Comorbid depression with AUD shows evidence of both genetic and environmental influences on susceptibility. In three phases of hypothesis generation and testing (NCBI database queries, PDG-ACE and GeneGo analyses) we established and tested a model of gene-by-environment interaction that shows evidence of influencing the comorbidity and is consistent with established knowledge about AUD and depression [37
]. We first hypothesized that common genetic influences affect AUD and depression. We tested this hypothesis by searching for candidate genes and found published evidence, via Entrez Gene and PubMed, supporting the roles of TNF and MTHFR in depression and AUD. Given evidence of a multi-gene influence on the comorbidity, we hypothesized that TNF and MTHR participate in a genetic interaction influencing the comorbidity. Mining the Entrez Gene records for TNF and MTHFR via the PDG-ACE algorithm, we found twenty one keywords that are common and significantly over-represented across the gene pair, consistent with interaction between these genes in comorbid AUD with depression. In addition, among the significant keywords, those that are most often associated with depression and AUD in the literature are suggestive of an environmental effect on this genetic interaction via ethanol intake or consumption. Given evidence that TNF and MTHFR participate in a genetic interaction that may be influenced by environmental exposure to ethanol, as well as evidence that TNF influences signal transduction pathways in response to the environment, we hypothesized signal transduction as the most appropriate model of the gene-by-environment interaction. Modeling this hypothesis via GeneGo, we found that both TNF and MTHFR are influenced by a genetic feedback cycle that incorporates environmental ethanol exposure into folate metabolism. Altered folate levels, as well as AUD, are consistently linked to depression [42
Mason and Choi [37
] review other mechanisms (decreased dietary intake of folate, decreased intestinal absorption, increased urinary secretion, and cleavage of the folate molecule) that have been purported to reduce the bio-availability of folate with excessive ethanol intake. In addition, they review the adverse effects that ethanol can have on one-carbon metabolism, a process that includes the synthesis of folate. Mason and Choi show five enzymes involved in one-carbon metabolism including MTHFR, Cystathionine beta-synthase (CBS, GeneID 875), Betaine Homocysteine Methyltransferase (BHMT, GeneID 635), Serine Hydroxymethyltransferase 1 (SHMT, GeneID 6470), and Methionine Synthase (MTR, GeneID 4548). Figure is a GeneGo graphic showing how TNF signaling may impact every one of these enzymes by regulating their expression. This network, still fairly simple, includes all of the elements of the proposed model (Figure ) and provides a suggestion of how AUD impacts one-carbon metabolism in a complex genotype-phenotype relationship. Arguably, because all of the enzymes seen in this network affect folate metabolism, they all are candidates for influencing comorbid depression with AUD.
Figure 4 GeneGo graphic illustrating how TNF signaling impacts one-carbon metabolism. Folate metabolism is one element of one-carbon metabolism and TNF signaling influences all of the enzymes involved. As a result, variations in any of the genes involved in one-carbon (more ...)
Based on the relationship between folate metabolism and one-carbon metabolism, we searched for evidence that the one-carbon metabolic process influences depression, AUD, and the comorbidity. Table shows evidence that several of these genes may have influences on depression or AUD. The larger hypotheses, depression AND folate, ethanol AND folate, show 133 and 237 citations, respectively, though we did not find evidence for depression AND ethanol AND folate. In Figure , two additional genes, p53 (TP53, GeneID 7157) and HNF4a (HNF4-alpha, GeneID 3172), are shown to participate in the network. Searching for evidence of these genes in depression, AUD, and the comorbidity, we found evidence for association between p53 and ethanol (Table ). Interestingly, "p53 gene" is one of the 21 keywords that we found to be common and significantly overrepresented across the TNF/MTHFR gene pair in the PDG-ACE analysis (Table ).
Additional hypotheses tested based on GeneGo modelling
Notably, while the evidence assembled in this analysis is consistent with our hypothesized model of gene-by-environment interaction of comorbid depression with AUD, much data remains missing. For example, we emphasize the environmental influence of alcohol consumption, though we have little information on how alcohol dosage or the duration of alcohol exposure might affect genetic influences in our model. Equally, while we have identified a network of genes that may influence the comorbidity, we have limited information on heritable variation that would be expected to increase or decrease susceptibility. To date, the C677T variant of MTHFR is associated with both susceptibility to depression [27
] and ethanol response [26
], and levels of TNF mRNA have been associated with depression [25
]. Cytogenetic band 6p21, the chromosomal location of TNF, has recently been associated with chromosomal aberrations in alcoholism [47
]. However, the genetic influences of this network are likely to be much more complex than what we know so far. Missing data on these influences await follow-on analyses (e.g., targeted genotyping in an affected population versus controls, animal modelling) that can be informed by the model developed here. Also, given the model proposed, future data from WGA or microarray studies can be tested on a reduced number of hypotheses, thus increasing the power of these tools.
Implications of this model are consistent with dietary guidance recommending monitoring and appropriate supplementation of folate for patients in treatment for depression [48
], AUD, or comorbid depression with AUD [37
]. In addition, identification of the variants associated with risk could be useful in prognosis and treatment of either or both conditions [51
]. Pharmacogenomic approaches are being successfully implemented in psychiatry, to the great benefit of patients with specific genetic variants [52
], and the identification of disease predisposing variants will likely improve the prognosis for depression with AUD.