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. 2022 Jan 3:12:778416.
doi: 10.3389/fgene.2021.778416. eCollection 2021.

Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop

Roger P Alexander  1 , Robert R Kitchen  2 , Juan Pablo Tosar  3 , Matthew Roth  4 , Pieter Mestdagh  5 , Klaas E A Max  6 , Joel Rozowsky  7 , Karolina Elżbieta Kaczor-Urbanowicz  8 , Justin Chang  7 , Leonora Balaj  9 , Bojan Losic  10 , Eric L Van Nostrand  11 , Emily LaPlante  4 , Bogdan Mateescu  12 , Brian S White  13 , Rongshan Yu  14 , Aleksander Milosavljevic  4 , Gustavo Stolovitzky  15 , Ryan M Spengler  16
Affiliations

Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop

Roger P Alexander et al. Front Genet. .

Abstract

We now know RNA can survive the harsh environment of biofluids when encapsulated in vesicles or by associating with lipoproteins or RNA binding proteins. These extracellular RNA (exRNA) play a role in intercellular signaling, serve as biomarkers of disease, and form the basis of new strategies for disease treatment. The Extracellular RNA Communication Consortium (ERCC) hosted a two-day online workshop (April 19-20, 2021) on the unique challenges of exRNA data analysis. The goal was to foster an open dialog about best practices and discuss open problems in the field, focusing initially on small exRNA sequencing data. Video recordings of workshop presentations and discussions are available (https://exRNA.org/exRNAdata2021-videos/). There were three target audiences: experimentalists who generate exRNA sequencing data, computational and data scientists who work with those groups to analyze their data, and experimental and data scientists new to the field. Here we summarize issues explored during the workshop, including progress on an effort to develop an exRNA data analysis challenge to engage the community in solving some of these open problems.

Keywords: DREAM challenge; RNA sequencing; RNA-seq; batch variation; biomarker discovery; deconvolulion; extracellular RNA; tissue of origin.

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Conflict of interest statement

EV is co-founder, member of the Board of Directors, on the SAB, equity holder, and paid consultant for Eclipse BioInnovations. EV’s interests have been reviewed and approved by the Baylor College of Medicine in accordance with its conflict of interest policies. RS is a paid consultant for Lacerta Therapeutics. Author RY was employed by the company Aginome Scientific, Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Key topics discussed during the 2021 ERCC exRNA data analysis workshop.
See this image and copyright information in PMC

References

    1. Czech B., Munafò M., Ciabrelli F., Eastwood E. L., Fabry M. H., Kneuss E., et al. (2018). piRNA-Guided Genome Defense: From Biogenesis to Silencing. Annu. Rev. Genet. 52, 131–157. 10.1146/annurev-genet-120417-031441 - DOI - PMC - PubMed
    1. Ellrott K., Buchanan A., Creason A., Mason M., Schaffter T., Hoff B., et al. (2019). Reproducible Biomedical Benchmarking in the Cloud: Lessons from Crowd-Sourced Data Challenges. Genome Biol. 20, 195. 10.1186/s13059-019-1794-0 - DOI - PMC - PubMed
    1. Fabbiano F., Corsi J., Gurrieri E., Trevisan C., Notarangelo M., D'Agostino V. G. (2020). RNA Packaging into Extracellular Vesicles: An Orchestra of RNA-Binding Proteins? J. Extracell Vesicles 10, e12043. 10.1002/jev2.12043 - DOI - PMC - PubMed
    1. Flynn R. A., Pedram K., Malaker S. A., Batista P. J., Smith B. A. H., Johnson A. G., et al. (2021). Small RNAs Are Modified with N-Glycans and Displayed on the Surface of Living Cells. Cell 184, 3109–3124. 10.1016/j.cell.2021.04.023 - DOI - PMC - PubMed
    1. Fromm B., Billipp T., Peck L. E., Johansen M., Tarver J. E., King B. L., et al. (2015). A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. Annu. Rev. Genet. 49, 213–242. 10.1146/annurev-genet-120213-092023 - DOI - PMC - PubMed