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Quantitative leukocyte BDNF promoter methylation analysis in bipolar disorder.

Strauss JS, Khare T, De Luca V, Jeremian R, Kennedy JL, Vincent JB, Petronis A - Int J Bipolar Disord (2013)

Bottom Line: Five CpG units, mostly in promoter 5, remained significant after false discovery rate correction (FDR) (p values ≤ 0.004) with medium to large effect sizes (Cohen's d ≥ 0.61).Statistically significant differences in mean methylation fraction at 5/36 CpG units (after FDR), some at or immediately adjacent to TFBSs, suggest possible relevance for the current findings to BD etiopathogenesis.Future studies should provide more exhaustive epigenetic study of the BDNF locus to better characterize the relationship between BDNF methylation differences and BD.

View Article: PubMed Central - PubMed

Affiliation: Centre for Addiction and Mental Health, University of Toronto, Toronto, ON M6J1H4 Canada.

ABSTRACT

Background: Bipolar disorder (BD) is a complex psychiatric phenotype with a high heritability and a multifactorial etiology. Multisite collaborative efforts using genome-wide association studies (GWAS) have identified only a portion of DNA sequence-based risk factors in BD. In addition to predisposing DNA sequence variants, epigenetic misregulation may play an etiological role in BD and account for monozygotic twin discordance, parental origin effects, and fluctuating course of BD. In this study, we investigated DNA methylation of the brain-derived neurotrophic factor (BDNF) gene in BD.

Methods: Fifty participants with BD were compared to the same number of age- and sex-matched controls for DNA methylation differences at BDNF promoters 3 and 5. DNA methylation reads were obtained using a mass spectrophotometer for 64 cytosine-guanine (CpG) sites in 36 CpG 'units' across three amplicons of BDNF promoters 3 and 5.

Results and discussion: Methylation fractions differed between BD participants and controls for 11 of 36 CpG units. Five CpG units, mostly in promoter 5, remained significant after false discovery rate correction (FDR) (p values ≤ 0.004) with medium to large effect sizes (Cohen's d ≥ 0.61). Several of the significant CpGs overlapped with or were immediately adjacent to transcription factor binding sites (TFBSs) - including two of the FDR-significant CpG units in promoter 5. For the CpGs in promoter 3, there was a positive and significant correlation between age at sample collection and DNA methylation fraction (rho = 0.56, p = 2.8 ×10(-5)) in BD cases, but not in controls. Statistically significant differences in mean methylation fraction at 5/36 CpG units (after FDR), some at or immediately adjacent to TFBSs, suggest possible relevance for the current findings to BD etiopathogenesis. The positive correlation between age and methylation seen in promoter 3 is consistent with age-related decline in BDNF expression previously reported. Future studies should provide more exhaustive epigenetic study of the BDNF locus to better characterize the relationship between BDNF methylation differences and BD.

No MeSH data available.


Related in: MedlinePlus

Graphical overview at BDNF gene. The BDNF gene structure and promoter locations are adopted from the study of Pruunsild et al. (2007). Arrow on the top shows the direction of BDNF transcript; exons (green), CpG islands (cyan), and investigated regions for DNA methylation (black) are mapped on NCBI accession number AF411339.1. CpG island were detected by CpGPlot using default parameters (http://www.ebi.ac.uk/Tools/seqstats/emboss_cpgplot/). Number of CpG dinucleotides in each amplicons is shown as lollipops on the lower panel.
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Fig1: Graphical overview at BDNF gene. The BDNF gene structure and promoter locations are adopted from the study of Pruunsild et al. (2007). Arrow on the top shows the direction of BDNF transcript; exons (green), CpG islands (cyan), and investigated regions for DNA methylation (black) are mapped on NCBI accession number AF411339.1. CpG island were detected by CpGPlot using default parameters (http://www.ebi.ac.uk/Tools/seqstats/emboss_cpgplot/). Number of CpG dinucleotides in each amplicons is shown as lollipops on the lower panel.

Mentions: BDNF sequence (AF411339.1) was used to map different known CpG promoters within the gene (Figure 1); two methods were used. First, the CSHL human promoter mapping using CpG islands (CpGpromoter) (Ioshikhes and Zhang 2000) enabled mapping of human promoters using Gardiner-Garden and Frommer's definition of CpG islands (Gardiner-Garden and Frommer 1987) (http://rulai.cshl.org/tools/CpG_promoter). CpGpromoter indicated CpG islands related to promoters at three regions of AF411339.1. Second is the BIMAS Promoter Scan (Center for Information Technology, NIH, http://www-bimas.cit.nih.gov/molbio/proscan/), which uses PROSCAN 1.7 to predict promoters based on scoring homologies with eukaryote Pol II sequences. BIMAS corroborated the three CpG island promoters noted with CpGpromoter, which correspond to BDNF promoters 1, 3, and 5 of the nine promoters described by Pruunsild et al. (2007) (see Figure 1).Figure 1


Quantitative leukocyte BDNF promoter methylation analysis in bipolar disorder.

