Among the known blood molecules is a new class, the extracellular RNAs (exRNAs.) Some of these are excellent biomarker candidates, but there are also a significant number of exRNAs derived from the microbiome. Both endogenous and exogenous exRNAs carry much information and could be effectors of cellular function. The NIH Common Fund exRNA consortium is now researching and applying exRNA in humans to diagnostics and therapeutics. A foundation for this effort, reliable profiles of the exRNA spectrum in healthy individuals, is needed. We have assembled an experienced, interdisciplinary team to carefully characterize these reference RNA profiles, and to improve the methods for doing so. The PI will work closely with Co-PI's Debbie Nickerson (UW Genomics Center co-Director, Sequencing), and Kai Wang (Institute for Systems Biology, data analysis), Co-Investigator, Elaine Peskind, VA Center and UW, selecting and providing samples), and co-investigators to provide advice, consultation, and collaboration (Paul Wilmes, Univ. of Luxembourg;Aleks Milosavljevic, Baylor;and Muneesh Tewari, Univ. of Mich.) We propose the generation, analysis, and dissemination of exRNA profiles of plasma, serum, CSF and saliva from the same healthy subjects: roughly equal numbers of men and women in three age categories (31 to 101 years.) These matched samples of serum, plasma, saliva and CSF collected at the same time from the same subjects are a key asset of this proposal. A new dimension in exRNA research was revealed by our recent work. The presence of microbial RNA (bacterial and fungal) in blood plasma raises important questions concerning its origins and functions. We will use our computational pipeline, including tools from the DMRR (DIAC), to characterize both endogenous exRNAs (en-exRNA) and exogenous exRNA (ex-exRNA) in and outside of lipid vesicles (in human serum, plasma, saliva and CSF.) We will do four NextGen libraries per sample: in and out of vesicles, and short and long insert libraries. We propose to characterize a set of 180 subjects over five years, and analyze and deposit profile data and metadata in the exRNA Atlas created and maintained by the DMRR of the ECRP consortium. We will complete the development and testing of a novel approach to generate sequence-specific library bias correction factors. We will periodically re-characterize the ex-exRNA due to microbial sequence database updates. The data generated will enable us to examine the variance in individual exRNAs and clusters of exRNAs as a function of subject attributes (including age and gender.) The project will be carried out in two phases. In the first phase (years 1 and 2), methods will be tested during data acquisition and analysis, including the bias correction method. The second phase (years 3-5) will consist of data generation and analysis only. A major emphasis and strength of our proposal is the rigorously collected, matched samples of multiple body fluids on the same subjects, with emphasis on accurate acquisition and analysis of exRNA and our extensive experience in all aspects of the proposed work.
The field of extracellular RNA (exRNA) is changing rapidly, but has already altered our view of communication between cells and has introduced a new class of diagnostic biomarkers. A foundation for research in this field will certainly be reliable, well- characterized profiles of the exRNA spectrum in healthy individuals. The Common Fund exRNA consortium is now leading research and application efforts in exRNA for understanding, diagnostics, and therapeutics. The work proposed here, including the newly developed methods, and the profiles in plasma, serum, CSF and saliva, will provide fundamental enablement to the scientific community in future efforts to harness the potential of exRNAs for the benefit of patients.
|Fallen, Shannon; Baxter, David; Wu, Xiaogang et al. (2018) Extracellular vesicle RNAs reflect placenta dysfunction and are a biomarker source for preterm labour. J Cell Mol Med 22:2760-2773|
|Malabirade, Antoine; Habier, Janine; Heintz-Buschart, Anna et al. (2018) The RNA Complement of Outer Membrane Vesicles From Salmonella enterica Serovar Typhimurium Under Distinct Culture Conditions. Front Microbiol 9:2015|
|Giraldez, Maria D; Spengler, Ryan M; Etheridge, Alton et al. (2018) Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling. Nat Biotechnol 36:746-757|
|Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne et al. (2018) Small RNA profiling of low biomass samples: identification and removal of contaminants. BMC Biol 16:52|
|Etheridge, Alton; Wang, Kai; Baxter, David et al. (2018) Preparation of Small RNA NGS Libraries from Biofluids. Methods Mol Biol 1740:163-175|
|Wu, Xiaogang; Kim, Taek-Kyun; Baxter, David et al. (2017) sRNAnalyzer-a flexible and customizable small RNA sequencing data analysis pipeline. Nucleic Acids Res 45:12140-12151|
|Lee, Inyoul; Baxter, David; Lee, Min Young et al. (2017) The Importance of Standardization on Analyzing Circulating RNA. Mol Diagn Ther 21:259-268|
|He, Yuqing; Ding, Yuanlin; Liang, Biyu et al. (2017) A Systematic Study of Dysregulated MicroRNA in Type 2 Diabetes Mellitus. Int J Mol Sci 18:|
|Fritz, Joëlle V; Heintz-Buschart, Anna; Ghosal, Anubrata et al. (2016) Sources and Functions of Extracellular Small RNAs in Human Circulation. Annu Rev Nutr 36:301-36|
|Wu, Shenghui; Kim, Taek-Kyun; Wu, Xiaogang et al. (2016) Circulating MicroRNAs and Life Expectancy Among Identical Twins. Ann Hum Genet 80:247-56|
Showing the most recent 10 out of 12 publications