reproducibility. These results will improve reproducibility and stimulate further progress in exRNA biomarker development. A systematic comparison of 10 extracellular RNA isolation methods across 5 biofluids will aid researchers in selecting optimal approaches for individual studies with the overall goal of enhancing reliability and reproducibility for a rapidly growing field.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 446-462.e16 |
| Journal | Cell |
| Volume | 177 |
| Issue number | 2 |
| DOIs | |
| State | Published - Apr 4 2019 |
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Keywords
- extracellular RNA
- extracellular vesicles
- lipoprotein
- ribonucleoprotein
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
Cite this
Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation. / Srinivasan, Srimeenakshi; Yeri, Ashish; Cheah, Pike See; Chung, Allen; Danielson, Kirsty; De Hoff, Peter; Filant, Justyna; Laurent, Clara D.; Laurent, Lucie D.; Magee, Rogan; Moeller, Courtney; Murthy, Venkatesh L.; Nejad, Parham; Paul, Anu; Rigoutsos, Isidore; Rodosthenous, Rodosthenis; Shah, Ravi V.; Simonson, Bridget; To, Cuong; Wong, David; Yan, Irene K.; Zhang, Xuan; Balaj, Leonora; Breakefield, Xandra O.; Daaboul, George; Gandhi, Roopali; Lapidus, Jodi; Londin, Eric; Patel, Tushar; Raffai, Robert L.; Sood, Anil K.; Alexander, Roger P.; Das, Saumya; Laurent, Louise C.
In: Cell, Vol. 177, No. 2, 04.04.2019, p. 446-462.e16.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation
AU - Srinivasan, Srimeenakshi
AU - Yeri, Ashish
AU - Cheah, Pike See
AU - Chung, Allen
AU - Danielson, Kirsty
AU - De Hoff, Peter
AU - Filant, Justyna
AU - Laurent, Clara D.
AU - Laurent, Lucie D.
AU - Magee, Rogan
AU - Moeller, Courtney
AU - Murthy, Venkatesh L.
AU - Nejad, Parham
AU - Paul, Anu
AU - Rigoutsos, Isidore
AU - Rodosthenous, Rodosthenis
AU - Shah, Ravi V.
AU - Simonson, Bridget
AU - To, Cuong
AU - Wong, David
AU - Yan, Irene K.
AU - Zhang, Xuan
AU - Balaj, Leonora
AU - Breakefield, Xandra O.
AU - Daaboul, George
AU - Gandhi, Roopali
AU - Lapidus, Jodi
AU - Londin, Eric
AU - Patel, Tushar
AU - Raffai, Robert L.
AU - Sood, Anil K.
AU - Alexander, Roger P.
AU - Das, Saumya
AU - Laurent, Louise C.
PY - 2019/4/4
Y1 - 2019/4/4
N2 - Poor reproducibility within and across studies arising from lack of knowledge regarding the performance of extracellular RNA (exRNA) isolation methods has hindered progress in the exRNA field. A systematic comparison of 10 exRNA isolation methods across 5 biofluids revealed marked differences in the complexity and reproducibility of the resulting small RNA-seq profiles. The relative efficiency with which each method accessed different exRNA carrier subclasses was determined by estimating the proportions of extracellular vesicle (EV)-, ribonucleoprotein (RNP)-, and high-density lipoprotein (HDL)-specific miRNA signatures in each profile. An interactive web-based application (miRDaR) was developed to help investigators select the optimal exRNA isolation method for their studies. miRDar provides comparative statistics for all expressed miRNAs or a selected subset of miRNAs in the desired biofluid for each exRNA isolation method and returns a ranked list of exRNA isolation methods prioritized by complexity, expression level, and reproducibility. These results will improve reproducibility and stimulate further progress in exRNA biomarker development. A systematic comparison of 10 extracellular RNA isolation methods across 5 biofluids will aid researchers in selecting optimal approaches for individual studies with the overall goal of enhancing reliability and reproducibility for a rapidly growing field.
AB - Poor reproducibility within and across studies arising from lack of knowledge regarding the performance of extracellular RNA (exRNA) isolation methods has hindered progress in the exRNA field. A systematic comparison of 10 exRNA isolation methods across 5 biofluids revealed marked differences in the complexity and reproducibility of the resulting small RNA-seq profiles. The relative efficiency with which each method accessed different exRNA carrier subclasses was determined by estimating the proportions of extracellular vesicle (EV)-, ribonucleoprotein (RNP)-, and high-density lipoprotein (HDL)-specific miRNA signatures in each profile. An interactive web-based application (miRDaR) was developed to help investigators select the optimal exRNA isolation method for their studies. miRDar provides comparative statistics for all expressed miRNAs or a selected subset of miRNAs in the desired biofluid for each exRNA isolation method and returns a ranked list of exRNA isolation methods prioritized by complexity, expression level, and reproducibility. These results will improve reproducibility and stimulate further progress in exRNA biomarker development. A systematic comparison of 10 extracellular RNA isolation methods across 5 biofluids will aid researchers in selecting optimal approaches for individual studies with the overall goal of enhancing reliability and reproducibility for a rapidly growing field.
KW - extracellular RNA
KW - extracellular vesicles
KW - lipoprotein
KW - ribonucleoprotein
UR - http://www.scopus.com/inward/record.url?scp=85063279270&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85063279270&partnerID=8YFLogxK
U2 - 10.1016/j.cell.2019.03.024
DO - 10.1016/j.cell.2019.03.024
M3 - Article
C2 - 30951671
AN - SCOPUS:85063279270
VL - 177
SP - 446-462.e16
JO - Cell
JF - Cell
SN - 0092-8674
IS - 2
ER -