3/3 High-resolution mapping of cell type-specific DNA (hydroxy)methylation in the human brain during postnatal development and in psychiatric disease

3/3 出生后发育和精神疾病期间人脑中细胞类型特异性 DNA（羟基）甲基化的高分辨率图谱

• 批准号: 10356882
• 负责人: ERAN A MUKAMEL
• 金额: $ 12.98万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-01 至 2025-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10356882
• 关键词: Aberrant DNA Methylation; Adolescence; Adult; Affect; Alleles; Attention; Autopsy; Base Pairing; Binding Sites; Bipolar Disorder; Brain; Brain region; Cell Nucleus; Cells; Childhood; Complement; DNA; DNA Methylation; Data; Data Set; Development; Disease; Enhancers; Epigenetic Process; Etiology; Fluorescence; Functional disorder; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Genetic; Genetic Risk; Genetic Transcription; Genome; Glutamates; Histones; Human; Interneurons; Link; Maps; Measures; Mediating; Mental disorders; Methods; Methylation; Minor Lymphocyte Stimulatory Loci; Modification; Molecular; Neuroglia; Neurons; Nuclear; Nucleic Acid Regulatory Sequences; Nucleotides; Patients; Population; Prefrontal Cortex; Process; Quantitative Trait Loci; Regulator Genes; Regulatory Element; Reporting; Resolution; Role; Sampling; Schizophrenia; Sex Bias; Site; Sorting - Cell Movement; Specimen; Techniques; Testing; Time; Tissues; Untranslated RNA; Variant; Work; base; bisulfite sequencing; brain cell; case control; cell type; disorder control; disorder risk; epigenome; epigenomics; excitatory neuron; gamma-Aminobutyric Acid; genetic association; genetic variant; genome wide association study; histone modification; individual patient; inhibitory neuron; insertion/deletion mutation; methylome; neuropsychiatric disorder; postnatal; postnatal development; promoter; recruit; relating to nervous system; risk variant; sex; spatiotemporal; transcription factor; transcriptome; transcriptome sequencing

Project Summary: Most genetic variants associated with disease in genome-wide association studies (GWAS) lie in non-coding gene regulatory elements (GRE; e.g., promoters and enhancers). GREs are tissue- and cell type-specific and are identified through their epigenomic signatures, including low DNA methylation (DNAm), DNA accessibility and certain histone modifications. The PsychENCODE Consortium has characterized brain GREs across brain regions and developmental time points, as well as in the brains of psychiatric patients using mostly DNA accessibility and histone modification marks. These marks, however, identify large regions of enrichment (~300-2,000bp), providing only low resolution coverage of the important regulatory nucleotides, e.g., transcription factor binding sites. DNAm (especially cell type-specific DNAm) has received less attention, although it has been linked to psychiatric disorders, including schizophrenia (SZ) and bipolar disorder (BD). In the adult human brain, ~80% of CG and 1.5% of non-CG (CH) sites are methylated, and can be converted to hydroxymethylcytosine (hmC) and further demethylated. In postmitotic neuronal genomes, mCH and hmC accumulate to a significantly higher level than in other tissues--a distinct feature of the brain's epigenome. Bisulfite sequencing (BS)-based approaches that are used to measure (h)mC can pinpoint GREs with single base resolution, presenting a unique opportunity to refine the gene regulatory landscape of the brain cell types. Here we aim to create reference DNAm maps [mC and hmC, using BS and oxidative (ox)BS sequencing] and transcriptional profiles (using RNA-seq) in two major subtypes of neurons in the human dorsolateral prefrontal cortex (DLPFC), namely excitatory glutamatergic (Glu) and inhibitory GABA-ergic neurons. The proposed work is based on fluorescence-activated nuclear sorting (FANS) methods that we recently developed to separate nuclei of different cell types from autopsied human brain, and on our recent findings that showed unexpected relationships between DNA(h)m, GREs, and gene expression in the DLPFC Glu and GABA neurons. We will perform these studies at key time points of postnatal brain development and adulthood to map DNA(h)m within active neuron subtype-specific GREs that may be vulnerable to disruption during childhood and adolescence periods that coincide with the critical processes of brain maturation and circuit refinement (Aim 1). This work will be complemented with single nucleus mC profiling, which will allow us to define the developmental trajectories of mC in discrete subpopulations of Glu and GABA neurons (Aim2). Finally, we will profile Glu and GABA neurons in 150 autopsied DLPFC samples obtained from controls and cases of SZ and BD, and will then map neuron subtype-specific gene expression and (hydroxy)methylation quantitative trait loci (eQTL, mQTLS, hmQTLs) (Aim3). We will integrate QTL, transcriptome, and DNA(h)m data with the results of SZ and BP GWAS to reveal DNA(h)m and gene expression-mediated causal risk variants and genes, and to distinguish specific neuronal subtype(s) that are critical in the etiology of these disorders.

项目概述：全基因组关联研究（GWAS）中与疾病相关的大多数遗传变异