Discovery, validation and characterization of Erbb4 and Nrg1 haplotypes using data from three genome-wide association studies of schizophrenia

Abstract

Schizophrenia is one of the most common and complex neuropsychiatric disorders, which is contributed both by genetic and environmental exposures. Recently, it is shown that NRG1-mediated ErbB4 signalling regulates many important cellular and molecular processes such as cellular growth, differentiation and death, particularly in myelin-producing cells, glia and neurons. Recent association studies have revealed genomic regions of NRG1 and ERBB4, which are significantly associated with risk of developing schizophrenia; however, inconsistencies exist in terms of validation of findings between distinct populations. In this study, we aim to validate the previously identified regions and to discover novel haplotypes of NRG1 and ERBB4 using logistic regression models and Haploview analyses in three independent datasets from GWAS conducted on European subjects, namely, CATIE, GAIN and nonGAIN. We identified a significant 6-kb block in ERBB4 between chromosome locations 212,156,823 and 212,162,848 in CATIE and GAIN datasets (p = 0.0206 and 0.0095, respectively). In NRG1, a significant 25-kb block, between 32,291,552 and 32,317,192, was associated with risk of schizophrenia in all CATIE, GAIN, and nonGAIN datasets (p = 0.0005, 0.0589, and 0.0143, respectively). Fine mapping and FastSNP analysis of genetic variation located within significantly associated regions proved the presence of binding sites for several transcription factors such as SRY, SOX5, CEPB, and ETS1. In this study, we have discovered and validated haplotypes of ERBB4 and NRG1 in three independent European populations. These findings suggest that these haplotypes play an important role in the development of schizophrenia by affecting transcription factor binding affinity.

Figure 1. Validation of previously identified and identification of novel haplotypes of ERBB4 in schizophrenia GWAS datasets.

A. ERBB4 polymorphims in three schizophrenia GWAS datasets are illustrated in GWADview software. SNPs are plotted by their location on the y-axis and by their genomic position on the x-axis. Blue represents CATIE, red GAIN and green nonGAIN. The lower panel shows haplotype blocks of this region in Hapmap CEU population. B. LD plots of ERBB4 with the most significant haplotypes in the region from 212,100,000 bp to 212,200,000 bp. Cut-off value for Hardy-Weinberg is 0.05 and for minor allele frequencies 0.001.

Figure 2. Validation of previously identified and identification of novel haplotypes of NRG1 in schizophrenia GWAS datasets.

A. NRG1 polymorphims in three schizophrenia GWAS datasets are illustrated in GWADview software. SNPs are plotted by their location and genomic position on the y and x-axis respectively. Blue represents CATIE, red GAIN and green nonGAIN. The lower panel shows haplotype blocks of this region in Hapmap CEU population. B. LD plots of NRG1 with the most significant haplotypes in the region from 32,250,000 bp to 32,400,000 bp. Cut-off value for Hardy-Weinberg is 0.05 and for minor allele frequencies 0.001.

Figure 3. Identification of gender-specific association of NRG1 in schizophrenia GWAS datasets.

LD plots of NRG1 with the most significant haplotypes A. in the region from 31,618,950 bp to 31,732,358 bp in females. B. in the region from 32,257,152 bp to 32,288,979 bp in males Cut-off value for Hardy-Weinberg is 0.05 and for minor allele frequencies 0.001.

Figure 4. Transcription factors that bind common and significant haplotypes of ERBB4.

The frequencies and p-values of transcription factors that bind to the 6-kb haplotype block of ERBB4 (chr 2: 212,156,823–212,162,848) in CATIE, GAIN and nonGAIN datasets are illustrated. A. The most common haplotype of 6-kb block in CATIE, GAIN and nonGAIN, T-A-G-C, and transcription factors that bind to this haplotype are shown. B, C and D depict the significant haplotypes of the same ERBB4 block in CATIE, GAIN and nonGAIN respectively.

Figure 5. Transcription factors that bind common and significant haplotypes of NRG1.

The frequencies and p-values of transcription factors that bind to the 25-kb haplotype block of ERBB4 NRG1 block (chr 8: 32,291,552–32,317,192) in CATIE, GAIN and nonGAIN datasets are illustrated. A. The most common haplotype of 25-kb block in CATIE, GAIN and nonGAIN, and transcription factors that bind to this haplotype are shown. B, C and D depict the significant haplotypes of the same NRG1 block in CATIE, GAIN and nonGAIN respectively.