Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research

Bogdan Mateescu^{1

2}, Jennifer C Jones³, Roger P Alexander⁴, Eric Alsop⁵, Ji Yeong An⁶, Mohammad Asghari², Alex Boomgarden⁷, Laura Bouchareychas^{8

9}, Alfonso Cayota^{10

11}, Hsueh-Chia Chang^{12

13}, Al Charest¹⁴, Daniel T Chiu¹⁵, Robert J Coffey^{16

17}, Saumya Das¹⁸, Peter De Hoff¹⁹, Andrew deMello², Crislyn D'Souza-Schorey⁷, David Elashoff²⁰, Kiarash R Eliato²¹, Jeffrey L Franklin^{16

17}, David J Galas²², Mark B Gerstein^{23

24

25}, Ionita H Ghiran¹⁴, David B Go^{12

13}, Stephen Gould²⁶, Tristan R Grogan²⁷, James N Higginbotham¹⁶, Florian Hladik^{28

29}, Tony Jun Huang³⁰, Xiaoye Huo¹², Elizabeth Hutchins⁵, Dennis K Jeppesen¹⁶, Tijana Jovanovic-Talisman²¹, Betty Y S Kim³¹, Sung Kim⁶, Kyoung-Mee Kim³², Yong Kim³³, Robert R Kitchen³⁴, Vaughan Knouse³, Emily L LaPlante³⁵, Carlito B Lebrilla³⁶, L James Lee³⁷, Kathleen M Lennon²¹, Guoping Li¹⁸, Feng Li³³, Tieyi Li³⁸, Tao Liu³⁹, Zirui Liu³⁸, Adam L Maddox²¹, Kyle McCarthy¹², Bessie Meechoovet⁵, Nalin Maniya¹², Yingchao Meng², Aleksandar Milosavljevic^{35

40}, Byoung-Hoon Min⁴¹, Amber Morey¹⁹, Martin Ng⁹, John Nolan⁴², Getulio P De Oliveira Junior¹⁴, Michael E Paulaitis⁴³, Tuan Anh Phu⁹, Robert L Raffai^{8

9

44}, Eduardo Reátegui³⁷, Matthew E Roth³⁵, David A Routenberg⁴⁵, Joel Rozowsky²³, Joseph Rufo³⁰, Satyajyoti Senapati¹², Sigal Shachar⁴⁵, Himani Sharma¹², Anil K Sood⁴⁶, Stavros Stavrakis², Alessandra Stürchler^{1

2}, Muneesh Tewari^{47

48

49

50}, Juan P Tosar^{10

51}, Alexander K Tucker-Schwartz⁴⁵, Andrey Turchinovich^{52

53}, Nedyalka Valkov¹⁸, Kendall Van Keuren-Jensen⁵, Kasey C Vickers⁵⁴, Lucia Vojtech⁵⁵, Wyatt N Vreeland⁵⁶, Ceming Wang¹², Kai Wang⁵⁷, ZeYu Wang³⁰, Joshua A Welsh³, Kenneth W Witwer^{58

59}, David T W Wong³³, Jianping Xia³⁰, Ya-Hong Xie³⁸, Kaichun Yang³⁰, Mikołaj P Zaborowski⁶⁰, Chenguang Zhang¹², Qin Zhang¹⁶, Angela M Zivkovic⁶¹, Louise C Laurent¹⁹

