A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder

Z. Kaminsky; M. Tochigi; P. Jia; M. Pal; J. Mill; A. Kwan; I. Ioshikhes; J. B. Vincent; J. L. Kennedy; J. Strauss; S. Pai; S. C. Wang; A. Petronis

doi:10.1038/mp.2011.64

A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder

Z. Kaminsky, M. Tochigi, P. Jia, M. Pal, J. Mill, A. Kwan, I. Ioshikhes, J. B. Vincent, J. L. Kennedy, J. Strauss, S. Pai, S. C. Wang, A. Petronis

Research output: Contribution to journal › Article › peer-review

86 Scopus citations

Abstract

Epigenetic studies of DNA and histone modifications represent a new and important activity in molecular investigations of human disease. Our previous epigenome-wide scan identified numerous DNA methylation differences in post-mortem brain samples from individuals affected with major psychosis. In this article, we present the results of fine mapping DNA methylation differences at the human leukocyte antigen (HLA) complex group 9 gene (HCG9) in bipolar disorder (BPD). Sodium bisulfite conversion coupled with pyrosequencing was used to interrogate 28 CpGs spanning ∼700 bp region of HCG9 in 1402 DNA samples from post-mortem brains, peripheral blood cells and germline (sperm) of bipolar disease patients and controls. The analysis of nearly 40 000 CpGs revealed complex relationships between DNA methylation and age, medication as well as DNA sequence variation (rs1128306). Two brain tissue cohorts exhibited lower DNA methylation in bipolar disease patients compared with controls at an extended HCG9 region (P=0.026). Logistic regression modeling of BPD as a function of rs1128306 genotype, age and DNA methylation uncovered an independent effect of DNA methylation in white blood cells (odds ratio (OR)=1.08, P=0.0077) and the overall sample (OR=1.24, P=0.0011). Receiver operating characteristic curve A prime statistics estimated a 69-72% probability of correct BPD prediction from a case vs control pool. Finally, sperm DNA demonstrated a significant association (P=0.018) with BPD at one of the regions demonstrating epigenetic changes in the post-mortem brain and peripheral blood samples. The consistent multi-tissue epigenetic differences at HCG9 argue for a causal association with BPD.

Original language	English (US)
Pages (from-to)	728-740
Number of pages	13
Journal	Molecular psychiatry
Volume	17
Issue number	7
DOIs	https://doi.org/10.1038/mp.2011.64
State	Published - Jul 2012
Externally published	Yes

Keywords

DNA methylation
bipolar disorder
epigenetics
pyrosequencing

ASJC Scopus subject areas

Molecular Biology
Psychiatry and Mental health
Cellular and Molecular Neuroscience

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10.1038/mp.2011.64

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title = "A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder",

abstract = "Epigenetic studies of DNA and histone modifications represent a new and important activity in molecular investigations of human disease. Our previous epigenome-wide scan identified numerous DNA methylation differences in post-mortem brain samples from individuals affected with major psychosis. In this article, we present the results of fine mapping DNA methylation differences at the human leukocyte antigen (HLA) complex group 9 gene (HCG9) in bipolar disorder (BPD). Sodium bisulfite conversion coupled with pyrosequencing was used to interrogate 28 CpGs spanning ∼700 bp region of HCG9 in 1402 DNA samples from post-mortem brains, peripheral blood cells and germline (sperm) of bipolar disease patients and controls. The analysis of nearly 40 000 CpGs revealed complex relationships between DNA methylation and age, medication as well as DNA sequence variation (rs1128306). Two brain tissue cohorts exhibited lower DNA methylation in bipolar disease patients compared with controls at an extended HCG9 region (P=0.026). Logistic regression modeling of BPD as a function of rs1128306 genotype, age and DNA methylation uncovered an independent effect of DNA methylation in white blood cells (odds ratio (OR)=1.08, P=0.0077) and the overall sample (OR=1.24, P=0.0011). Receiver operating characteristic curve A prime statistics estimated a 69-72% probability of correct BPD prediction from a case vs control pool. Finally, sperm DNA demonstrated a significant association (P=0.018) with BPD at one of the regions demonstrating epigenetic changes in the post-mortem brain and peripheral blood samples. The consistent multi-tissue epigenetic differences at HCG9 argue for a causal association with BPD.",

keywords = "DNA methylation, bipolar disorder, epigenetics, pyrosequencing",

author = "Z. Kaminsky and M. Tochigi and P. Jia and M. Pal and J. Mill and A. Kwan and I. Ioshikhes and Vincent, {J. B.} and Kennedy, {J. L.} and J. Strauss and S. Pai and Wang, {S. C.} and A. Petronis",

note = "Funding Information: We would like to thank the Stanley Medical Research Institute (SMRI) and Dr Francine Benes of the McLean Hospital Brain Bank for the provided brain tissues. ZK and JM were CIHR fellows. MT was supported by the Japan Society for the Promotion of Science Postdoctoral Fellowships for Research Abroad. AP is Senior Fellow, Ontario Mental Health Foundation, and Tapscott Chair in Schizophrenia Studies, University of Toronto. This work was supported by the Canadian Institutes for Health and Research (186007) and the National Institutes of Health (MH074127; MH088413) to AP.",

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doi = "10.1038/mp.2011.64",

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AU - Tochigi, M.

