Detailed analysis of the serotonin transporter gene (SLC6A4) shows no association with bipolar disorder in the Northern Swedish population

Exploring the Structural and Functional Effects of Nonsynonymous SNPs in the Human Serotonin Transporter Gene Through In Silico Approaches

The sodium-dependent serotonin transporter SLC6A4 (solute carrier family 6 member 4) gene encodes an intrinsic membrane protein that transmits the serotonin neurotransmitter from synaptic clefts into presynaptic neurons. The product of the SLC6A4 gene is related to the regulation of mood and social behavior, sleep, appetite, memory, digestion, and sexual desire. This protein is a target for antidepressant and psychostimulant drugs, thus prolonged neurotransmitter signaling remains blocked. In this study, the functional consequences of nsSNPs in the human SLC6A4 gene were explored through computational tools: PhD-SNP, SIFT, Align GVGD, PROVEAN, PMut, nsSNP Analyzer, SNPs&GO, SNAP2, PolyPhen2, and PANTHER to identify the most deleterious and damaging nsSNPs. Then the mutant protein stabilities were assessed using I-Mutant, MUpro, and MutPred2; amino acid conservation using ConSurf, and posttranslational modification analysis using MusiteDEEP and PROSPER. Furthermore, the 3-dimensional (3D) model of the mutated proteins was predicted and validated using SPARKS-X, Verify3D, and PROCHECK. The protein–ligand binding sites were analyzed using the COACH meta-server. Results from this study predicted that T192M, G342E, R607C, W282S, R104C, P131L, P156L, and N351S were the most structurally and functionally significant nsSNPs in the human SLC6A4 gene. Arg607 and Pro156 were the predicted sites for posttranslational modifications, and Thr192 and Try282 were the ligand-binding sites in the human SLC6A4 gene. The analyzed data also suggested that R104C, P131L, P156L, T192M, G342E, and W282S mutants might affect the binding of sodium ions with this protein. Taken together, this study provided important information on structurally and functionally important nsSNPs of the human SLC6A4 gene for further experimental validation. In the future, these damaging nsSNPs of the SLC6A4 gene have the potential to be evaluated as prognostic biomarkers for SLC6A4-related disorder diagnosis and research.

A functional SNP in MIR124-1, a brain expressed miRNA gene, is associated with aggressiveness in a Colombian sample

Background:

Interpersonal violence and suicide are among the main causes of mortality and morbidity around the world. In several developing countries, such as Colombia, they are among the first five entities of public health concern. Aggressiveness is an important endophenotype for aggression and suicidal behavior, having a heritability of around 50%. Exploration of classical candidate genes, involved in serotoninergic and dopaminergic neurotransmission, has identified few consistent risk factors for aggressiveness. miRNAs are a novel class of molecules with a growing role in normal neural function and neuropsychiatric disorders; of special interest, miR-124 is a brain-specific miRNA that is key for neuronal plasticity. We evaluated the hypothesis that a functional polymorphism in MIR124-1 gene might be associated with aggressiveness in a Colombian sample.

Methods:

The Spanish adaptation of the refined version of the Aggression Questionnaire and the abbreviated Barratt Impulsiveness Scale were applied to 170 young subjects. The functional SNP in MIR124-1 (rs531564) was genotyped by a TaqMan assay.

Results:

We found a significant association between the MIR124-1 and aggressiveness in our sample, with G/G carriers having lower scores (P = 0.01). This association seemed to be specific for aggressiveness, as it was not significant for impulsiveness.

Conclusions:

We showed for the first time the association of a functional polymorphism in MIR124-1 and aggressiveness. Known targets of miR-124 (such as BDNF and DRD4 genes) could explain the effect of this miRNA on behavior. A future analysis of additional novel functional polymorphisms in other brain expressed miRNAs could be useful for a deeper understanding of aggression in humans.

