Optimization of circulating miRNA library preparation for next-generation sequencing and an exploratory pharmacogenomics investigation of psoriatic arthritis patients treated with IL-12/23 or IL-17 inhibitors

Abstract

Optimization for circulating miRNA library preparations, multiplexing capacity, and sequencing with the Ion Torrent System was executed in order to process patient samples effectively. Multiple modifications were attempted in two published protocols before miRNA library preparations reached adequate quality for sequencing. A cohort of nine psoriatic arthritis patients, recruited for a pharmacogenomics investigation of treatment with IL-12/23 or IL-17 inhibitors, had blood samples drawn at baseline, as well as one- and three-month post treatment. The pharmacogenomics samples from baseline were sequenced and the resultant data underwent several analyses in order to identify predictive miRNA markers or profiles. Differential miRNA expression analyses were performed both between the American College of Rheumatology response criteria groupings and on clinical datasets, followed by a comprehensive literature review to examine potential implications of identified miRNAs. Pathway analyses, network analyses, and an in silico functional enrichment analysis were performed on the data to identify associations with signalling cascades, collectively targeted genes, and biological functions, respectively. The results of this exploratory study demonstrate the potential of the miRNA sequencing framework for identifying predictive miRNA markers and profiles associated with response to pharmaceuticals.