Principal Investigator: Mark Bender Gerstein

Contributors: Aleksandar Milosavljevic, David Galas

DESCRIPTION (provided by applicant): The last decade has seen the discovery of miRNAs in body fluids including plasma and serum. This lead to the hypothesis that RNAs play roles as extracellular signaling molecules. It is now clear that these RNAs exist not only in exosomes or other vesicles, but also outside vesicles bound to carrier proteins, such as Argonaute (Ago) proteins In vesicle-mediated RNA signaling, the vesicles are secreted by a large variety of cells, and contain RNAs (e.g. mRNA, miRNA and other ncRNA) that can be taken up by other cells. Strong evidence shows that they can be functional in other cells. In vesicle-free RNA signaling, exRNAs (e.g. siRNA and miRNA) could also be transported across cell membranes by specific receptors or channels, but evidence is much weaker for this mode. Signaling via RNAs has the potential to play roles as autocrine, paracrine or endocrine signaling , and is therefore of great potential significance in many biological processes. It is now clear that most body fluids contain miRNA and other ncRNAs Moreover, these exRNAs are markers for various pathological states, including cancers and toxicity. Although previous studies have observed widespread signaling exRNAs, it is still not fully understood how and why source cells emit RNA, how they are transported, and how the target cells uptake and interpret the RNAs. It is also not clear when and why exosomal inclusion is needed, and how the inclusion affects biological function. In order to develop a comprehensive understanding of the complex mechanisms of this intercellular communication, a set of reference maps, an exRNA Atlas, is needed including a map of proteins and other carrier molecules that bind exRNA, as well as profiles of RNA content of exosomes and body fluids. To enable the construction of an exRNA Atlas we will construct an automated en-exRNA pipeline for creating an exRNA Atlas Database by adapting existing RNA-seq workflows for mRNAs and miRNAs and develop advanced enexRNA analysis methods and tools for the community and for creating and exRNA Atlas Knowledge Base.

The DMRR DIAC will coordinate multiple teams for analyzing consortium data in different ways.  The DMRR DIAC should plan to facilitate data analysis efforts of smaller projects and also provide substantial support for consortium-wide integrative analysis efforts.  The majority of datasets that will be analyzed are expected to be RNA-seq, small RNA-seq or related datatypes, however other datatypes (e.g. proteomic, metabolomic, individual variation) may require analysis as well. Activities of the DMRR DIAC include:

  • developing analysis tools and strategies to address the extent to which ExRNAs may be transferred from food, the environment, and the microbiome.
  • developing analysis strategies to integrate the ExRNA datasets in synergistic ways with other relevant datasets (e.g. inter-individual variation, proteomic, metabolomic) as well as developing user-friendly analysis tools for the consortium and “apps” for investigators with limited experience in RNA data mining
  • publishing integrative ExRNA consortium papers which might include analyses of classes of ExRNAs, cells or organisms of origin, relative abundance, and/or other properties including the use of ExRNA profiles/signatures as biomarkers
  • generating comprehensive and accurate catalogs of ExRNAs for different body fluid and/or define biological roles for these ExRNAs
  • facilitating interactions between ERCP Consortium members or outside investigators to identify any additional datasets from outside of the ERCP Consortium for use in integrative analyses
  • possibly developing software relevant to the analysis of ExRNA datasets.  Any software proposed to be developed should be modular, open-source,  and include appropriate documentation, so that it can work as a stand-alone package.  Software should not duplicate existing software with similar features and should leverage existing software projects as much as possible. Software should use standard formats for data input and output, to facilitate its use and interoperability with other software.
  • performing analyses requested by ERCP consortium members or NIH staff to assess the quality and coverage of the ExRNA datasets.
  • planing and implementing regular conference calls with ERCP consortium PD(s)/PI(s) to develop Data Analysis Working Groups to coordinate and facilitate integrative analysis of ExRNA consortium data.
  • coordinating with the DMRR DCC to provide support, including data transformations and preparation of data freezes, for any data analyses.
  • providing resources and coordination activities that will enable the ERCP Consortium to share useful information about ExRNA species and profiles to the larger biomedical research community.
  • supporting activities that include but are not limited to developing uniform data processing pipelines to standardize the ExRNA data analyses, assessing the quality of the ExRNA data, and integrating datasets and data types.

 

Related Projects

Data Coordination Component of the Data Management and Resource Repository for the exRNA atlas (DMRR DCC)

Aleksandar Milosavljevic
Baylor College of Medicine

Scientific Outreach Component of the Data Management and Resource Repository for the exRNA atlas (DMRR SOC)

David Galas
Pacific Northwest Diabetes Research Institute

Administrative Core of the Data Management and Resource Repository for the exRNA Atlas (DMRR AC)

Aleksandar Milosavljevic
Baylor College of Medicine