Associations of the serotonin transporter promoter polymorphism (5-HTTLPR) with bipolar disorder and treatment response: A systematic review and meta-analysis

BACKGROUND

Associations of the serotonin transporter promoter polymorphism (5-HTTLPR) with bipolar disorder (BPD) and treatment response in bipolar patients were not conclusive. This study not only assessed the association between the 5-HTTLPR and BPD with accumulating relevant studies, but also in the first time evaluated the effect of the 5-HTTLPR on both anti-depressive and anti-manic treatment responses in bipolar patients.

METHODS

PubMed, Embase, PsycINFO, Cochrane Library and Cochrane Control Trials databases were systematically searched before February 2017. This meta-analysis followed the PRISMA guidelines.

RESULTS

A total of 32 population-based studies (5567 cases and 6993 controls) and 9 family-based studies (837 trios) were finally screened out and statistically joined into a single meta-analysis that revealed an association between S allele and an increased risk of BPD (OR = 1.06, p = .038). Pooled analysis of the 32 population-based studies indicated an association of S-carrier genotypes with an increased risk of BPD (OR = 1.10, p = .029). Meanwhile, the association remained significant in Caucasians (OR = 1.15, p = .004), which could provide an enough power (88%) to detect a significant association. Regarding the treatment response studies, 6 studies reporting the relationship of the 5-HTTLPR in anti-depressive remission rate (1034 patients) and 7 studies reporting in response rate (1098 patients) were included for pooled analyses. We observed a significant association of S-carrier genotypes with a reduced anti-depressive remission rate (OR = 0.64, p = .006) but not with anti-depressive response rate. The association between the 5-HTTLPR with anti-manic response rate was not observed in the included 6 studies (676 patients).

CONCLUSIONS

The present study supported the presence of a marginal but detectable effect of the 5-HTTLPR on susceptibility to BPD. Moreover, the detected association in Caucasian was statistically reliable. Besides, the 5-HTTLPR was identified as a useful predictor for anti-depressive remission but not for anti-depressive or anti-manic response.

Situation Awareness Performance in Healthy Young Adults Is Associated With a Serotonin Transporter Gene Polymorphism

Background Situation awareness (SA) is defined in three levels: SA1 is the perception of the elements in a specific context, SA2 is the comprehension of their meaning, and SA3 is the projection of their status. Purpose To analyze the possible association of a genetic polymorphism in the serotonin transporter ( SLC6A4) gene and performance on the Situational Awareness test (SAtest). Methods SAtest was applied to a sample of 230 healthy Colombian subjects, using the Psychology Experiment Building Language platform and a functional polymorphism in the SLC6A4 gene was genotyped by polymerase chain reaction. Results In the SA1 level, s/s genotype carriers had worse accuracy, in comparison with s/l and l/l genotypes. At SA2 level, l/l genotype carriers had better accuracy than s/s and s/l individuals and that in the SA3 level, l/l carriers also had better accuracy. These associations were significant after correction for multiple testing. Conclusions It is possible that l/l carriers have a better ability to perceive and focus their attention on the elements of their environment and to have the capacity to understand and predict what will happen with those elements. This is the first genetic study of SA performance in healthy participants. Additional investigations of other genes could contribute to the understanding of the molecular correlates of SA in healthy subjects and in neuropsychiatric patients.

Development of Novel High-Resolution Melting-Based Assays for Genotyping Two Alu Insertion Polymorphisms (FXIIIB and PV92)

Insertion/Deletion polymorphisms (InDels) are a common type of genetic variation, with a growing role in population genetics and applied genomics. There is the need for the development of novel cost-effective assays for genotyping InDels of high importance. The main objective of this study was to develop high-resolution melting-based assays for genotyping two commonly studied Alu insertion polymorphisms: FXIIIB and PV92 (rs70942849 and rs3138523). Three primers (two forward and one reverse) were designed for each marker, and high-resolution melting (HRM) analyses in a qPCR platform were performed, using EvaGreen fluorescent dye. For each one of the two Alu insertion polymorphisms, HRM analyses identified distinguishable peaks for the three genotypes, allowing a robust genotyping. Results were validated using 96 DNA samples previously genotyped and the assays worked with different DNA concentrations. In this study, we developed novel cost-effective assays, using qPCR, for genotyping two Alu insertion polymorphisms (widely used as ancestry markers). Our results highlight the feasibility of using HRM analyses for genotyping InDel polymorphisms of medical and biotechnological importance.

