Biology subjects

Zeliff, D.

Publications and source records attributed to Zeliff, D..

2 recordsLinked to original sources

bioRxiv2025

RNA-sequencing Strain-specific Genome Alignment Increases Differential Expression Findings in Comparison of C57BL/6J and DBA/2J Nucleus Accumbens

Alcohol Use Disorder (AUD) is a polygenic disease defined by the inability to regulate alcohol consumption despite adverse consequences. C57BL/6J (B6) and DBA/2J (D2) mice, the progenitor strains to the BXD recombinant inbred strain, exhibit differences in voluntary ethanol consumption and other ethanol behaviors, making them frequently used models for studying genetic influences on ethanol responses. The B6 genome is the standard reference genome for the majority of mouse RNA-sequencing (RNAseq) studies, including studies on D2 mice. We hypothesized that aligning B6 and D2 RNAseq data to their strain specific genome would allow improved detection of differentially expressed genes (DEGs) in comparison of brain gene expression between these two strains. RNA samples obtained from B6 and D2 nucleus accumbens (NAc) tissue were analyzed using a standard RNAseq analysis pipeline except from genome alignment. Following quality control, samples were aligned to either the B6 reference genome (Release 108) or the D2 samples were aligned to a recent homologous genome assembly (GCA_921998315.2). Alignment of D2 samples to the D2 genome showed significantly higher alignment compared to the B6 reference genome (93.82% vs 92.02%, p = 0.0272), but also showed a decrease in the number of total reads assigned (72.30%% vs 74.36%, p <0.0001). When comparing B6 and D2 expression, using the D2 alignment resulted in large increases in the number of differentially expressed genes (DEGs) (10,777 vs 6,191) and differentially utilized exons (DUEs) (81,206 vs 21,223) with resulting changes in gene ontology functional analyses. The gene ontology identified substantial overlap between the two analyses while also adding novel categories. These studies highlight the importance of using strain-specific alignment in increasing the number of reads aligned and the number of DEGs and DUEs identified. The use of strain-specific alignment in RNA-seq studies may provide greater accuracy in investigating gene expression and pathways regulated by ethanol in model organism studies on molecular mechanisms of AUD.

genomics↗

bioRxiv2025

GSK3B inhibition partially reverses brain ethanol-induced transcriptomic changes in C57BL/6J mice: Expression network co-analysis with human genome-wide association studies

Alcohol use disorder (AUD) is a chronic behavioral disease with greater than 50% of its risk due to complex genetic contributions. Existing pharmacological and behavioral treatments for AUD are minimally effective and underutilized. Animal model behavioral genetics and human genome-wide association studies have begun to identify individual genes contributing to the progressive compulsive consumption of ethanol that occurs with AUD, promising possible new therapeutic targets. Our laboratory has previously identified Gsk3b as a central member in a network of ethanol-responsive genes in mouse prefrontal cortex, which altered ethanol consumption with genetic manipulation and was also significantly associated with risk for alcohol dependence in human genome-wide association studies. Here we perform detailed brain RNA sequencing transcriptomic studies to characterize a highly specific and clinically available GSK3B pharmacological inhibitor, tideglusib, as a possible therapeutic for clinical trials on treatment of AUD. A model of chronic intermittent ethanol consumption was used to study gene expression changes in prefrontal cortex and nucleus accumbens in the presence or absence of tideglusib treatment. Multivariate analysis of differentially expressed genes showed that tideglusib largely reversed ethanol- induced expression changes for two prominent clusters of genes in both prefrontal cortex and nucleus accumbens. Bioinformatic analysis showed these genes to have prominent roles in neuronal functioning and synaptic activity. Additionally, mouse brain differential gene expression data was analyzed together with human protein-protein interaction and genome-wide association studies on AUD to derive networks responding to tideglusib and relevant to human genetic risk for alcohol dependence. These studies identified discrete networks significantly enriched with genes provisionally associated with AUD, and provide key information on central hubs of such networks. Together these studies document tideglusib as a major modulator of chronic ethanol consumption-evoked brain gene expression signatures, and identify possible new targets for therapeutic modulation of AUD.

genomics↗