Sequence variations of ABCB1, SLC6A2, SLC6A3, SLC6A4, CREB1, CRHR1 and NTRK2: association with major depression and antidepressant response in Mexican-Americans

Abstract

We studied seven genes that reflect events relevant to antidepressant action at four sequential levels: (1) entry into the brain, (2) binding to monoaminergic transporters, and (3) distal effects at the transcription level, resulting in (4) changes in neurotrophin and neuropeptide receptors. Those genes are ATP-binding cassette subfamily B member 1 (ABCB1), the noradrenaline, dopamine, and serotonin transporters (SLC6A2, SLC6A3 and SLC6A4), cyclic AMP-responsive element binding protein 1 (CREB1), corticotropin-releasing hormone receptor 1 (CRHR1) and neurotrophic tyrosine kinase type 2 receptor (NTRK2). Sequence variability for those genes was obtained in exonic and flanking regions. A total of 56 280 000 bp across were sequenced in 536 unrelated Mexican Americans from Los Angeles (264 controls and 272 major depressive disorder (MDD)). We detected in those individuals 419 single nucleotide polymorphisms (SNPs); the nucleotide diversity was 0.00054 + or - 0.0001. Of those, a total of 204 novel SNPs were identified, corresponding to 49% of all previously reported SNPs in those genes: 72 were in untranslated regions, 19 were in coding sequences of which 7 were non-synonymous, 86 were intronic and 27 were in upstream/downstream regions. Several SNPs or haplotypes in ABCB1, SLC6A2, SLC6A3, SLC6A4, CREB1 and NTRK2 were associated with MDD, and in ABCB1, SLC6A2 and NTRK2 with antidepressant response. After controlling for age, gender and baseline 21-item Hamilton Depression Rating Scale (HAM-D21) score, as well as correcting for multiple testing, the relative reduction of HAM-D21 score remained significantly associated with two NTRK2-coding SNPs (rs2289657 and rs56142442) and the haplotype CAG at rs2289658 (splice site), rs2289657 and rs2289656. Further studies in larger independent samples will be needed to confirm these associations. Our data indicate that extensive assessment of sequence variability may contribute to increase understanding of disease susceptibility and drug response. Moreover, these results highlight the importance of direct re-sequencing of key candidate genes in ethnic minority groups in order to discover novel genetic variants that cannot be simply inferred from existing databases.

Figure 1

Minor allele frequency (MAF), nucleotide diversity and F_ST measure in seven candidate genes in Mexican-American major depressive disorder (MDD) patients and controls. Histograms show the total number of single nucleotide polymorphisms (SNPs) detected in intronic (black bar) and exonic (gray bar) regions in the seven genes by MAF in 272 MDD patients and 264 healthy controls (a); the nucleotide diversity in noncoding (black bar) and coding (gray bar) (b) or intronic (black bar) and exonic (gray bar) regions (c) by gene in the combined sample of 272 MDD patients and 264 healthy controls; the total number of SNPs shared by Mexican-American (MA) sample and HapMap samples by pairwise F_ST value (d) or represent the average F_ST by gene (e) in MA vs CEU (black bar), MA vs HCB (dark gray bar), MA vs JPT (gray bar) and MA vs YRI (White bar).

Figure 2

Linkage disequilibrium (LD) pattern in seven genes: cyclic AMP-responsive element binding protein 1 (CREB1) (a), SLC6A3 (b), ATP-binding cassette subfamily B member 1 (ABCB1) (c), neurotrophic tyrosine kinase type 2 receptor (NTRK2) (d), SLC6A2 (e), SLC6A4 (f) and corticotropin-releasing hormone receptor 1 (CRHR1) (g). Standard color scheme in Haploview program is used to display the level of logarithm of odds (LODs) and the D′. Shown in each box are estimated statistics of the D′, which indicates the LD relationship between each pair of single nucleotide polymorphisms (SNPs) and are not labeled if D′=1.00. Regions are shown in bright red, light blue, shades of pink/red and white for D′=1+LOD⩾2, D′=1+LOD<2, D′<1+LOD⩾2 and D′<1+LOD<2, respectively. Vertical lines on the long horizontal white indicate the relative positions of SNPs in the gene.