Polymorphism of rs3813034 in Serotonin Transporter Gene SLC6A4 Is Associated With the Selective Serotonin and Serotonin-Norepinephrine Reuptake Inhibitor Response in Depressive Disorder: Sequencing Analysis of SLC6A4

Selective serotonin and serotonin-norepinephrine reuptake inhibitors (SSRI/SNRI) are commonly used for treating major depression. Regretfully, significant heterogeneity exists regarding the benefits of SSRI/SNRI in individual cases. We previously reported that a polymorphism located in the serotonin transporter linked promoter region (5-HTT LPR) is associated with an interindividual difference in SSRI treatment efficacy. However, this explains only a small part of the variation of this complex phenotype. Other 5-HTT variants in the coding regions, 3' untranslated region (3' UTR), and introns adjacent to each exon could also contribute to treatment response. Therefore, we performed a sequencing analysis of the SLC6A4 gene (coding for 5-HTT) and investigated the association between variants detected in this study and the antidepressant response to SSRI/SNRI in 201 Japanese depressive patients. Seventeen novel mutations were identified by sequencing analysis. We found that the polymorphism G2563T (rs3813034) as a tag single-nucleotide polymorphism of IVS9 A-90G (rs140701), G2356T (rs1042173), and A3641C (rs7224199) is associated with interindividual variability of SSRI/SNRI efficacy at week 6, independent from clinical variables and effect of 5-HTT LPR (P < 0.001 by multiple regression analysis). This polymorphism could help determine individualized SSRI/SNRI treatments for depressive patients in combination with 5-HTT LPR.

Functional polymorphisms in BDNF and COMT genes are associated with objective differences in arithmetical functioning in a sample of young adults

BACKGROUND

Understanding the molecular genetics of complex human behaviors and functions remains a substantial challenge for the neurosciences. Previous studies have shown a genetic basis for individual differences in mathematical functioning; however, the specific genes remain to be completely identified. In the present study, we explored the possibility that 2 functional polymorphisms in candidate genes could be associated with differences in arithmetical performance.

METHODS

A computerized test to analyze performance in basic arithmetical calculations (additions and subtractions) was applied to 168 healthy young Colombian participants using the PEBL (Psychology Experiment Building Language) battery. DNA samples were genotyped for 2 functional SNPs in candidate genes: brain-derived neurotrophic factor (BDNF)-Val66Met and catechol-O-methyltransferase (COMT)-Val158Met.

RESULTS

We found significant differences for arithmetical processing scores between genotypes. For BDNF, Val/Val subjects had a worse performance (p value: 0.025) and for COMT, Val/Val carriers had a better performance (p value: 0.006). A multivariate model, including both BDNF and COMT genes, accounted for 7.1% of the variance in math processing scores.

DISCUSSION

To our knowledge, this is the first study finding associations of polymorphisms in BDNF and COMT genes with quantitative measures of numerical aptitude in healthy young participants. A future study of other genes involved in neural plasticity could be helpful to identify genetic correlates of arithmetical functioning, which will be important for the understanding of normal human behaviors and related neuropsychiatric disorders.

Differences in planning performance, a neurocognitive endophenotype, are associated with a functional variant in PER3 gene

