Profiling Extracellular Long RNA Transcriptome in Human Plasma and Extracellular Vesicles for Biomarker Discovery

Rodosthenis S Rodosthenous; Elizabeth Hutchins; Rebecca Reiman; Ashish S Yeri; Srimeenakshi Srinivasan; Timothy G Whitsett; Ionita Ghiran; Michael G Silverman; Louise C Laurent; Kendall Van Keuren-Jensen; Saumya Das

doi:10.1016/j.isci.2020.101182

Profiling Extracellular Long RNA Transcriptome in Human Plasma and Extracellular Vesicles for Biomarker Discovery

iScience. 2020 Jun 26;23(6):101182. doi: 10.1016/j.isci.2020.101182. Epub 2020 May 18.

Affiliations

¹ Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Simches 3(rd) Floor, Boston, MA 02114, USA.
² Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA.
³ Department of Obstetrics, Gynecology, and Reproductive Sciences, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
⁴ Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
⁵ Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA. Electronic address: kjensen@tgen.com.
⁶ Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Simches 3(rd) Floor, Boston, MA 02114, USA. Electronic address: sdas@mgh.harvard.edu.

Abstract

The recent discovery of extracellular RNAs in blood, including RNAs in extracellular vesicles (EVs), combined with low-input RNA-sequencing advances have enabled scientists to investigate their role in human disease. To date, most studies have been focusing on small RNAs, and methodologies to optimize long RNAs measurement are lacking. We used plasma RNA to assess the performance of six long RNA sequencing methods, at two different sites, and we report their differences in reads (%) mapped to the genome/transcriptome, number of genes detected, long RNA transcript diversity, and reproducibility. Using the best performing method, we further compare the profile of long RNAs in the EV- and no-EV-enriched RNA plasma compartments. These results provide insights on the performance and reproducibility of commercially available kits in assessing the landscape of long RNAs in human plasma and different extracellular RNA carriers that may be exploited for biomarker discovery.

Keywords: Medical Laboratory Technology; Omics; Transcriptomics.

Grants and funding

T32 HD007203/HD/NICHD NIH HHS/United States