Project Leader: Zez Williams. This project addresses fundamental gaps in our knowledge of Extracellular RNAs (exRNAs) in circulation and will provide the foundation for understanding both their physiological and pathological functions as well as their potential clinical utility. We currently lack a reference profile of circulating coding and non-coding RNAs?and we lack the knowledge of the normal variability to the reference profile within a single individual over time, between similar individuals and between populations differing in gender, body mass index and age.
In Aim 1 we will generate a comprehensive and quantitative reference atlas of extracellular RNAs (exRNAs) in circulation from a few healthy individuals and examine the normal variability within an individual and between individuals based on gender, age, and BMl. This atlas will be produce utilizing RNAseq technology developed in our laboratories. This atlas will serve as a foundation for discovery of new biomarkers associated with disease and inform our understanding of potential roles for exRNA in circulation in physiology and disease. We do not understand how different cell- and tissue- types contribute to the total pool of extracellular circulating RNAs.
In Aim 2 we will determine the tissue- and cell-specific contribution to total circulating exRNA using the human placenta as a model organ and combining that information with tissue-specific RNAseq data. We will examine which tissues and RNA types contribute to the overall pool of exRNA in circulation. We do not understand the dynamics within the extracellular circulating RNA compartment?how quickly the component RNAs enter and are cleared from this space. This project seeks to systematically address these areas In Aim 3 we will determine the clearance rate and kinetics of circulating exRNA. This will be accomplished by serially monitoring the plasma and urine of women post-partum and using placenta-specific exRNAs as markers. In summary, we propose to analyze exRNAs in using RNAseq to produce a comprehensive and quantitative reference profile for single individuals over time as well as between populations and to determine the tissue- and cellular origin for these exRNAs as well as their dynamics. Collectively, these results will answer basic questions regarding the full RNA composition of serum, provide a firm foundation for future studies of exRNAs and provide important biomedical insights.

Public Health Relevance

This project utilizes RNAseq technology that we have recently developed and the pregnancy model in the setting of a diverse population to comprehensively profile circulating exRNAs and capture their normal variation as well as to provide insights into the origins and dynamics the RNAs. The findings will provide the essential foundation for understanding how circulating exRNAs are formed, how they function in health and disease, and how they may be used as diagnostic and therapeutic agents

Agency
National Institute of Health (NIH)
Type
Research Program--Cooperative Agreements (U19)
Project #
5U19CA179564-02
Application #
8736237
Study Section
Special Emphasis Panel (ZRG1)
Project Start
Project End
Budget Start
Budget End
Support Year
2
Fiscal Year
2014
Total Cost
Indirect Cost
Name
Rockefeller University
Department
Type
DUNS #
City
New York
State
NY
Country
United States
Zip Code
Wei, Shan; Williams, Zev (2016) Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology. Genetics 202:37-44
Ren, Aiming; Vušurović, Nikola; Gebetsberger, Jennifer et al. (2016) Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage. Nat Chem Biol 12:702-8
Ben-Dov, Iddo Z; Whalen, Veronica M; Goilav, Beatrice et al. (2016) Cell and Microvesicle Urine microRNA Deep Sequencing Profiles from Healthy Individuals: Observations with Potential Impact on Biomarker Studies. PLoS One 11:e0147249
Gao, Pu; Yang, Hui; Rajashankar, Kanagalaghatta R et al. (2016) Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition. Cell Res 26:901-13
Li, Xin; Mauro, Maurizio; William, Zev (2015) Comparison of plasma extracellular RNA isolation kits reveals kit-dependent biases. Biotechniques 59:13-7
Ren, Aiming; Wang, Xin C; Kellenberger, Colleen A et al. (2015) Structural basis for molecular discrimination by a 3',3'-cGAMP sensing riboswitch. Cell Rep 11:1-12
Ho, Gloria Y F; Jung, Hwa J; Schoen, Robert E et al. (2015) Differential expression of circulating microRNAs according to severity of colorectal neoplasia. Transl Res 166:225-32
Li, Xin; Ben-Dov, Iddo Z; Mauro, Maurizio et al. (2015) Lowering the quantification limit of the QubitTM RNA HS assay using RNA spike-in. BMC Mol Biol 16:9
Ren, Aiming; Xue, Yi; Peselis, Alla et al. (2015) Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch. Cell Rep 13:1800-13
Košutić, Marija; Neuner, Sandro; Ren, Aiming et al. (2015) A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class. Angew Chem Int Ed Engl 54:15128-33

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