Strauss JS, Khare T, De Luca V, Jeremian R, Kennedy JL, Vincent JB, Petronis A - Int J Bipolar Disord (2013)

Graphical overview at BDNF gene. The BDNF gene structure and promoter locations are adopted from the study of Pruunsild et al. (2007). Arrow on the top shows the direction of BDNF transcript; exons (green), CpG islands (cyan), and investigated regions for DNA methylation (black) are mapped on NCBI accession number AF411339.1. CpG island were detected by CpGPlot using default parameters (http://www.ebi.ac.uk/Tools/seqstats/emboss_cpgplot/). Number of CpG dinucleotides in each amplicons is shown as lollipops on the lower panel.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4215812&req=5

Fig1: Graphical overview at BDNF gene. The BDNF gene structure and promoter locations are adopted from the study of Pruunsild et al. (2007). Arrow on the top shows the direction of BDNF transcript; exons (green), CpG islands (cyan), and investigated regions for DNA methylation (black) are mapped on NCBI accession number AF411339.1. CpG island were detected by CpGPlot using default parameters (http://www.ebi.ac.uk/Tools/seqstats/emboss_cpgplot/). Number of CpG dinucleotides in each amplicons is shown as lollipops on the lower panel.
Mentions: BDNF sequence (AF411339.1) was used to map different known CpG promoters within the gene (Figure 1); two methods were used. First, the CSHL human promoter mapping using CpG islands (CpGpromoter) (Ioshikhes and Zhang 2000) enabled mapping of human promoters using Gardiner-Garden and Frommer's definition of CpG islands (Gardiner-Garden and Frommer 1987) (http://rulai.cshl.org/tools/CpG_promoter). CpGpromoter indicated CpG islands related to promoters at three regions of AF411339.1. Second is the BIMAS Promoter Scan (Center for Information Technology, NIH, http://www-bimas.cit.nih.gov/molbio/proscan/), which uses PROSCAN 1.7 to predict promoters based on scoring homologies with eukaryote Pol II sequences. BIMAS corroborated the three CpG island promoters noted with CpGpromoter, which correspond to BDNF promoters 1, 3, and 5 of the nine promoters described by Pruunsild et al. (2007) (see Figure 1).Figure 1

Bottom Line: Five CpG units, mostly in promoter 5, remained significant after false discovery rate correction (FDR) (p values ≤ 0.004) with medium to large effect sizes (Cohen's d ≥ 0.61).Statistically significant differences in mean methylation fraction at 5/36 CpG units (after FDR), some at or immediately adjacent to TFBSs, suggest possible relevance for the current findings to BD etiopathogenesis.Future studies should provide more exhaustive epigenetic study of the BDNF locus to better characterize the relationship between BDNF methylation differences and BD.

View Article: PubMed Central - PubMed

Affiliation: Centre for Addiction and Mental Health, University of Toronto, Toronto, ON M6J1H4 Canada.

ABSTRACT

Background: Bipolar disorder (BD) is a complex psychiatric phenotype with a high heritability and a multifactorial etiology. Multisite collaborative efforts using genome-wide association studies (GWAS) have identified only a portion of DNA sequence-based risk factors in BD. In addition to predisposing DNA sequence variants, epigenetic misregulation may play an etiological role in BD and account for monozygotic twin discordance, parental origin effects, and fluctuating course of BD. In this study, we investigated DNA methylation of the brain-derived neurotrophic factor (BDNF) gene in BD.

Methods: Fifty participants with BD were compared to the same number of age- and sex-matched controls for DNA methylation differences at BDNF promoters 3 and 5. DNA methylation reads were obtained using a mass spectrophotometer for 64 cytosine-guanine (CpG) sites in 36 CpG 'units' across three amplicons of BDNF promoters 3 and 5.

Results and discussion: Methylation fractions differed between BD participants and controls for 11 of 36 CpG units. Five CpG units, mostly in promoter 5, remained significant after false discovery rate correction (FDR) (p values ≤ 0.004) with medium to large effect sizes (Cohen's d ≥ 0.61). Several of the significant CpGs overlapped with or were immediately adjacent to transcription factor binding sites (TFBSs) - including two of the FDR-significant CpG units in promoter 5. For the CpGs in promoter 3, there was a positive and significant correlation between age at sample collection and DNA methylation fraction (rho = 0.56, p = 2.8 ×10(-5)) in BD cases, but not in controls. Statistically significant differences in mean methylation fraction at 5/36 CpG units (after FDR), some at or immediately adjacent to TFBSs, suggest possible relevance for the current findings to BD etiopathogenesis. The positive correlation between age and methylation seen in promoter 3 is consistent with age-related decline in BDNF expression previously reported. Future studies should provide more exhaustive epigenetic study of the BDNF locus to better characterize the relationship between BDNF methylation differences and BD.

No MeSH data available.


Related in: MedlinePlus