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• RNAseq transcriptomes revealed that alcohol affects the three organs differentially. • Alcohol and KYNA affect gene transcription differently from alcohol or KYNA alone. • Tryptophan metabolism was skewed towards the kynurenine pathway in the brain. Excessive alcohol (ethanol) use has long been known to affect human health negatively. However, the underlying molecular basis is incompletely understood. Moreover, consumption of alcohol is often mixed with kynurenic acid (KYNA), an abundant tryptophan metabolite produced during fermentation. The combined effect of ethanol and KYNA on host gene expression has not been investigated. The current study used mice as the model to interrogate the impact of ethanol and/or KYNA on global gene transcription. Adult male mice were administered with 2 g/kg ethanol and/or 0.1 mg/kg KYNA by gavage once a day for a week. Three organs: brain, kidney, and liver were collected and their total RNAs extracted for transcriptome sequencing and quantitative real-time PCR. Gene ontology, Kyoto encyclopedia of genes, and genomes pathway analyses revealed that alcohol affects the three organs differentially. Furthermore, the gene expression profile from alcohol and KYNA co-administration was significantly different from that of alcohol or KYNA administration alone. Strikingly, Indolamine 2,3-dioxygenase 1, a rate-limiting enzyme in tryptophan metabolism, was significantly increased in the brain after a combined exposure of alcohol and KYNA, suggesting that Trp metabolism was skewed towards the kynurenine pathway in the brain. Our systemic analysis provides new insights into the mechanism whereby alcohol and KYNA affects organ functions. [ABSTRACT FROM AUTHOR]