GSE111754
miRNA-Seq identifies a serum miRNA panel which can detect and monitor liver disease in pediatric cystic fibrosis
Purpose: Cystic fibrosis (CF)-associated liver disease (CFLD) is a hepatobiliary complication of CF. Current diagnostic modalities rely on non-specific assessments, while liver biopsy is the gold standard to assess severity of disease. Using miRNA-sequencing we investigated the use of serum miRNA to diagnose and monitor CFLD progression in children with CF. Methods: This was a cross-sectional cohort study of the circulatory miRNA signature of 90 children grouped by clinical, biochemical and imaging assessments as follows: healthy controls (n=30), CF patients with no evidence of liver disease (CFnoLD, n=30) and CFLD (n=30). Serum miRNAs were analysed by miRNA-sequencing. Following total circulatory RNA extraction, RNA samples were pooled together to create three libraries (i.e., 10 patients/library) per study cohort.  Libraries were prepared using the Ion Total RNA-Seq Kit v2 protocol (Thermo Fisher, Revision E) and sequenced on the Ion Proton System, using the Ion PI Chip v3 following the Ion PI Hi-Q Sequencing 200 Kit protocol (Thermo Fisher, Revision C).  Selected differentially expressed serum miRNA candidates were further validated in 124 individual children serum samples by qRT-PCR and statistical analysis performed to evaluate utility to predict CFLD and hepatic fibrosis severity validated by liver biopsy. Results: The nine libraries  sequenced by the Ion Proton System produced 64,658,545 total reads. During processing of the sequencing data, we noticed significant low counts mapped from the CFnoLD library 3. Following principal component analysis this library was confirmed to be an outlier and excluded from the analysis. For the remaining libraries, initial threshold filtering was performed by discarding miRNAs with 10 or less counts and normalized for compositional bias in sequenced libraries and library size. After threshold filtering, 659 miRNAs were identified with a minimum average count of 10. Overall design: Serum miRNA profiles of healthy controls (n=30), CF no liver disease (n=30) and CF liver disease (n=30) children were generated by miRNA-sequencing, using the Ion Torrent Proton System.