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AU - Mill, J.

AU - Kwan, A.

AU - Ioshikhes, I.

AU - Vincent, J. B.

AU - Kennedy, J. L.

AU - Strauss, J.

AU - Pai, S.

AU - Wang, S. C.

AU - Petronis, A.

N1 - Funding Information: We would like to thank the Stanley Medical Research Institute (SMRI) and Dr Francine Benes of the McLean Hospital Brain Bank for the provided brain tissues. ZK and JM were CIHR fellows. MT was supported by the Japan Society for the Promotion of Science Postdoctoral Fellowships for Research Abroad. AP is Senior Fellow, Ontario Mental Health Foundation, and Tapscott Chair in Schizophrenia Studies, University of Toronto. This work was supported by the Canadian Institutes for Health and Research (186007) and the National Institutes of Health (MH074127; MH088413) to AP.

PY - 2012/7

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N2 - Epigenetic studies of DNA and histone modifications represent a new and important activity in molecular investigations of human disease. Our previous epigenome-wide scan identified numerous DNA methylation differences in post-mortem brain samples from individuals affected with major psychosis. In this article, we present the results of fine mapping DNA methylation differences at the human leukocyte antigen (HLA) complex group 9 gene (HCG9) in bipolar disorder (BPD). Sodium bisulfite conversion coupled with pyrosequencing was used to interrogate 28 CpGs spanning ∼700 bp region of HCG9 in 1402 DNA samples from post-mortem brains, peripheral blood cells and germline (sperm) of bipolar disease patients and controls. The analysis of nearly 40 000 CpGs revealed complex relationships between DNA methylation and age, medication as well as DNA sequence variation (rs1128306). Two brain tissue cohorts exhibited lower DNA methylation in bipolar disease patients compared with controls at an extended HCG9 region (P=0.026). Logistic regression modeling of BPD as a function of rs1128306 genotype, age and DNA methylation uncovered an independent effect of DNA methylation in white blood cells (odds ratio (OR)=1.08, P=0.0077) and the overall sample (OR=1.24, P=0.0011). Receiver operating characteristic curve A prime statistics estimated a 69-72% probability of correct BPD prediction from a case vs control pool. Finally, sperm DNA demonstrated a significant association (P=0.018) with BPD at one of the regions demonstrating epigenetic changes in the post-mortem brain and peripheral blood samples. The consistent multi-tissue epigenetic differences at HCG9 argue for a causal association with BPD.

AB - Epigenetic studies of DNA and histone modifications represent a new and important activity in molecular investigations of human disease. Our previous epigenome-wide scan identified numerous DNA methylation differences in post-mortem brain samples from individuals affected with major psychosis. In this article, we present the results of fine mapping DNA methylation differences at the human leukocyte antigen (HLA) complex group 9 gene (HCG9) in bipolar disorder (BPD). Sodium bisulfite conversion coupled with pyrosequencing was used to interrogate 28 CpGs spanning ∼700 bp region of HCG9 in 1402 DNA samples from post-mortem brains, peripheral blood cells and germline (sperm) of bipolar disease patients and controls. The analysis of nearly 40 000 CpGs revealed complex relationships between DNA methylation and age, medication as well as DNA sequence variation (rs1128306). Two brain tissue cohorts exhibited lower DNA methylation in bipolar disease patients compared with controls at an extended HCG9 region (P=0.026). Logistic regression modeling of BPD as a function of rs1128306 genotype, age and DNA methylation uncovered an independent effect of DNA methylation in white blood cells (odds ratio (OR)=1.08, P=0.0077) and the overall sample (OR=1.24, P=0.0011). Receiver operating characteristic curve A prime statistics estimated a 69-72% probability of correct BPD prediction from a case vs control pool. Finally, sperm DNA demonstrated a significant association (P=0.018) with BPD at one of the regions demonstrating epigenetic changes in the post-mortem brain and peripheral blood samples. The consistent multi-tissue epigenetic differences at HCG9 argue for a causal association with BPD.

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A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder

Abstract

Keywords

ASJC Scopus subject areas

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