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 |
Keywords
- extracellular RNA
- extracellular vesicles
- lipoprotein
- ribonucleoprotein
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
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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 › peer-review
}
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.
N1 - Funding Information: This publication is part of the NIH Extracellular RNA Communication Consortium paper package and was supported by the NIH Common Fund's exRNA Communication Program. We would like to thank Aileen Fernando, Fabian Flores, and the UCSD Clinical and Translational Research Institute for assisting us with collection of the standardized plasma and serum samples used in this study. We would like to thank Thomas Touboul for assisting us with collection of hESC supernatant for this study. This study was supported by the Extracellular RNA Communication Consortium funded by the NIH Common Fund (NIH UH3TR000906 [S.S. P.D.H. C.D.L. L.D.L. C.M. C.T. L.C.L.], NIH U19179563 [P.S.C. X.Z. L.B. X.O.B.], NIH UH3TR000901 [K.D. R.V.S. B.S. S.D. J.L.]; NIH UH3TR000943 [A.K.S.], NIH UH3TR000890 [P.N. A.P. R.G.]), NIH UH3TR000884 [I.K.Y. T.P.], NIH U19CA179512 [R.L.R.]; NIH U54DA036134 [R.P.A.]) and other funding sources (NIH P01069246 [P.S.C. X.Z. L.B. X.O.B.]; NIH RO1HL122547 [K.D. R.V.S. B.S. S.D. J.L.]; NIH R35CA209904 and CA217685, the American Cancer Society Research Professor Award, and the Frank McGraw Memorial Chair in Cancer Research [A.K.S.]; NIH K23 HL127099 [R.V.S.]; NIH R01HL133575 [R.L.R.]; NIH T32 HD007203 [S.S.]; NIH/NHLBI HL141424 [I.R.]; NIH/NCI CA195204 [E.L. I.R. R.M.]; Thomas Jefferson University Institutional Funds [E.L. I.R. R.M.]). Conceptualization, L.C.L. S.D. A.K.S. T.P. R.G. X.O.B. L.B. R.L.R.; Formal Analysis, L.C.L. A.Y. V.L.M. R.V.S. J.L. I.R. E.L. C.T.; Investigation, S.S. P.S.C. A.C. K.D. P.D.H. J.F. C.D.L. R.M. C.M. V.L.M. P.N. A.P. I.R. R.R. R.V.S. B.S. C.T. D.W. I.K.Y. X.Z. L.B. G.D. E.L. J.L. R.P.A. Data Curation, S.S. L.C.L.; Writing?Original Draft, S.S. V.L.M. R.V.S. E.L. R.L.R. L.C.L.; Writing?Review & Editing, S.S. L.B. X.O.B. R.G. E.L. T.P. R.L.R. A.K.S. S.D. L.C.L.; Visualization, L.D.L. R.P.A. L.C.L.; Supervision, L.B. X.O.B. R.G. E.L. T.P. R.L.R. A.K.S. S.D. L.C.L.; Project Administration, S.S. L.C.L.; Funding Acquisition, X.O.B. R.G. T.P. R.L.R. A.K.S. S.D. L.C.L. S.D. is a founding member of Dyrnamix, which did not play any role in this study and has a patent on extracellular RNA biomarkers for cardiac remodeling. Over the past 12 months, R.V.S. has received funds from Amgen (scientific advisory board), Myokardia (consulting), and Best Doctors (consulting). R.V.S. is a co-inventor on a patent for ex-RNAs signatures of cardiac remodeling. R.G. has been employed by Sanofi Genzyme since September 2017, working on a multiple sclerosis treatment. A.K.S. has the following interests: Advisory board member for Kiyatec and Merck; research funding from M-Trap; stock holder for Biopath; patents for EGFL6 antibodies and siRNA delivery systems. Funding Information: This publication is part of the NIH Extracellular RNA Communication Consortium paper package and was supported by the NIH Common Fund's exRNA Communication Program. We would like to thank Aileen Fernando, Fabian Flores, and the UCSD Clinical and Translational Research Institute for assisting us with collection of the standardized plasma and serum samples used in this study. We would like to thank Thomas Touboul for assisting us with collection of hESC supernatant for this study. This study was supported by the