Affiliations

¹ Brain Research Institute, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
² Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
³ Laboratory of Pathology Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
⁴ Extracellular RNA Communication Consortium, Phoenix, AZ 85254, USA.
⁵ Neurogenomics Division, TGen, Phoenix, AZ 85004, USA.
⁶ Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
⁷ Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
⁸ Department of Surgery, Division of Vascular and Endovascular Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.
⁹ Northern California Institute for Research and Education, San Francisco, CA 94121, USA.
¹⁰ Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.
¹¹ University Hospital, Universidad de la República, Montevideo 11600, Uruguay.
¹² Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
¹³ Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
¹⁴ Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
¹⁵ Department of Chemistry and Bioengineering, University of Washington, Seattle, WA 98195, USA.
¹⁶ Department of Medicine/Gastroenterology and Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
¹⁷ Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA.
¹⁸ Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
¹⁹ Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, La Jolla, San Diego, CA 92093, USA.
²⁰ Statistics Core, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
²¹ Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA.
²² Pacific Northwest Research Institute, Seattle, WA 98122, USA.
²³ Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
²⁴ Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT 06520, USA.
²⁵ Department of Computer Science, Yale University, New Haven, CT 06520, USA.
²⁶ Department of Biological Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA.
²⁷ Department of Medicine Statistics Core, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, USA.
²⁸ Departments of Obstetrics and Gynecology, and Medicine, University of Washington, Seattle, WA, USA.
²⁹ Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
³⁰ Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA.
³¹ Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
³² Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
³³ Department of Oral Biology and Medicine, UCLA School of Dentistry, Los Angeles, CA 90095, USA.
³⁴ Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA.
³⁵ Bioinformatics Research Laboratory, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
³⁶ Department of Chemistry, University of California, Davis, CA 95616, USA.
³⁷ Department of Chemical and Biomolecular Engineering and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
³⁸ Department of Materials Science & Engineering, University of California Los Angeles, Los Angeles, CA 90095-1595, USA.
³⁹ Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
⁴⁰ Program in Quantitative and Computational Biosciences Baylor College of Medicine, Houston, TX 77030, USA.
⁴¹ Department of Medicine, Samsung Medical Center, Sungkyunkwan University, School of Medicine, Seoul, South Korea.
⁴² Scintillon Institute, San Diego, CA, USA.
⁴³ Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁴⁴ Department of Veterans Affairs, Surgical Service (112G), San Francisco VA Medical Center, San Francisco, CA 94121, USA.
⁴⁵ Meso Scale Diagnostics, LLC, Rockville, MD 20850, USA.
⁴⁶ Department of Gynecologic Oncology & Reproductive Medicine, University of Texas MD Aderson Cancer Center, Houston, TX 77030, USA.
⁴⁷ Department of Internal Medicine, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI 48109, USA.
⁴⁸ Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
⁴⁹ Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
⁵⁰ Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
⁵¹ Analytical Biochemistry Unit, School of Science, Universidad de la República, Montevideo 11400, Uruguay.
⁵² Cancer Genome Research (B063), German Cancer Research Center DKFZ, Heidelberg 69120, Germany.
⁵³ Heidelberg Biolabs GmbH, Heidelberg 69120, Germany.
⁵⁴ Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
⁵⁵ Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA.
⁵⁶ Bioprocess Measurement Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
⁵⁷ Institute for Systems Biology, Seattle, WA 98109, USA.
⁵⁸ Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁵⁹ Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁶⁰ Department of Gynecology, Obstetrics and Gynecologic Oncology, Division of Gynecologic Oncology, Poznan University of Medical Sciences, 60-535 Poznań, Poland.
⁶¹ Department of Nutrition, University of California, Davis, CA 95616, USA.

PMID: 35958027
PMCID: PMC9358052
DOI: 10.1016/j.isci.2022.104653

Review

Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research

Bogdan Mateescu et al. iScience. 2022.

. 2022 Jun 23;25(8):104653.

doi: 10.1016/j.isci.2022.104653. eCollection 2022 Aug 19.

