TY - JOUR
T1 - An approach for prioritizing candidate genes from RNA-seq using preclinical cocaine self-administration datasets as a test case
AU - Vannan, Annika
AU - Dell'Orco, Michela
AU - Perrone-Bizzozero, Nora I.
AU - Neisewander, Janet L.
AU - Wilson, Melissa A.
N1 - Publisher Copyright:
© The Author(s) 2023.
PY - 2023/10
Y1 - 2023/10
N2 - 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. 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 2 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 in either dataset after correcting for multiple testing with false discovery rate (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 the use of our pipeline on a third dataset with differentially expressed genes 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.
AB - 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. 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 2 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 in either dataset after correcting for multiple testing with false discovery rate (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 the use of our pipeline on a third dataset with differentially expressed genes 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.
KW - addiction
KW - animal model
KW - bioinformatics
KW - brain gene expression
KW - differential expression analysis
KW - drug seeking behavior
KW - evolutionary conservation
KW - experimental design
KW - translational value
UR - http://www.scopus.com/inward/record.url?scp=85172940988&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85172940988&partnerID=8YFLogxK
U2 - 10.1093/g3journal/jkad143
DO - 10.1093/g3journal/jkad143
M3 - Article
C2 - 37433118
AN - SCOPUS:85172940988
SN - 2160-1836
VL - 13
JO - G3: Genes, Genomes, Genetics
JF - G3: Genes, Genomes, Genetics
IS - 10
M1 - jkad143
ER -