New study reveals gene expression differences in brain regions tied to addiction, highlighting pathways for innovative alcohol use disorder treatments and drug repurposing opportunities.
Study: Gene expression differences associated with alcohol use disorder in human brain. Image Credit: Roman Zaiets / Shutterstock
A recent study in the journal Molecular Psychiatry provided neurobiological insights into AUD by exploring the meta-analyzed gene expression pattern in two addiction-relevant brain regions, namely, the nucleus accumbens (NAc) and dorsolateral prefrontal cortex (DLPFC).
By conducting meta-analyses across multiple independent datasets, the study identified differentially expressed genes (DEGs) linked with AUD, providing robust findings due to increased statistical power and a large sample size.
The meta-analyses revealed a total of 476 DEGs, with 25 overlapping between the NAc and PFC, highlighting both shared and region-specific gene expression patterns associated with AUD.
The prevalence of and neurological insights into AUD
Millions of deaths occur every year due to alcoholic abuse. Although multiple genome-based studies have indicated the heritable nature of AUD, the gene regulatory landscape linked with this disorder has remained unclear. Understanding the neurobiological mechanisms should help identify a potential target to develop effective interventions to alleviate AUD.
The brain’s NAc, prefrontal cortex (PFC), and DLPFC regions are associated with reward pathways and addiction as components of the dopaminergic mesolimbic system. These brain regions are closely linked with addiction; for example, NAc is associated with the binge/intoxication stage, and DLPFC implicates the preoccupation/anticipation stage.
The PFC regulates the dopamine release into the NAc. Multiple studies have shown that PFC impairment negatively affects executive function and impulsivity and elevates involvement with risky behavior. Taken together, the NAc and PFC brain regions are highly connected with AUD.
A limited number of studies have explored AUD-related bulk RNA-seq gene expression in the human brain. This study’s use of meta-analysis across independent datasets significantly strengthens the reliability of the findings. These studies enabled the identification of differential gene expression (DGE) in the brains of patients with AUD.
About the study
The post-mortem human NAc and DLPFC samples were obtained from 122 candidates, i.e., 61 AUD and 61 non-AUD, as part of the Lieber Institute for Brain Development (LIBD) Human Brain Repository.
AUD cases and controls were determined based on the Diagnostic and Statistical Manual of Mental Disorders-5th edition (DSM-5) symptoms. AUD cases were those who developed more than two symptoms within twelve months, while non-AUD controls were those with no lifetime history of DSM-5 AUD symptoms. Furthermore, non-AUD cases exhibited post-mortem ethanol toxicology of less than 0.06 g/dL.
AUD cases and controls were matched with major depressive disorder (MDD) and smoking status. It must be noted that MDD and tobacco smoking are the two most common comorbidities of AUD.
RNA was extracted from AUD and non-AUD tissues, and Illumina TruSeq Total RNA Stranded RiboZero Gold was used for library preparation. These samples were referred to as NAc_LIBD and PFC_LIBD datasets. Other samples obtained from UT Austin and the NYGC were referred to as NAc_UT, PFC_UT, and PFC_NYGC, respectively.
All RNA-seq data from different sources were processed using various bioinformatic tools, including Trimmomatic and GENCODE v40 (GRCh38) transcriptome, and quality control (QC) metrics were calculated. The proportion of different cell types, such as microglia, macrophages, excitatory neurons, oligodendrocyte precursor cells (OPCs), GABAergic neurons, oligodendrocytes, T-cells, astrocytes, and medium spiny neurons (MSNs), was estimated for PFC and the NAc.
Linear regression analysis was conducted to establish the association between cell type proportions and AUD status based on smoking, age, sex, and MDD. Bioinformatic tools were also used to determine DGE linked with AUD cases and understand gene co-expression. Notably, gene co-expression analysis using weighted gene co-expression network analysis (WGCNA) revealed shared and region-specific gene networks across the NAc and PFC, further deepening insights into AUD-related molecular mechanisms.
Study findings
In the NAc_LIBD and PFC_LIBD datasets, 90 and 98 differentially expressed genes (DEGs) were identified, respectively. Twelve genes were found to overlap in both datasets. No DEGs were identified out of 20,958 genes tested in the NAc_UT dataset. In the PFC_UT and PFC_NYGC datasets, 14 and 53 DEGs, respectively, were recognized. These newly identified DEGs linked with AUD provided insights into gene expression signatures of AUD in specific brain regions.
A total of 447 DEGs associated with AUD in PFC were identified. However, 25 genes were found to differentially express in NAc and PFC that were linked with AUD. The top five DEG genes identified in the meta-analysis of overlapping genes across the NAc samples were ODC1, ZNF844, ARRDC3, FAM225A, and GUSBP11, and across the PFC samples were TXNIP, ODC1, HMGN2, SLC16A9, and SLC16A6.
The current study identified CSPP1 as the only gene significantly linked with AUD in the caudate nucleus (CN); no NAc meta-analysis genes were associated with AUD in the ventral striatum (VS) and putamen (PUT). No PFC meta-analysis significant genes were found to be associated with AUD in CN, VS, or PUT.
Gene set enrichment analysis (GSEA) for the NAc and PFC meta-analyses uncovered four KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. The cross-region weighted gene co-expression network analysis (WGCNA) revealed that no modules were associated with AUD. NAc_LIBD and PFC_LIBD modules were compared, showing that 97.8% of genes in these modules overlapped, suggesting high levels of cross-region co-expression.
Therapeutic intervention for AUD
The Drug Repurposing Database tool was used to identify potential DEG as a therapeutic target for AUD. Of particular interest, 29 drug compounds targeting DEGs in NAc and 436 drug compounds targeting DEGs in PFC were identified, underscoring the potential for drug repurposing to treat AUD. Out of 54 identified DEG genes in NAc, 11 genes were targeted by 29 drug compounds. Furthermore, 64 of the top 100 genes with AUD-associated DGE in PFC could be targeted by 436 drug compounds. Therefore, the current study uncovered potential pharmacotherapies for AUD.