Authors

Affiliations

¹ Brain Research Institute, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
² Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
³ Laboratory of Pathology Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
⁴ Extracellular RNA Communication Consortium, Phoenix, AZ 85254, USA.
⁵ Neurogenomics Division, TGen, Phoenix, AZ 85004, USA.
⁶ Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
⁷ Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
⁸ Department of Surgery, Division of Vascular and Endovascular Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.
⁹ Northern California Institute for Research and Education, San Francisco, CA 94121, USA.
¹⁰ Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.
¹¹ University Hospital, Universidad de la República, Montevideo 11600, Uruguay.
¹² Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
¹³ Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
¹⁴ Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
¹⁵ Department of Chemistry and Bioengineering, University of Washington, Seattle, WA 98195, USA.
¹⁶ Department of Medicine/Gastroenterology and Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
¹⁷ Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA.
¹⁸ Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
¹⁹ Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, La Jolla, San Diego, CA 92093, USA.
²⁰ Statistics Core, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
²¹ Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA.
²² Pacific Northwest Research Institute, Seattle, WA 98122, USA.
²³ Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
²⁴ Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT 06520, USA.
²⁵ Department of Computer Science, Yale University, New Haven, CT 06520, USA.
²⁶ Department of Biological Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA.
²⁷ Department of Medicine Statistics Core, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, USA.
²⁸ Departments of Obstetrics and Gynecology, and Medicine, University of Washington, Seattle, WA, USA.
²⁹ Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
³⁰ Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA.
³¹ Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
³² Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
³³ Department of Oral Biology and Medicine, UCLA School of Dentistry, Los Angeles, CA 90095, USA.
³⁴ Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA.
³⁵ Bioinformatics Research Laboratory, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
³⁶ Department of Chemistry, University of California, Davis, CA 95616, USA.
³⁷ Department of Chemical and Biomolecular Engineering and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
³⁸ Department of Materials Science & Engineering, University of California Los Angeles, Los Angeles, CA 90095-1595, USA.
³⁹ Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
⁴⁰ Program in Quantitative and Computational Biosciences Baylor College of Medicine, Houston, TX 77030, USA.
⁴¹ Department of Medicine, Samsung Medical Center, Sungkyunkwan University, School of Medicine, Seoul, South Korea.
⁴² Scintillon Institute, San Diego, CA, USA.
⁴³ Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁴⁴ Department of Veterans Affairs, Surgical Service (112G), San Francisco VA Medical Center, San Francisco, CA 94121, USA.
⁴⁵ Meso Scale Diagnostics, LLC, Rockville, MD 20850, USA.
⁴⁶ Department of Gynecologic Oncology & Reproductive Medicine, University of Texas MD Aderson Cancer Center, Houston, TX 77030, USA.
⁴⁷ Department of Internal Medicine, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI 48109, USA.
⁴⁸ Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
⁴⁹ Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
⁵⁰ Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
⁵¹ Analytical Biochemistry Unit, School of Science, Universidad de la República, Montevideo 11400, Uruguay.
⁵² Cancer Genome Research (B063), German Cancer Research Center DKFZ, Heidelberg 69120, Germany.
⁵³ Heidelberg Biolabs GmbH, Heidelberg 69120, Germany.
⁵⁴ Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
⁵⁵ Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA.
⁵⁶ Bioprocess Measurement Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
⁵⁷ Institute for Systems Biology, Seattle, WA 98109, USA.
⁵⁸ Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁵⁹ Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁶⁰ Department of Gynecology, Obstetrics and Gynecologic Oncology, Division of Gynecologic Oncology, Poznan University of Medical Sciences, 60-535 Poznań, Poland.
⁶¹ Department of Nutrition, University of California, Davis, CA 95616, USA.

PMID: 35958027
PMCID: PMC9358052
DOI: 10.1016/j.isci.2022.104653

Abstract

The extracellular RNA communication consortium (ERCC) is an NIH-funded program aiming to promote the development of new technologies, resources, and knowledge about exRNAs and their carriers. After Phase 1 (2013-2018), Phase 2 of the program (ERCC2, 2019-2023) aims to fill critical gaps in knowledge and technology to enable rigorous and reproducible methods for separation and characterization of both bulk populations of exRNA carriers and single EVs. ERCC2 investigators are also developing new bioinformatic pipelines to promote data integration through the exRNA atlas database. ERCC2 has established several Working Groups (Resource Sharing, Reagent Development, Data Analysis and Coordination, Technology Development, nomenclature, and Scientific Outreach) to promote collaboration between ERCC2 members and the broader scientific community. We expect that ERCC2's current and future achievements will significantly improve our understanding of exRNA biology and the development of accurate and efficient exRNA-based diagnostic, prognostic, and theranostic biomarker assays.

Keywords: Biochemistry; Biological sciences; Cell biology; Molecular biology.

PubMed Disclaimer

Conflict of interest statement

Crislyn D’Souza-Schorey, Satyajyoti Senapati and Hsueh-Chia Chang hold equity in AgenDx Biosciences. Hsueh-Chia Chang is a cofounder of Aopia Biosciences and holds equity. Daniel T. Chiu has financial interest and is a scientific founder and/or board member of the following companies and their respective affiliates: Micareo, Inc, Lamprogen, Inc, Cellectricon AB, and Fluicell AB. Saumya Das is a founding member of Dyrnamix Inc. that did not play any role in this study. Kendal Van Keuren-Jensen is a board member of Dyrnamix Inc. and HTG that did not play any role in this study. Aleksandar Milosavljevic is a founder of IP Genesis, Inc. that did not play any role in this study. Louise C. Laurent has stock in Illumina, Inc. Anil K. Sood has the following disclosures: Consultant (Merck, Kiyatec), shareholder (BioPath), research funding (MTrap). John Nolan holds equity in Cellarcus Biosciences Inc. L. James Lee holds equity at Spot Biosystems. David A. Routenberg, Sigal Shachar and Alexander K. Tucker-Schwartz are employees of Meso Scale Diagnostics, LLC. Andrey Turchinovich is founder of SciBerg e.Kfm, Mannheim, Germany. Angela M. Zivkovic is cofounder and board member at Innate Biology, Inc.