Performance alterations in executive function have been studied as potential endophenotypes for several neuropsychiatric diseases. Planning is an important component of executive function and has been shown to be affected in diseases such as attention deficit hyperactivity disorder, schizophrenia, obsessive-compulsive disorder and Parkinson's disease. Several genes related to dopaminergic systems, such as COMT, have been explored as candidates for influencing planning performance. The circadian clock gene PERIOD3 (PER3) has been shown to be associated with several complex behaviors in humans and could be involved in different signaling mechanisms. In this study, we evaluated the possible association between a functional polymorphism in the PER3 gene (PER3-VNTR, rs57875989) and performance in a commonly used test of planning (Tower of London, TOL) in 229 healthy subjects from Bogotá, Colombia. PER3-VNTR genotyping was carried out with conventional PCR and all participants completed the TOL test using the computerized Psychology Experiment Building Language (PEBL) battery. A linear regression model was used for the analysis of association with the SNPStats program. We found that 4/4 genotype carriers showed a better performance and made fewer moves, in comparison to 4/5 and 5/5 genotype carriers (p = 0.003). These results appear to be independent from effects of this polymorphism on self-reported average hours of sleep during work days in our sample. This is the first evidence of an association between PER3-VNTR and planning performance in a sample of healthy subjects and our results are consistent from previous findings for alterations in other cognitive domains. Future studies examining additional genes could lead to the identification of novel molecular underpinnings of planning in healthy subjects and in patients with neuropsychiatric disorders.

No Association of BDNF, COMT, MAOA, SLC6A3, and SLC6A4 Genes and Depressive Symptoms in a Sample of Healthy Colombian Subjects

Background. Major depressive disorder (MDD) is the second cause of years lived with disability around the world. A large number of studies have been carried out to identify genetic risk factors for MDD and related endophenotypes, mainly in populations of European and Asian descent, with conflicting results. The main aim of the current study was to analyze the possible association of five candidate genes and depressive symptoms in a Colombian sample of healthy subjects. Methods and Materials. The Spanish adaptation of the Hospital Anxiety and Depression Scale (HADS) was applied to one hundred eighty-eight healthy Colombian subjects. Five functional polymorphisms were genotyped using PCR-based assays: BDNF-Val66Met (rs6265), COMT-Val158Met (rs4680), SLC6A4-HTTLPR (rs4795541), MAOA-uVNTR, and SLC6A3-VNTR (rs28363170). Result. We did not find significant associations with scores of depressive symptoms, derived from the HADS, for any of the five candidate genes (nominal p values >0.05). In addition, we did not find evidence of significant gene-gene interactions. Conclusion. This work is one of the first studies of candidate genes for depressive symptoms in a Latin American sample. Study of additional genetic and epigenetic variants, taking into account other pathophysiological theories, will help to identify novel candidates for MDD in populations around the world.

A functional polymorphism in the promoter region of MAOA gene is associated with daytime sleepiness in healthy subjects

Excessive daytime sleepiness (EDS) is one of the main causes of car and industrial accidents and it is associated with increased morbidity and alterations in quality of life. Prevalence of EDS in the general population around the world ranges from 6.2 to 32.4%, with a heritability of 38-40%. However, few studies have explored the role of candidate genes in EDS. Monoamine oxidase A (MAOA) gene has an important role in the regulation of neurotransmitter levels and a large number of human behaviors. We hypothesized that a functional VNTR in the promoter region of the MAOA gene might be associated with daytime sleepiness in healthy individuals. The Epworth sleepiness scale (ESS) was applied to 210 Colombian healthy subjects (university students), which were genotyped for MAOA-uVNTR. MAOA-uVNTR showed a significant association with ESS scores (p = 0.01): 3/3 genotype carriers had the lowest scores. These results were supported by differences in MAOA-uVNTR frequencies between diurnal somnolence categories (p = 0.03). Our finding provides evidence for the first time that MAOA-uVNTR has a significant association with EDS in healthy subjects. Finally, these data suggest that functional variations in MAOA gene could have a role in other phenotypes of neuropsychiatric relevance.

Evidence for single nucleotide polymorphisms and their association with bipolar disorder

