microRNA profiling of amniotic fluid samples from CAKUT fetuses

Summary

Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) is the leading cause of childhood end-stage renal disease and a significant cause of chronic kidney disease in adults. Genetic and environmental factors have been shown to influence CAKUT development, but the known disease mechanism remains incomplete. Our goal is to identify affected pathways and networks in CAKUT through multi-omics analysis, including miRNome, peptidome and proteome data. The peptidome and proteome data of the corresponding samples were previously published [pmid: 32750455, pmid: 33987838].

Study design

Amniotic fluid samples were collected in a prospective multicenter observational study focusing on fetal bilateral CAKUT as part of a clinical trial. In addition, 21 samples were collected from non-CAKUT individuals. The severity was defined based on the renal status after 2 years of postnatal clinical follow-up.

The total RNA was isolated using the Agilent RNA 6000 Pico kit protocol (5067-1513) and microRNAs were profiled using Agilent microRNA slides (Sanger miRBase release 21). The samples were labelled and hybridized according to the Agilent's microRNA Complete Labeling and Hybridization Kit protocol (5190-0456), followed by Spike-ins with the Agilent's microRNA Spike-In Kit protocol (5190-1934) and analyzed using Aligent's High-Resolution Microarray Scanner GS2505_C. Features were called using the Agilent Feature Extraction software (version 11.0.1.1) and sample intensities were normalized using quantile normalization (RMA).