Background: Acamprosate and Naltrexone are FDA approved drugs for the treatment of AUD. GWAS for clinical trials of acamprosate and/or naltrexone treatment of AUD that enrolled 1083 participants identified single nucleotide polymorphisms (SNPs) in the BRE gene (p = 1.6E−8) associated with time to relapse to heavy drinking during the first 3 months of drug or placebo therapy. The GTEx database reported that those SNPs were a splicing quantitative trait locus for the FNDC4 gene--which mapped 400 kb distant from BRE. The splice variant resulted in early termination of transcription. FNDC4 is a secreted protein highly expressed in neurons and was included among top genes identified in an ethanol withdrawal mouse model. Methods: We analyzed human brain tissue Hi-C data to determine a possible link between the GWAS SNP signal and FNDC4. Wild type and alternatively spliced FNDC4 cDNA constructs were generated to compare their effect on FNDC4 protein secretion from 293T cells. Finally, RNA sequencing was applied to study FNDC4 function in iPSC-derived human neurons. Results: We identified chromatin looping between the GWAS SNPs and the distant FNDC4 gene. GWAS SNP-dependent FNDC4 splicing at exon 6 changed its secretion after expression in 293T cells. We found that FNDC4 dysregulated a series of AUD-associated pathways in iPSC-derived neurons. Finally, we observed that FNDC4 expression in neurons could be regulated by ethanol-dependent induction of TGFβ2. Conclusion: GWAS identified AUD drug treatment outcomes associated with SNPs that regulated FNDC4 splicing and reduced FNDC4 protein secretion from neurons. FNDC4 may influence alcohol intake by regulating AUD-associated genes such as BDNF. These observations may help explain biological mechanisms for the association of SNPs at the BRE locus with response to AUD drug therapy.
