Extracellular RNA (exRNA) from pathogens plays a key role as activator of innate immunity in mammals. However, the presence of host exRNA in serum and other body fluids challenges the current models of RNA based immune recognition. To understand its basis of specificity, it is important to catalog host exRNAs and their associated proteins in serum, investigate mechanisms leading to circulating ribonucleoprotein (RNP) homeostasis, and identify protein factors contributing to cellular RNA release. Genetic alterations in RNA targets or interacting proteins may contribute to imbalances in normal versus stress-triggered release of RNPs and push adaptive long-term pathogen-directed immunity towards autoimmunity. ExRNAs may also play a broader role in extracellular signaling similar to peptide hormones, which would also be captured by this experimental approach. This application brings together a team of multiple investigators with complementary expertise and history of close collaboration to build a solid foundation regarding identification, mechanism and function of extracellular RNAs and the proteins involved in their biogenesis, export, recognition, and turnover.
The specific aims of the proposed project are: 1. Catalogue and quantify all classes of extracellular RNAs in human serum from normal subjects using various established and novel RNA seq approaches and examine normal variability of circulating RNA profiles within an individual, between individuals and the influence of gender, age, race, and disease. Establish a core facility for processing and archiving clinical materials (Williams, Putterman, Tuschi). 2. Determine exRNA composition in patients suffering from systemic lupus erythematosus (SLE), for whom antibodies against different classes of RBPs is a hallmark. Considering that these RBPs alter their subcellular localization upon stress and appear in stress granules with immature RNA and/or RNA targeted for turnover, we will evaluate in as much the composition of RNPs in stress granules harvested from immortalized B cells of normal and SLE subjects possesses immunostimulatory function and if these RNP granules are also released during stress (Tuschi, Putterman, Williams). 3. Develop a molecular and mechanistic understanding of stress granule formation and RNA/RNP mediated innate immune responses. Identify the RNA targets and RNP structures of autoantigens in tRNA stress responses, their turnover, and their immune receptors.

Public Health Relevance

This application has the potential to allow us to come to a molecular understanding of the triggers of SLE and possibly other autoimmune diseases. The role of stress-induced RNA- and RBP-containing cytoplasmic granules may also reveal molecular aspects that may contribute to their deposition in inclusion bodies and amyloids in myopathies and neurodegenerative diseases. Our approach may also benchmark future developments of RNA as biomarkers and may discovery of previously unknown RNA secretory mechanism. DESCRIPTION (provided by applicant): Extracellular RNA (exRNA) from pathogens plays a key role as activator of innate immunity in mammals. However, the presence of host exRNA in serum and other body fluids challenges the current models of RNA based immune recognition. To understand its basis of specificity, it is important to catalog host exRNAs and their associated proteins in serum, investigate mechanisms leading to circulating ribonucleoprotein (RNP) homeostasis, and identify protein factors contributing to cellular RNA release. Genetic alterations in RNA targets or interacting proteins may contribute to imbalances in normal versus stress-triggered release of RNPs and push adaptive long-term pathogen-directed immunity towards autoimmunity. ExRNAs may also play a broader role in extracellular signaling similar to peptide hormones, which would also be captured by this experimental approach. This application brings together a team of multiple investigators with complementary expertise and history of close collaboration to build a solid foundation regarding identification, mechanism and function of extracellular RNAs and the proteins involved in their biogenesis, export, recognition, and turnover. The specific aims of the proposed project are: 1. Catalogue and quantify all classes of extracellular RNAs in human serum from normal subjects using various established and novel RNA seq approaches and examine normal variability of circulating RNA profiles within an individual, between individuals and the influence of gender, age, race, and disease. Establish a core facility for processing and archiving clinical materials (Williams, Putterman, Tuschi). 2. Determine exRNA composition in patients suffering from systemic lupus erythematosus (SLE), for whom antibodies against different classes of RBPs is a hallmark. Considering that these RBPs alter their subcellular localization upon stress and appear in stress granules with immature RNA and/or RNA targeted for turnover, we will evaluate in as much the composition of RNPs in stress granules harvested from immortalized B cells of normal and SLE subjects possesses immunostimulatory function and if these RNP granules are also released during stress (Tuschi, Putterman, Williams). 3. Develop a molecular and mechanistic understanding of stress granule formation and RNA/RNP mediated innate immune responses. Identify the RNA targets and RNP structures of autoantigens in tRNA stress responses, their turnover, and their immune receptors.

Agency
National Institute of Health (NIH)
Type
Research Program--Cooperative Agreements (U19)
Project #
5U19CA179564-02
Application #
8719066
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Howcroft, Thomas K
Project Start
Project End
Budget Start
Budget End
Support Year
2
Fiscal Year
2014
Total Cost
Indirect Cost
Name
Rockefeller University
Department
Genetics
Type
Graduate Schools
DUNS #
City
New York
State
NY
Country
United States
Zip Code
10065
Akat, Kemal Marc; Moore-McGriff, D'Vesharronne; Morozov, Pavel et al. (2014) Comparative RNA-sequencing analysis of myocardial and circulating small RNAs in human heart failure and their utility as biomarkers. Proc Natl Acad Sci U S A 111:11151-6
Ren, Aiming; Patel, Dinshaw J (2014) c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets. Nat Chem Biol 10:780-6