NeuroMolecular Medicine

, Volume 16, Issue 4, pp 697–703 | Cite as

Aberrant DNA Methylation of Blood in Schizophrenia by Adjusting for Estimated Cellular Proportions

  • Makoto Kinoshita
  • Shusuke NumataEmail author
  • Atsushi Tajima
  • Kazutaka Ohi
  • Ryota Hashimoto
  • Shinji Shimodera
  • Issei Imoto
  • Masatoshi Takeda
  • Tetsuro Ohmori
Original Paper


DNA methylation, which is the transference of a methyl group to the 5′-carbon position of the cytosine in a CpG dinucleotide, is one of the major mechanisms of epigenetic modifications. A number of studies have demonstrated altered DNA methylation of peripheral blood cells in schizophrenia (SCZ) in previous studies. However, most of these studies have been limited to the analysis of the CpG sites in CpG islands in gene promoter regions, and cell-type proportions of peripheral leukocytes, which may be one of the potential confounding factors for DNA methylation, have not been adjusted in these studies. In this study, we performed a genome-wide DNA methylation profiling of the peripheral leukocytes from patients with SCZ and from non-psychiatric controls (N = 105; 63 SCZ and 42 control subjects) using a quantitative high-resolution DNA methylation microarray which covered across the whole gene region (485,764 CpG dinucleotides). In the DNA methylation data analysis, we first estimated the cell-type proportions of each sample with a published algorithm. Next, we performed a surrogate variable analysis to identify potential confounding factors in our microarray data. Finally, we conducted a multiple linear regression analysis in consideration of these factors, including estimated cell-type proportions, and identified aberrant DNA methylation in SCZ at 2,552 CpG loci at a 5 % false discovery rate correction. Our results suggest that altered DNA methylation may be involved in the pathophysiology of SCZ, and cell heterogeneity adjustments may be necessary for DNA methylation analysis.


Epigenetics DNA methylation Schizophrenia Microarray Leukocyte Blood Cell heterogeneity 



The authors thank Dr. Jörg Tost for his valuable comments and suggestions on SNP-associated probes in the Illumina HumanMethylation450 platform. The authors would also like to thank Mrs. Akemi Okada and Mrs. Kumiko Kikuchi for their technical assistance. The authors appreciate all the volunteers who understood our study purpose and participated in this study, and the physicians who helped us to collect clinical data and blood samples at the mental hospitals. This work was supported in part by a Grant-in-Aid for Scientific Research from the Japanese Ministry of Education, Culture, Sports, Science and Technology (Grant Number 24791216), SENSHIN Medical Research Foundation, and the Research Group for Schizophrenia.

Conflict of interest

The all authors report no biomedical financial interests or potential conflicts of interest.

Supplementary material

12017_2014_8319_MOESM1_ESM.tif (391 kb)
DNA methylation levels of three CpG sites in the AR gene. The AR gene is a X-linked gene. Three CpG sites in CpG islands in the AR gene showed higher DNA methylation in female. (TIFF 391 kb)
12017_2014_8319_MOESM2_ESM.docx (27 kb)
Supplementary material 2 (DOCX 27 kb)
12017_2014_8319_MOESM3_ESM.docx (351 kb)
Supplementary material 3 (DOCX 350 kb)


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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Makoto Kinoshita
    • 1
  • Shusuke Numata
    • 1
    Email author
  • Atsushi Tajima
    • 2
  • Kazutaka Ohi
    • 3
  • Ryota Hashimoto
    • 3
    • 5
  • Shinji Shimodera
    • 4
  • Issei Imoto
    • 2
  • Masatoshi Takeda
    • 5
  • Tetsuro Ohmori
    • 1
  1. 1.Department of Psychiatry, Course of Integrated Brain Sciences, Medical Informatics, Institute of Health BiosciencesThe University of Tokushima Graduate SchoolTokushimaJapan
  2. 2.Department of Human Genetics, Institute of Health BiosciencesThe University of Tokushima Graduate SchoolTokushimaJapan
  3. 3.Department of PsychiatryOsaka University Graduate School of MedicineSuitaJapan
  4. 4.Department of NeuropsychiatryKochi Medical SchoolNankokuJapan
  5. 5.Molecular Research Center for Children’s Mental Development, United Graduate School of Child DevelopmentOsaka UniversitySuitaJapan

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