Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins

• Published in: Journal of extracellular vesicles Vol. 7; no. 1; pp. 1506198 - n/a
• Main Authors: Allen, Ryan M., Zhao, Shilin, Ramirez Solano, Marisol A., Zhu, Wanying, Michell, Danielle L., Wang, Yuhuan, Shyr, Yu, Sethupathy, Praveen, Linton, MacRae F., Graf, Gregory A., Sheng, Quanhu, Vickers, Kasey C.
• Format: Journal Article
• Language: English
• Published: Sweden Taylor & Francis 01.12.2018; John Wiley & Sons, Inc; Wiley
• Subjects: APOB; Bile; Bioinformatics; Biomarkers; Cardiovascular disease; Cholesterol; Data analysis; Datasets; Diabetes; E coli; exogenous RNA; extracellular RNA; Gene expression; Genomes; Genomic analysis; HDL; High density lipoprotein; high-throughput sequencing; lipoprotein; Lipoproteins; Liver; Microbiomes; MicroRNA; MicroRNAs; miRNA; Multivariate analysis; Pipelines; Plasma; Proteins; Protocol; rRNA; small RNA; Transfer RNA; Triglycerides; Urine; HDL; MicroRNA; exogenous RNA; lipoprotein; urine; extracellular RNA; small RNA; APOB; bile; high-throughput sequencing
• ISSN: 2001-3078; 2001-3078
• DOI: 10.1080/20013078.2018.1506198

To comprehensively study extracellular small RNAs (sRNA) by sequencing (sRNA-seq), we developed a novel pipeline to overcome current limitations in analysis entitled, "Tools for Integrative Genome analysis of Extracellular sRNAs (TIGER)". To demonstrate the power of this tool, sRNA-seq was performed on mouse lipoproteins, bile, urine and livers. A key advance for the TIGER pipeline is the ability to analyse both host and non-host sRNAs at genomic, parent RNA and individual fragment levels. TIGER was able to identify approximately 60% of sRNAs on lipoproteins and >85% of sRNAs in liver, bile and urine, a significant advance compared to existing software. Moreover, TIGER facilitated the comparison of lipoprotein sRNA signatures to disparate sample types at each level using hierarchical clustering, correlations, beta-dispersions, principal coordinate analysis and permutational multivariate analysis of variance. TIGER analysis was also used to quantify distinct features of exRNAs, including 5ʹ miRNA variants, 3ʹ miRNA non-templated additions and parent RNA positional coverage. Results suggest that the majority of sRNAs on lipoproteins are non-host sRNAs derived from bacterial sources in the microbiome and environment, specifically rRNA-derived sRNAs from Proteobacteria. Collectively, TIGER facilitated novel discoveries of lipoprotein and biofluid sRNAs and has tremendous applicability for the field of extracellular RNA.