Extracellular microRNA 3’ end modification across diverse body fluids

ABSTRACT

microRNAs (miRNAs) are small non-coding RNAs that play critical roles in gene regulation. The presence of miRNAs in extracellular biofluids is increasingly recognized. However, most previous characterization of extracellular miRNAs focused on their overall expression levels. Alternative sequence isoforms and modifications of miRNAs were rarely considered in the extracellular space. Here, we developed a highly accurate bioinformatic method, called miNTA, to identify 3’ non-templated additions (NTAs) of miRNAs using small RNA-sequencing data. Using miNTA, we conducted an in-depth analysis of miRNA 3’ NTA profiles in 1047 extracellular RNA-sequencing data sets of 4 types of biofluids. This analysis identified hundreds of miRNAs with 3’ uridylation or adenylation, with the former being more prevalent. Among these miRNAs, up to 53% (22%) had an average 3’ uridylation (adenylation) level of at least 10% in a specific biofluid. Strikingly, we found that 3’ uridylation levels enabled segregation of different types of biofluids, more effectively than overall miRNA expression levels. This observation suggests that 3’ NTA levels possess fluid-specific information relatively robust to batch effects. In addition, we observed that extracellular miRNAs with 3’ uridylations are enriched in processes related to angiogenesis, apoptosis, and inflammatory response, and this type of modification may stabilize base-pairing between miRNAs and their target genes. Together, our study provides a comprehensive landscape of miRNA NTAs in human biofluids, which paves way for further biomarker discoveries. The insights generated in our work built a foundation for future functional, mechanistic, and translational discoveries.

KEYWORDS:

• microRNA
• non-templated additions
• extracellular RNA
• computational analysis
• biofluids

Acknowledgments

We thank members of the Xiao laboratory for helpful discussions and comments on this work. We acknowledge the data production efforts and the subject donors for making available the data sets used in this study. The Extracellular Small RNA Profiles in Plasma, Urine and Saliva from College Athletes Study (dbGAP phs001258) was made possible by the NIH Common Fund Program on Extracellular RNA Communication Grant UH3 TR000891, Riddell and BRG Sports, the Flinn Foundation grant awards #1994 and #2307, the staff and athletes at Arizona State University, and TGen faculty and interns. Thanks to The Michael J Fox Foundation for supporting the collection of dbGAP phs00727, the subject donors to the program at Sun Health Research Institute. This work was supported in part by grants from the National Institute of Health (U01HG009417, R01AG056476 to X.X) and the Jonsson Comprehensive Cancer Center at UCLA. K.K. was supported by a Eureka Scholarship from the Department of Integrative Biology and Physiology at UCLA.

Disclosure statement

No potential conflicts of interest were disclosed.

Supplementary material

Supplemental data for this article can be accessed here.

Additional information

Funding

This work was supported by the National Human Genome Research Institute [U01HG009417]; National Institute on Aging (US) [R01AG056476].