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

Authors

Roger P Alexander
Robert R Kitchen
Juan Pablo Tosar
Matthew Roth
Pieter Mestdagh
Klaas E A Max
Joel Rozowsky
Karolina Elżbieta Kaczor-Urbanowicz
Justin Chang
Leonora Balaj
Bojan Losic
Eric L Van Nostrand
Emily LaPlante
Bogdan Mateescu
Brian S White
Rongshan Yu
Aleksander Milosavljevic
Gustavo Stolovitzky
Ryan M Spengler

Publication Date

1-1-2021

Journal

Frontiers in Genetics

DOI

10.3389/fgene.2021.778416

PMID

35047007

PMCID

PMC8762274

PubMedCentral® Posted Date

1-3-2022

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes

Keywords

extracellular RNA, RNA-seq, RNA sequencing, deconvolulion, batch variation, DREAM challenge, tissue of origin, biomarker discovery

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.

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