Our goal is to generate reference profiles of short, long and circular non-coding regulatory exRNAs, including environmentally-derived exRNAs, in samples of 12 different body fluids from healthy humans using comprehensive RNA sequencing. We have assembled a multidisciplinary team with expertise in clinical investigation, genomics technologies, bioinformatics and statistics to achieve this goal. One major strength of this proposal is that we benefit from close interactions with other investigators participating in two UCSF-based U19 projects supported by the Common Fund Extracellular RNA Communication Program. Another major strength is that we will make use of very large sets of carefully curated body fluid samples collected from ethnically diverse populations of female and male children and adults who participated in NIH-funded cohort studies. Our three specific aims are:
Aim 1) Obtain a large and diverse set of samples from 12 human body fluids (plasma, serum, cord blood, urine, cerebrospinal fluid (CSF), sputum, bronchoalveolar lavage (BAL), saliva, seminal fluid, amniotic fluid, peri-embryonic fluid and ovarian follicle fluid), Aim 2) Use state of the art approaches to sequence the full range of exRNAs in body fluid samples, and Aim 3) Apply appropriate analytical approaches to identify human and exogenous RNAs and establish normal reference values for representative ethnically-diverse US populations. We will approach the project in two phases. In phase I (years 1-2), we will study ~200 samples representing 12 body fluids using three complementary sequencing approaches. These studies will fill major gaps in our understanding of the diversity of exRNAs in human body fluids and provide important insights about which sequencing-based approaches are most valuable for exRNA identification and quantification. During phase II (years 3-5), we will build on our phase I studies and other work performed by Extracellular RNA Communication Program participants by analyzing 2,880 plasma and urine samples that have been banked from 2,160 subjects enrolled in three large, ethnically-diverse, NIH cohort studies (CARDIA, REGARDS and GALA/SAGE). These studies will be adequately powered to establish normal reference ranges for exRNAs stratified by age, sex, and ethnicity. Each phase is associated with realistic milestone assessments and can form the basis for collaboration with other consortium participants. This project is relevant to public health in thatit will establish the healthy control reference data necessary to apply exRNAs as biomarkers in patients with or at risk for disease.
Recently, extracellular RNA (i.e. ribonucleic acid outside of cells, also known as exRNA) has been found in a range of human body fluids, and these exRNAs may represent a new type of disease biomarker. The goal of this multidisciplinary research project is to generate reference profiles of the full range of exRNAs, including environmentally-derived exRNAs, from 12 different healthy human body fluids including plasma, serum, cord blood, urine, cerebrospinal fluid (CSF), sputum, bronchoalveolar lavage (BAL), saliva, seminal fluid, amniotic fluid, peri-embryonic fluid and ovarian follicle fluid through the application of comprehensive RNA sequencing. This project is relevant to public health in that it will establish the healthy control reference data necessary to apply exRNAs as biomarkers in patients with or at risk for disease.
|Li, Kang; Wong, David K; Luk, Fu Sang et al. (2018) Isolation of Plasma Lipoproteins as a Source of Extracellular RNA. Methods Mol Biol 1740:139-153|
|Godoy, Paula M; Bhakta, Nirav R; Barczak, Andrea J et al. (2018) Large Differences in Small RNA Composition Between Human Biofluids. Cell Rep 25:1346-1358|
|Bhakta, Nirav R; Christenson, Stephanie A; Nerella, Srilaxmi et al. (2018) IFN-stimulated Gene Expression, Type 2 Inflammation, and Endoplasmic Reticulum Stress in Asthma. Am J Respir Crit Care Med 197:313-324|
|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|
|Pua, Heather H; Steiner, David F; Patel, Sana et al. (2016) MicroRNAs 24 and 27 Suppress Allergic Inflammation and Target a Network of Regulators of T Helper 2 Cell-Associated Cytokine Production. Immunity 44:821-32|