Human brain multi-omics to decipher major depression pathophysiology

人脑多组学破译重度抑郁症病理生理学

基本信息

批准号：
10715962
负责人：
Maura Boldrini
金额：
$ 79.76万
依托单位：
NEW YORK STATE PSYCHIATRIC INSTITUTE DBA RESEARCH FOUNDATION FOR MENTAL HYGIENE, INC
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-09-01 至 2028-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10715962
关键词：
ATAC-seq Adult Age Amygdaloid structure Anatomy Animal Model Antidepressive Agents Apoptosis Astrocytes Atlases Autopsy Bar Codes Biological Assay Brain Brain Diseases Cell Adhesion Cell Cycle Inhibition Cell Lineage Cell Nucleus Cell Survival Cell model Cell physiology Cells Chromatin Complex Custom Cytoplasmic Granules DNA Repair Data Decision Making Disease Emotional Epigenetic Process Female Functional disorder Gene Expression Regulation Genes Genomics Glucocorticoid Receptor Heterogeneity Hippocampus Human Hydrocortisone Immunity Inflammation Life Link Longevity Major Depressive Disorder Maps Mass Spectrum Analysis Memory Messenger RNA Meta-Analysis Microglia Mitosis Molecular Mus Neurites Neuroglia Neuronal Plasticity Neurons Ontology Pathogenesis Pathogenicity Patients Phenotype Pilot Projects Predisposition Prefrontal Cortex Proliferating Proteins Proteomics Published Database Publishing RNA RNA Splicing Reporting Resolution Rewards Rodent Sampling Severities Slide Stress Sudden Death Technology Testing Tissues Toxicology Transposase Uniport Variant Woman XCL1 gene adult neurogenesis allostatic load biomarker identification cell determination cognitive function dentate gyrus depressive symptoms differential expression early life adversity economic cost emotional functioning epigenomics excitatory neuron genetic variant genome wide association study granule cell high risk hippocampal pyramidal neuron inhibitory neuron mRNA Expression male mood regulation multiple omics neurogenesis neuron loss neuropsychiatry new technology new therapeutic target prevent progenitor response single nucleus RNA-sequencing social stem cell proliferation suicidal risk synaptogenesis transcription factor transcriptomics treatment response

项目摘要

Major depressive disorder (MDD) is a common disease with high risk of suicide, great social and economic costs, and poor treatment response. Hippocampus neuroplasticity is altered in MDD, susceptible to stress exposure and critical for mood regulation and the establishment of emotional memories in MDD. At the cellular level, our group and others reported fewer granule neurons, fewer astrocytes, and smaller dentate gyrus in MDD. There are conflicting findings about the extent to which new neurons are generated in adult humans, and we showed this happens into the eighth decade of life, while other groups were unable to confirm these findings. Adult neurogenesis is linked to both the pathogenesis of depressive phenotypes and the action of antidepressants in mouse studies. Pathogenic mechanisms underlying cellular and anatomical changes in MDD remain largely unknown. A meta-analysis from the three largest genome-wide association studies identified 102 independent variants, 269 genes, and 15 gene-sets associated with MDD. There is an urgent need for using new technologies to investigate cell lineages in human hippocampus. This project will identify differentially expressed proteins (DEPs) and genes (DEGs) between MDD and non- psychiatric control (CTRL) hippocampus, at a regional and single cell level. In homogenized hippocampus tissue, we will implement our proteomics pipeline using high resolution mass spectrometry (HRMS), single nuclei (sn)RNA-seq and snATAC (Assay for Transposase-Accessible Chromatin) sequencing. In slide-mounted tissue we will apply Visium (10X Genomics) and our custom-made slide-seq technology, using deterministic barcoding for spatial omics sequencing, co-mapping mRNAs, ATAC and proteins (DBiT-seq). Our pilot proteomics studies showed that DEPs lower in uMDD vs. CTRL promote mitosis, differentiation, and prevent apoptosis. Pilot snRNA-seq and snATAC-seq identified all types of neurons and glia, vasculature, and immature cell clusters, which mapped with Visium onto the expected hippocampus subfields. DBiT-seq pilot studies showed higher variability of RNA splicing in MDD vs. CTRL, RNA velocity revealed high transcriptomic instability in MDD leading to high inter-patient heterogeneity in the pyramidal neuron cluster, and epigenetic ATAC profiling identified markers potentially related to MDD pathogenesis. Studying 80 MDD and 80 CTRL, age 14-90 yrs., 60% males and 40% females, with sudden death, short agonal state, clear toxicology, postmortem interval<24 hrs., RNA integrity number (RIN)>8, tissue pH>6, we will: 1. Identify hippocampus DEPs between MDD and CTRL applying HRMS. 2. Identify cell clusters’ DEGs in MDD vs. CTRL hippocampus applying snRNA- seq and snATAC-seq. 3. Deliver the first hippocampus spatial transcriptomic atlas and epigenomic atlas for chromatin accessibility, identify region-specific RNA dynamics, and determine MDD vs. CTRL multiome differences applying DBiT-seq. Identified molecular regulators of hippocampus cell viability and function will provide potential druggable targets for new MDD treatments, to be later tested in cellular and animal models.

重度抑郁症（MDD）是一种自杀风险高、社会和经济成本巨大的常见疾病，海马神经可塑性较差，容易受到压力暴露的影响。在MDD中，我们的情绪调节和情绪记忆的建立至关重要。研究小组和其他人报告称，重度抑郁症患者的颗粒神经元、星形胶质细胞和齿状回较小。关于成年人新神经元生成程度的发现是相互矛盾的，我们证明了这种情况发生在八岁的时候，而其他研究小组无法证实这些发现。神经发生与抑郁表型的发病机制和抗抑郁药的作用有关 MDD 的细胞和解剖学变化的致病机制在很大程度上仍然存在。三个最大的全基因组关联研究的荟萃分析确定了 102 项独立的研究。与 MDD 相关的变体、269 个基因和 15 个基因组。迫切需要使用新技术来研究人类海马体的细胞谱系。项目将鉴定 MDD 和非 MDD 之间的差异表达蛋白 (DEP) 和基因 (DEG) 精神控制（CTRL）海马，在区域和单细胞水平上，在同质化海马组织中，我们将使用高分辨率质谱 (HRMS)、单核来实施我们的蛋白质组学流程 (sn)RNA-seq 和 snATAC（转座酶可及染色质测定）在载玻片组织中进行测序。我们将应用 Visium (10X Genomics) 和我们定制的幻灯片测序技术，使用确定性条形码用于空间组学测序、共同绘制 mRNA、ATAC 和蛋白质 (DBiT-seq)。我们的初步蛋白质组学研究表明，与 CTRL 相比，uMDD 中的 DEP 较低，可促进有丝分裂、分化和试点 snRNA-seq 和 snATAC-seq 鉴定了所有类型的神经元和神经胶质细胞、脉管系统和未成熟细胞簇，使用 Visium 映射到预期的 DBiT-seq 试点区域。研究表明，MDD 与 CTRL 中的 RNA 剪接变异性更高，RNA 速度揭示了高转录组学 MDD 的不稳定性导致锥体神经元簇的患者间高度异质性，以及表观遗传 ATAC 分析确定了可能与 MDD 发病机制相关的标记物，研究 80 MDD 和 80 CTRL、年龄。 14-90岁，60%男性和40%女性，猝死，短暂的临终状态，明确的毒理学，尸检间隔<24小时，RNA完整性数（RIN）>8，组织pH>6，我们将： 1. 识别之间的海马DEP 应用 HRMS 的 MDD 和 CTRL 2. 应用 snRNA- 识别 MDD 与 CTRL 海马中的细胞簇的 DEG。 seq 和 snATAC-seq 3. 提供第一个海马空间转录组图谱和表观基因组图谱。染色质可及性，识别区域特异性 RNA 动力学，并确定 MDD 与 CTRL 多组应用 DBiT-seq 确定的海马细胞活力和功能的分子调节剂将为新的 MDD 治疗提供潜在的药物靶标，随后在细胞和动物模型中进行测试。