Dissecting GWAS Identified Risk Variants in Parkinson's Disease – Functional Role of GPNMB in the Pathogenesis of PD

剖析 GWAS 确定的帕金森病风险变异 — GPNMB 在帕金森病发病机制中的功能作用

基本信息

批准号：
10680117
负责人：
Riana Lo Bu
金额：
$ 4.77万
依托单位：
ALBERT EINSTEIN COLLEGE OF MEDICINE
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：
2023-04-01 至 2025-03-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10680117
关键词：
Affect Age Aging Autophagocytosis Autophagosome Binding Brain CRISPR/Cas technology Chromatin Structure Chronic Complex DNA Data Data Set Development Disease Disease susceptibility Distal Electrophoretic Mobility Shift Assay Elements Enhancers Environmental Risk Factor Epidemiology Etiology Functional disorder Gene Deletion Gene Expression Gene Expression Profile Gene Expression Profiling Genes Genetic Enhancer Element Genetic Risk Genetic Transcription Genomic Segment Glycoproteins Impairment Individual Inflammasome Inflammation Inflammatory Integral Membrane Protein Link Literature Macrophage Mediating Membrane Microglia Molecular Molecular Chaperones Nerve Degeneration Neurodegenerative Disorders Nonmetastatic Parkinson Disease Pathogenesis Pathway interactions Patients Phagocytes Phagocytosis Play Population Genetics Probability Proteins Quantitative Reverse Transcriptase PCR Regulatory Element Reverse Transcriptase Polymerase Chain Reaction Risk Role Single Nucleotide Polymorphism Stress Substantia nigra structure System Testing Transcriptional Regulation Untranslated RNA Up-Regulation Upstream Enhancer Variant Work brain tissue cytokine disorder risk epigenomics gain of function genetic risk factor genome editing genome wide association study genomic locus glial activation human pluripotent stem cell inhibitor insight loss of function lysosome membrane melanoma migration neuroinflammation new therapeutic target novel protein B protein expression risk variant sporadic Parkinson&apos s Disease theories transcription factor transcriptome transcriptome sequencing zinc finger nuclease

项目摘要

ABSTRACT Parkinson’s Disease (PD) is the second most common chronic progressive neurodegenerative disease. Epide- miology and population genetics suggest that sporadic PD (>95% of cases) results from a complex interaction between genetic risk, aging, and environmental factors. A detailed understanding of the genetic risk is the first step to elucidating this complex interaction. Genome wide association studies (GWAS) have identified numer- ous risk variants (e.g., single nucleotide polymorphisms [SNPs]) present in 78 genomic regions associated with an increased risk of developing PD. However, there is little insight regarding which and how these SNPs mech- anistically contribute to the development and progression of PD. Since most of the functional SNPs are highly enriched in non-coding regulatory DNA elements such as distal enhancers, the prevailing theory is that cis- acting effects of the functional non-coding SNPs on gene expression play a significant role in the development of complex diseases. To compile a list of probable causal SNPs in brain enhancers, we integrated GWAS-iden- tified PD-risk variants with epigenomic data identifying brain-specific enhancers and gene expression datasets in primary brain tissue. This analysis revealed multiple candidate PD-risk variants in a microglia-specific en- hancer element in the glycoprotein nonmetastatic melanoma protein B (GPNMB) locus. GPNMB is a type 1 transmembrane protein known to be upregulated in the substantia nigra of PD patients. Very little is known re- garding its molecular function and how the dysregulation of GPNMB contributes to PD. Our preliminary analy- sis of changes in the cellular transcriptome after GPNMB gene deletion in hPSC-derived microglia identified alterations in expression levels of multiple key genes associated with CNS inflammation (i.e. NLRP2, NLRP12). In addition, there is compelling evidence indicating a role for GPNMB in autophagy (macroautoph- agy, mitophagy, and CMA). Based on previous literature and our preliminary data, I speculate that the cis-act- ing effect of a PD-risk associated sequence variant in a microglia-specific GPNMB enhancer leads to in- creased GPNMB expression, resulting in autophagy dysregulation and ultimately culminating in the activation of inflammatory pathways in microglia which contribute to the neurodegeneration observed in PD. To test this hypothesis this project aims to: (1) to identify the causal risk variant present in this upstream enhancer of GPNMB and characterize the molecular mechanisms by which the causal risk variant dysregulates GPNMB expression in microglia using CRISPR/Cas9-risk variant edited hPSCs, (2) characterize the functional effects of gain and loss of GPNMB on microglial inflammation associated with microglial activation and neurodegener- ation associated-inducers, and (3) characterize the functional effect of GPNMB on autophagy and determine if autophagy is an intermediate mechanism by which GPNMB influences inflammation. This work will provide in- valuable insight into the novel link between non-coding PD risk variants, GPNMB, autophagy, and inflamma- tion.

抽象的帕金森病（PD）是第二常见的慢性进行性神经退行性疾病。微生物学和群体遗传学表明，散发性 PD（>95% 的病例）是复杂相互作用的结果遗传风险、衰老和环境因素之间的关系首先要详细了解遗传风险。阐明这种复杂相互作用的步骤已确定为全基因组关联研究（GWAS）。 78 个基因组区域中存在与以下疾病相关的风险变异（例如单核苷酸多态性 [SNP]）：然而，对于这些 SNP 的机制以及如何发挥作用，人们还知之甚少。由于大多数功能性 SNP 具有高度的功能性，因此对 PD 的发生和进展具有重要意义。富含非编码调控DNA元件，例如远端增强子，流行的理论是顺式- 功能性非编码SNP对基因表达的作用在发育中发挥重要作用为了编制大脑增强剂中可能的因果 SNP 列表，我们整合了 GWAS-ide- 通过表观基因组数据识别大脑特异性增强子和基因表达数据集，对 PD 风险变异进行了强化该分析揭示了小胶质细胞特异性 en-中的多个候选 PD 风险变异。糖蛋白非转移性黑色素瘤蛋白 B (GPNMB) 基因座中的突变元件是 1 型。已知 PD 患者黑质中的跨膜蛋白上调。我们初步分析了其分子功能以及 GPNMB 的失调如何导致 PD。鉴定出 hPSC 来源的小胶质细胞中 GPNMB 基因缺失后细胞转录组的变化与中枢神经系统炎症相关的多个关键基因（即 NLRP2、此外，有令人信服的证据表明 GPNMB 在自噬（宏自噬）中发挥作用。 agy、mitophagy 和 CMA）根据之前的文献和我们的初步数据，我推测 cis-act- 小胶质细胞特异性 GPNMB 增强子中 PD 风险相关序列变异的作用导致 GPNMB 表达增加，导致自噬失调并最终导致激活小胶质细胞中导致 PD 中观察到的神经变性的炎症途径的研究。假设该项目旨在：（1）识别该上游增强子中存在的因果风险变异 GPNMB 并描述了因果风险变异导致 GPNMB 失调的分子机制使用 CRISPR/Cas9 风险变异编辑的 hPSC 在小胶质细胞中表达，(2) 表征功能效应 GPNMB 的获得和损失对与小胶质细胞激活和神经退行性疾病相关的小胶质细胞炎症的影响化相关诱导剂，以及 (3) 表征 GPNMB 对自噬的功能影响，并确定是否自噬是 GPNMB 影响炎症的一种中间机制。这项工作将提供信息。对非编码 PD 风险变异、GPNMB、自噬和炎症之间新联系的宝贵见解。