Figures

**Figure 1**
Diversity of exRNA carriers in biofluids exRNA are associated with a plethora of carriers ranging from a few nanometers to several microns. Although EVs are the most studied exRNA carriers, RNPs, exomeres, supermeres, lipoproteins, and extracellular organelles are associated with a high proportion of exRNA in biofluids. Their relative abundance may explain the specific exRNA biotype composition observed in distinct biofluids. During viral infection, RNA viruses also constitute a significant exRNA carrier in specific biofluids, a property exploited for diagnostics. Here, all known exRNA carriers are represented at scale thereby illustrating their high size heterogeneity, and the challenge to fractionate them in parallel. Acronyms: RNP: ribonucleoprotein; HDL. High-density lipoprotein; LDL: Low-density lipoprotein; VLDL: Very-Low Density Lipoprotein; EVs: extracellular vesicles; SARS-Cov-2: severe acute respiratory syndrome coronavirus two; HIV-1: Human immunodeficiency virus 1.

**Figure 2**
ERCC2 Integrated technological development for exRNA separation and detection The aim of ERCC2 is not only to combine and refine existing methods, but also to develop innovative technologies, in order to improve the multiplexed characterization of cargo-specific exRNA signatures from clinical samples, toward their implementation in disease biomarkers strategies. AF4, Asymmetric flow field flow fractionation; HF-TFF, hollow fiber tangential flow filtration; GF, gel filtration; F, filtration; RPS, resistive pulse sensing; NTA, nanoparticle tracking analysis; SERS, Surface-enhanced Raman spectroscopy; FLUO, fluorescence; DC, differential centrifugation; DGUC, density-gradient ultracentrifugation

**Figure 3**
The ERCC2 benchmarking initiative The ERCC2 groups are working together on a benchmarking study aiming at evaluating the performance of the ERCC2-driven technologies. This initiative not only aims at homogenizing practice and calibration tools, but also to promote rigor and reproducibility within ERCC2 and members of the scientific community at large.

See this image and copyright information in PMC

References

1. Ahn J.Y., Datta S., Bandeira E., Cano M., Mallick E., Rai U., Powell B., Tian J., Witwer K.W., Handa J.T., Paulaitis M.E. Release of extracellular vesicle miR-494-3p by ARPE-19 cells with impaired mitochondria. Biochim. Biophys. Acta Gen. Subj. 2021;1865:129598. doi: 10.1016/j.bbagen.2020.129598. - DOI - PubMed
1. Al Amir Dache Z., Otandault A., Tanos R., Pastor B., Meddeb R., Sanchez C., Arena G., Lasorsa L., Bennett A., Grange T., et al. Blood contains circulating cell-free respiratory competent mitochondria. FASEB. J. 2020;34:3616–3630. doi: 10.1096/fj.201901917RR. - DOI - PubMed
1. Andronico L.A., Jiang Y., Jung S.-R., Fujimoto B.S., Vojtech L., Chiu D.T. Sizing extracellular vesicles using membrane dyes and a single molecule-sensitive flow analyzer. Anal. Chem. 2021;93:5897–5905. doi: 10.1021/acs.analchem.1c00253. - DOI - PMC - PubMed
1. Arab T., Mallick E.R., Huang Y., Dong L., Liao Z., Zhao Z., Gololobova O., Smith B., Haughey N.J., Pienta K.J., et al. Characterization of extracellular vesicles and synthetic nanoparticles with four orthogonal single-particle analysis platforms. J. Extracell. Vesicles. 2021;10:e12079. doi: 10.1101/2020.08.04.237156. - DOI - PMC - PubMed
1. Arroyo J.D., Chevillet J.R., Kroh E.M., Ruf I.K., Pritchard C.C., Gibson D.F., Mitchell P.S., Bennett C.F., Pogosova-Agadjanyan E.L., Stirewalt D.L., et al. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc. Natl. Acad. Sci. USA. 2011;108:5003–5008. doi: 10.1073/pnas.1019055108. - DOI - PMC - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research

Affiliations

Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

Grants and funding

LinkOut - more resources

Full Text Sources

Research Materials