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 Wong; Irene 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

doi:10.1016/j.cell.2019.03.024

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

Cell. 2019 Apr 4;177(2):446-462.e16. doi: 10.1016/j.cell.2019.03.024.

Authors

Srimeenakshi Srinivasan¹, Ashish Yeri², Pike See Cheah³, Allen Chung⁴, Kirsty Danielson², Peter De Hoff¹, Justyna Filant⁵, Clara D Laurent⁶, Lucie D Laurent¹, Rogan Magee⁷, Courtney Moeller¹, Venkatesh L Murthy⁸, Parham Nejad⁹, Anu Paul⁹, Isidore Rigoutsos⁷, Rodosthenis Rodosthenous², Ravi V Shah², Bridget Simonson², Cuong To¹, David Wong⁴, Irene K Yan¹⁰, Xuan Zhang¹¹, Leonora Balaj¹², Xandra O Breakefield¹¹, George Daaboul¹³, Roopali Gandhi⁹, Jodi Lapidus¹⁴, Eric Londin⁷, Tushar Patel¹⁰, Robert L Raffai⁴, Anil K Sood¹⁵, Roger P Alexander¹⁶, Saumya Das², Louise C Laurent¹⁷

Affiliations

¹ Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.
² Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
³ Neurology and Radiology Services and Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA; Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Malaysia.
⁴ Department of Surgery, University of California, San Francisco and VA Medical Center San Francisco, San Francisco, CA 94121, USA.
⁵ Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
⁶ Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
⁷ Computational Medicine Center, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA, USA.
⁸ Department of Medicine, Division of Cardiovascular Medicine, Frankel Cardiovascular Center, University of Michigan, Ann Arbor, MI, USA.
⁹ Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
¹⁰ Mayo Clinic Florida, Jacksonville, FL, USA.
¹¹ Neurology and Radiology Services and Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.
¹² Neurology and Radiology Services and Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA; Department of Neurosurgery, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.
¹³ NanoView Biosciences, Boston, MA, USA.
¹⁴ Oregon Health Sciences University, Portland, OR, USA.
¹⁵ Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
¹⁶ Pacific Northwest Research Institute, Seattle, WA 98122, USA.
¹⁷ Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA. Electronic address: [email protected].

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.

Keywords: extracellular RNA; extracellular vesicles; lipoprotein; ribonucleoprotein.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Adult
Body Fluids / chemistry
Cell Line
Cell-Free Nucleic Acids / isolation & purification*
Circulating MicroRNA / isolation & purification*
Extracellular Vesicles / metabolism
Female
Healthy Volunteers
Humans
Male
MicroRNAs / isolation & purification
MicroRNAs / metabolism
RNA / isolation & purification*
RNA / metabolism
Reproducibility of Results
Sequence Analysis, RNA / methods

Substances

Cell-Free Nucleic Acids
Circulating MicroRNA
MicroRNAs
RNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding