Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation

Srimeenakshi Srinivasan, Ashish Yeri, Pike See Cheah, Allen Chung, Kirsty Danielson, Peter De Hoff, Justyna Filant, Clara D. Laurent, Lucie D. Laurent, Rogan Magee, Courtney Moeller, Venkatesh L. Murthy, Parham Nejad, Anu Paul, Isidore Rigoutsos, Rodosthenis Rodosthenous, Ravi V. Shah, Bridget Simonson, Cuong To, David WongIrene K. Yan, Xuan Zhang, Leonora Balaj, Xandra O. Breakefield, George Daaboul, Roopali Gandhi, Jodi Lapidus, Eric Londin, Tushar Patel, Robert L. Raffai, Anil K. Sood, Roger P. Alexander, Saumya Das, Louise C. Laurent

Research output: Contribution to journal › Article

16 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)446-462.e16
JournalCell
Volume177
Issue number2
DOIs
StatePublished - Apr 4 2019

Fingerprint

RNA Sequence Analysis
RNA
MicroRNAs
Research Personnel
Ribonucleoproteins
Biomarkers
HDL Lipoproteins
Set theory
Statistics

Keywords

  • extracellular RNA
  • extracellular vesicles
  • lipoprotein
  • ribonucleoprotein

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Srinivasan, S., Yeri, A., Cheah, P. S., Chung, A., Danielson, K., De Hoff, P., ... Laurent, L. C. (2019). Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation. Cell, 177(2), 446-462.e16. https://doi.org/10.1016/j.cell.2019.03.024

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

Srinivasan, S, Yeri, A, Cheah, PS, Chung, A, Danielson, K, De Hoff, P, Filant, J, Laurent, CD, Laurent, LD, Magee, R, Moeller, C, Murthy, VL, Nejad, P, Paul, A, Rigoutsos, I, Rodosthenous, R, Shah, RV, Simonson, B, To, C, Wong, D, Yan, IK, Zhang, X, Balaj, L, Breakefield, XO, Daaboul, G, Gandhi, R, Lapidus, J, Londin, E, Patel, T, Raffai, RL, Sood, AK, Alexander, RP, Das, S & Laurent, LC 2019, 'Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation', Cell, vol. 177, no. 2, pp. 446-462.e16. https://doi.org/10.1016/j.cell.2019.03.024
Srinivasan S, Yeri A, Cheah PS, Chung A, Danielson K, De Hoff P et al. Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation. Cell. 2019 Apr 4;177(2):446-462.e16. https://doi.org/10.1016/j.cell.2019.03.024
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. / Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation. In: Cell. 2019 ; Vol. 177, No. 2. pp. 446-462.e16.
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AU - Moeller, Courtney

AU - Murthy, Venkatesh L.

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AU - Shah, Ravi V.

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AU - To, Cuong

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AU - Daaboul, George

AU - Gandhi, Roopali

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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.

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