Cell type-specific epigenetic links to schizophrenia risk in the brain

Isabel Mendizabal, Stefano Berto, Noriyoshi Usui, Kazuya Toriumi, Paramita Chatterjee, Connor Douglas, Iksoo Huh, Hyeonsoo Jeong, Thomas Layman, Carol A. Tamminga, Todd M. Preuss, Genevieve Konopka, Soojin V. Yi

Research output: Contribution to journalArticle

Abstract

Background: The importance of cell type-specific epigenetic variation of non-coding regions in neuropsychiatric disorders is increasingly appreciated, yet data from disease brains are conspicuously lacking. We generate cell type-specific whole-genome methylomes (N = 95) and transcriptomes (N = 89) from neurons and oligodendrocytes obtained from brain tissue of patients with schizophrenia and matched controls. Results: The methylomes of the two cell types are highly distinct, with the majority of differential DNA methylation occurring in non-coding regions. DNA methylation differences between cases and controls are subtle compared to cell type differences, yet robust against permuted data and validated in targeted deep-sequencing analyses. Differential DNA methylation between control and schizophrenia tends to occur in cell type differentially methylated sites, highlighting the significance of cell type-specific epigenetic dysregulation in a complex neuropsychiatric disorder. Conclusions: Our results provide novel and comprehensive methylome and transcriptome data from distinct cell populations within patient-derived brain tissues. This data clearly demonstrate that cell type epigenetic-differentiated sites are preferentially targeted by disease-associated epigenetic dysregulation. We further show reduced cell type epigenetic distinction in schizophrenia.

Original languageEnglish (US)
Article number135
JournalGenome Biology
Volume20
Issue number1
DOIs
StatePublished - Jul 9 2019

Fingerprint

Epigenomics
epigenetics
brain
Schizophrenia
methylation
Brain
DNA
cells
DNA methylation
DNA Methylation
Transcriptome
transcriptome
genome
schizophrenia
High-Throughput Nucleotide Sequencing
central nervous system diseases
Oligodendroglia
Brain Diseases
neurons
Genome

Keywords

  • Brain cell type
  • DNA methylation
  • Epigenetics
  • Neurogenomics
  • Neuron
  • Oligodendrocyte
  • Schizophrenia
  • Transcriptome

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

Mendizabal, I., Berto, S., Usui, N., Toriumi, K., Chatterjee, P., Douglas, C., ... Yi, S. V. (2019). Cell type-specific epigenetic links to schizophrenia risk in the brain. Genome Biology, 20(1), [135]. https://doi.org/10.1186/s13059-019-1747-7

Cell type-specific epigenetic links to schizophrenia risk in the brain. / Mendizabal, Isabel; Berto, Stefano; Usui, Noriyoshi; Toriumi, Kazuya; Chatterjee, Paramita; Douglas, Connor; Huh, Iksoo; Jeong, Hyeonsoo; Layman, Thomas; Tamminga, Carol A.; Preuss, Todd M.; Konopka, Genevieve; Yi, Soojin V.

In: Genome Biology, Vol. 20, No. 1, 135, 09.07.2019.

Research output: Contribution to journalArticle

Mendizabal, I, Berto, S, Usui, N, Toriumi, K, Chatterjee, P, Douglas, C, Huh, I, Jeong, H, Layman, T, Tamminga, CA, Preuss, TM, Konopka, G & Yi, SV 2019, 'Cell type-specific epigenetic links to schizophrenia risk in the brain', Genome Biology, vol. 20, no. 1, 135. https://doi.org/10.1186/s13059-019-1747-7
Mendizabal I, Berto S, Usui N, Toriumi K, Chatterjee P, Douglas C et al. Cell type-specific epigenetic links to schizophrenia risk in the brain. Genome Biology. 2019 Jul 9;20(1). 135. https://doi.org/10.1186/s13059-019-1747-7
Mendizabal, Isabel ; Berto, Stefano ; Usui, Noriyoshi ; Toriumi, Kazuya ; Chatterjee, Paramita ; Douglas, Connor ; Huh, Iksoo ; Jeong, Hyeonsoo ; Layman, Thomas ; Tamminga, Carol A. ; Preuss, Todd M. ; Konopka, Genevieve ; Yi, Soojin V. / Cell type-specific epigenetic links to schizophrenia risk in the brain. In: Genome Biology. 2019 ; Vol. 20, No. 1.
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