Department of Clinical Medicine, Palle Juul-Jensens Boulevard 165, DK-8200, Aarhus N, Denmark.
Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, DK-8000, Aarhus C, Denmark.
Sci Data. 2023 Jul 6;10(1):432. doi: 10.1038/s41597-023-02338-1.
The discovery of surrogate biomarkers reflecting neuronal dysfunction in neurodegenerative diseases (NDDs) remains an active area of research. To boost these efforts, we demonstrate the utility of publicly available datasets for probing the pathogenic relevance of candidate markers in NDDs. As a starting point, we introduce the readers to several open access resources, which contain gene expression profiles and proteomics datasets from patient studies in common NDDs, including proteomics analyses of cerebrospinal fluid (CSF). Then, we illustrate the method for curated gene expression analyses across select brain regions from four cohorts of Parkinson disease patients (and from one study in common NDDs), probing glutathione biogenesis, calcium signaling and autophagy. These data are complemented by findings of select markers in CSF-based studies in NDDs. Additionally, we enclose several annotated microarray studies, and summarize reports on CSF proteomics across the NDDs, which the readers can utilize for translational purposes. We anticipate that this "beginner's guide" will benefit the research community in NDDs, and would serve as a useful educational tool.
在神经退行性疾病（NDDs）中发现反映神经元功能障碍的替代生物标志物仍然是一个活跃的研究领域。为了推动这些努力，我们展示了使用公开数据集来探究候选标志物在 NDDs 中的发病相关性的实用性。作为起点，我们向读者介绍了几个开放获取资源，其中包含来自常见 NDDs 患者研究的基因表达谱和蛋白质组学数据集，包括脑脊液（CSF）的蛋白质组学分析。然后，我们说明了针对来自四个帕金森病患者队列的选定脑区进行经过策展的基因表达分析的方法（以及一个常见 NDDs 研究），探查谷胱甘肽生物合成、钙信号和自噬。这些数据补充了基于 CSF 的 NDDs 研究中选定标志物的发现。此外，我们还附上了几个注释的微阵列研究，并总结了跨 NDDs 的 CSF 蛋白质组学报告，读者可以将其用于转化研究。我们预计，这本“初学者指南”将使 NDDs 研究界受益，并成为有用的教育工具。