Bipolar disorder (BD) is a complex disorder with a number of susceptibility genes and environmental risk factors involved in its pathogenesis. In recent years, huge progress has been made in molecular techniques for genetic studies, which have enabled identification of numerous genomic regions and genetic variants implicated in BD across populations. Despite the abundance of genetic findings, the results have often been inconsistent and not replicated for many candidate genes/single nucleotide polymorphisms (SNPs). Therefore, the aim of the review presented here is to summarize the most important data reported so far in candidate gene and genome-wide association studies. Taking into account the abundance of association data, this review focuses on the most extensively studied genes and polymorphisms reported so far for BD to present the most promising genomic regions/SNPs involved in BD. The review of association data reveals evidence for several genes (SLC6A4/5-HTT [serotonin transporter gene], BDNF [brain-derived neurotrophic factor], DAOA [D-amino acid oxidase activator], DTNBP1 [dysbindin], NRG1 [neuregulin 1], DISC1 [disrupted in schizophrenia 1]) to be crucial candidates in BD, whereas numerous genome-wide association studies conducted in BD indicate polymorphisms in two genes (CACNA1C [calcium channel, voltage-dependent, L type, alpha 1C subunit], ANK3 [ankyrin 3]) replicated for association with BD in most of these studies. Nevertheless, further studies focusing on interactions between multiple candidate genes/SNPs, as well as systems biology and pathway analyses are necessary to integrate and improve the way we analyze the currently available association data.

Behavioural genetics of the serotonin transporter

The serotonin transporter is a key regulator of the bioavailability of serotonin and therefore any modulation in the expression or action of the transporter would be expected to have consequences on behaviour. The transporter has therefore become a target for pharmaceutical intervention in behavioural and mood disorders. The search for polymorphic variants in the transporter that would associate with neurological disorders has been extensive but has become focused on two domains which are both termed variable number tandem repeat (VNTR)polymorphisms. Both of these VNTRs are in non-coding DNA and therefore proposed to be mechanistically involved in a disorder through their ability to modulate transcriptional or post-transcriptional regulation of the transporter. The most extensively studied is in the promoter and is a bi-allelic insertion/deletion found in the 50 promoter region of the gene 1.2 kb upstream of the transcriptional start site. This VNTR, termed, 5-HTTLPR was initially identified as two variants containing either, 14 (short/deletion) or 16 (long/insertion) copies of a 22 bp repeat. A second widely studied VNTR found in the non-coding region of the transporter is located within intron 2 and comprises 9, 10 or 12 copies of a16–17 bp repeat termed, STin2.9, STin2.10 and STin2.12, respectively. These VNTR polymorphisms have been associated with a range of behavioural and psychiatric disorders including depression, OCD, anxiety and schizophrenia, however often the lack of reproducibility in different cohorts has led to debate on the actual association of the polymorphisms with this extensive range of neurological conditions. Here we review these two polymorphic VNTRs in depth and relate that to pharmaceutical response, their ability to regulate differential transporter expression, their core involvement in gene-environment interaction and their genetic association with specific disorders.

Variants of the serotonin transporter gene and NEO-PI-R Neuroticism: No association in the BLSA and SardiNIA samples

The polymorphism in the serotonin transporter gene promoter region (5-HTTLPR) is by far the most studied variant hypothesized to influence Neuroticism-related personality traits. The results of previous studies have been mixed and appear moderated by the personality questionnaire used. Studies that used the TCI to assess Harm Avoidance or the EPQ to assess Neuroticism have found no association with the 5-HTTLPR. However, studies that used the NEO-PI-R or related instruments (NEO-PI, NEO-FFI) to measure Neuroticism have found some evidence of association. This study examines the association of variants in the serotonin transporter gene in a sample from a genetically isolated population within Sardinia (Italy) that is several times larger than previous samples that used the NEO-PI-R (N = 3,913). The association was also tested in a sample (N = 548) from the Baltimore Longitudinal Study of Aging (BLSA), in which repeated NEO-PI-R assessments were obtained. In the SardiNIA sample, we found no significant association of the 5-HTTLPR genotypes with Neuroticism or its facets (Anxiety, Angry-Hostility, Depression, Self-Consciousness, Impulsiveness, and Vulnerability). In the BLSA sample, we found lower scores on Neuroticism traits for the heterozygous group, which is inconsistent with previous studies. We also examined eight SNPs in the SardiNIA (N = 3,972) and nine SNPs in the BLSA (N = 1,182) that map within or near the serotonin transporter gene (SLC6A4), and found no association. Along with other large studies that used different phenotypic measures and found no association, this study substantially increases the evidence against a link between 5-HTT variants and Neuroticism-related traits.