Extracellular RNA Communication Consortium funded by the NIH Common Fund (NIH UH3TR000906 [S.S. P.D.H. C.D.L. L.D.L. C.M. C.T. L.C.L.], NIH U19179563 [P.S.C. X.Z. L.B. X.O.B.], NIH UH3TR000901 [K.D. R.V.S. B.S. S.D. J.L.]; NIH UH3TR000943 [A.K.S.], NIH UH3TR000890 [P.N. A.P. R.G.]), NIH UH3TR000884 [I.K.Y. T.P.], NIH U19CA179512 [R.L.R.]; NIH U54DA036134 [R.P.A.]) and other funding sources (NIH P01069246 [P.S.C. X.Z. L.B. X.O.B.]; NIH RO1HL122547 [K.D. R.V.S. B.S. S.D. J.L.]; NIH R35CA209904 and CA217685, the American Cancer Society Research Professor Award, and the Frank McGraw Memorial Chair in Cancer Research [A.K.S.]; NIH K23 HL127099 [R.V.S.]; NIH R01HL133575 [R.L.R.]; NIH T32 HD007203 [S.S.]; NIH/NHLBI HL141424 [I.R.]; NIH/NCI CA195204 [E.L. I.R. R.M.]; Thomas Jefferson University Institutional Funds [E.L. I.R. R.M.]). Conceptualization, L.C.L. S.D. A.K.S. T.P. R.G. X.O.B. L.B. R.L.R.; Formal Analysis, L.C.L. A.Y. V.L.M. R.V.S. J.L. I.R. E.L. C.T.; Investigation, S.S. P.S.C. A.C. K.D. P.D.H. J.F. C.D.L. R.M. C.M. V.L.M. P.N. A.P. I.R. R.R. R.V.S. B.S. C.T. D.W. I.K.Y. X.Z. L.B. G.D. E.L. J.L. R.P.A. Data Curation, S.S. L.C.L.; Writing—Original Draft, S.S. V.L.M. R.V.S. E.L. R.L.R. L.C.L.; Writing—Review & Editing, S.S. L.B. X.O.B. R.G. E.L. T.P. R.L.R. A.K.S. S.D. L.C.L.; Visualization, L.D.L. R.P.A. L.C.L.; Supervision, L.B. X.O.B. R.G. E.L. T.P. R.L.R. A.K.S. S.D. L.C.L.; Project Administration, S.S. L.C.L.; Funding Acquisition, X.O.B. R.G. T.P. R.L.R. A.K.S. S.D. L.C.L. S.D. is a founding member of Dyrnamix, which did not play any role in this study and has a patent on extracellular RNA biomarkers for cardiac remodeling. Over the past 12 months, R.V.S. has received funds from Amgen (scientific advisory board), Myokardia (consulting), and Best Doctors (consulting). R.V.S. is a co-inventor on a patent for ex-RNAs signatures of cardiac remodeling. R.G. has been employed by Sanofi Genzyme since September 2017, working on a multiple sclerosis treatment. A.K.S. has the following interests: Advisory board member for Kiyatec and Merck; research funding from M-Trap; stock holder for Biopath; patents for EGFL6 antibodies and siRNA delivery systems. Funding Information: This publication is part of the NIH Extracellular RNA Communication Consortium paper package and was supported by the NIH Common Fund’s exRNA Communication Program. We would like to thank Aileen Fernando, Fabian Flores, and the UCSD Clinical and Translational Research Institute for assisting us with collection of the standardized plasma and serum samples used in this study. We would like to thank Thomas Touboul for assisting us with collection of hESC supernatant for this study. This study was supported by the Extracellular RNA Communication Consortium funded by the NIH Common Fund ( NIH UH3TR000906 [S.S., P.D.H., C.D.L., L.D.L., C.M., C.T., L.C.L.], NIH U19179563 [P.S.C., X.Z., L.B., X.O.B.], NIH UH3TR000901 [K.D., R.V.S., B.S., S.D., J.L.]; NIH UH3TR000943 [A.K.S.], NIH UH3TR000890 [P.N., A.P., R.G.]), NIH UH3TR000884 [I.K.Y., T.P.], NIH U19CA179512 [R.L.R.]; NIH U54DA036134 [R.P.A.]) and other funding sources (NIH P01069246 [P.S.C., X.Z., L.B., X.O.B.]; NIH RO1HL122547 [K.D., R.V.S., B.S., S.D., J.L.]; NIH R35CA209904 and CA217685 , the American Cancer Society Research Professor Award, and the Frank McGraw Memorial Chair in Cancer Research [A.K.S.]; NIH K23 HL127099 [R.V.S.]; NIH R01HL133575 [R.L.R.]; NIH T32 HD007203 [S.S.]; NIH/NHLBI HL141424 [I.R.]; NIH/NCI CA195204 [E.L., I.R., R.M.]; Thomas Jefferson University Institutional Funds [E.L., I.R., R.M.]).
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 -