An approach for prioritizing candidate genes from RNA-seq using preclinical cocaine self-administration datasets as a test case.

Abstract

RNA-sequencing (RNA-seq) technology has led to a surge of neuroscience research using animal models to probe the complex molecular mechanisms underlying brain function and behavior, including substance use disorders (SUDs). However, findings from rodent studies often fail to be translated into clinical treatments. Here, we developed a novel pipeline for narrowing candidate genes from preclinical studies by translational potential and demonstrated its utility in two RNA-seq studies of rodent self-administration. This pipeline uses evolutionary conservation and preferential expression of genes across brain tissues to prioritize candidate genes, increasing the translational utility of RNA-seq in model organisms. Initially, we demonstrate the utility of our prioritization pipeline using an uncorrected p-value. However, we found no differentially-expressed genes (DEGs) in either dataset after correcting for multiple testing (FDR < 0.05 or < 0.1). This is likely due to low statistical power that is common across rodent behavioral studies, and therefore we additionally illustrate use of our pipeline on a third dataset with DEGs corrected for multiple testing (FDR < 0.05). We also advocate for improved RNA-seq data collection, statistical testing, and metadata reporting that will bolster the field's ability to identify reliable candidate genes and improve the translational value of bioinformatics in rodent research.