Differential gene expression analysis reveals NF-kB subunit as a potential biomarker for alcohol use disorder

Alcohol Use Disorder is a chronic disease that causes an individual to lose control of their ability to stop drinking, diagnosed by state markers and biomarkers. We analyzed a publicly available RNA-seq dataset comparing patients with Alcohol Dependence (now AUD) to controls. We hypothesized that after analysis of the dataset, there would be a differential gene expression between the control and disease (Alcohol Dependence) groups indicating that expression levels for specific genes vary which can provide insights into biological processes. Using Gene Expression Omnibus 2R, we identified differentially expressed genes with a P-value threshold of 0.05. The 250 most upregulated genes by P-value were inserted in the Search Tool for the Retrieval of Interacting Genes/Proteins database (StringDB) to find out the relationships between genes through the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology.

Furthermore, through the analysis, RELA (NF-κB Subunit p65) emerged as one of the significant genes since it is an activator of AUD symptoms in the “AGE-RAGE signaling pathway in diabetic complications,” possibly serving as a minimal biomarker for AUD. RELA has a Log2FC of 0.384 and approximately 1.3 times the expression level compared to the control group. This biomarker is more reliable than others through its low false discovery rate of 0.014919. The level of expression in RELA along with the candidate genes can be used to diagnose AUD which would provide a high sensitivity along with a low false discovery rate, making it ideal compared to other markers. Gamma-Glutamyltransferase (GGT) and Carbohydrate-Deficient Transferrin (CDT), current markers for AUD, were not seen in the differential gene expression analysis possibly due to them not being highly expressed in the Post-mortem brain tissue compared to the control. RELA has some benefits compared to other markers like GGT and CDT in the sense that RELA has a relatively low false discovery rate and does not have a low sensitivity. Both GGT and CDT are considered to be low sensitivity with GGT being 61% and CDT ranging from 26-83%.

Additionally, the CDT marker results in a significant rate of false negative results while the GGT marker can be affected by certain medications along with pancreatitis or prostate disease in an individual. These weaknesses can be alleviated with RELA since this gene can also be used alongside the other candidate genes to ensure that it does not have a low sensitivity or false negative results. The candidate genes can serve as potential biomarkers since they have a higher fold-change than RELA but they do not directly affect the symptoms in the “AGE-RAGE signaling pathway” so due to confounding variables, these genes were not the main focus of our research. Alcohol can also stimulate NF-κB activity and cytokine expression in the brain which is seen through the dataset since it was derived from brain biopsies. The increased levels in the samples could serve NF-κB as a mediator of addiction-related gene expression.