The etiology of Parkinson's disease is largely unknown. Genome-wide transcriptomic studies in bulk brain tissue have identified several molecular signatures associated with the disease. While these studies have the potential to shed light into the pathogenesis of Parkinson's disease, they are also limited by two major confounders: RNA post-mortem degradation and heterogeneous cell type composition of bulk tissue samples. We performed RNA sequencing following ribosomal RNA depletion in the prefrontal cortex of 49 individuals from two independent case-control cohorts. Using cell type specific markers, we estimated the cell type composition for each sample and included this in our analysis models to compensate for the variation in cell type proportions. Ribosomal RNA depletion followed by capture by random primers resulted in substantially more even transcript coverage, compared to poly(A) capture, in post-mortem tissue. Moreover, we show that cell type composition is a major confounder of differential gene expression analysis in the Parkinson's disease brain. Accounting for cell type proportions attenuated numerous transcriptomic signatures that have been previously associated with Parkinson's disease, including vesicle trafficking, synaptic transmission, immune and mitochondrial function. Conversely, pathways related to endoplasmic reticulum, lipid oxidation and unfolded protein response were strengthened and surface as the top differential gene expression signatures in the Parkinson's disease prefrontal cortex. Our results indicate that differential gene expression signatures in Parkinson's disease bulk brain tissue are significantly confounded by underlying differences in cell type composition. Modeling cell type heterogeneity is crucial in order to unveil transcriptomic signatures that represent regulatory changes in the Parkinson's disease brain and are, therefore, more likely to be associated with underlying disease mechanisms.

中文翻译：

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帕金森氏病中常见的基因表达特征是由细胞组成的变化驱动的。

帕金森氏病的病因很大程度上未知。全脑组织中的全基因组转录组研究已经确定了与该疾病相关的几种分子标记。虽然这些研究有可能阐明帕金森氏病的发病机理，但它们也受到两个主要混杂因素的限制：RNA验尸降解和大块组织样品的异质细胞类型组成。在来自两个独立的病例对照队列的49位个体的前额叶皮层中，核糖体RNA消耗后，我们进行了RNA测序。使用细胞类型特异性标记，我们估算了每个样品的细胞类型组成，并将其包括在我们的分析模型中，以补偿细胞类型比例的变化。与死后组织中的poly（A）捕获相比，核糖体RNA耗竭后被随机引物捕获的转录本覆盖率要大得多。此外，我们表明细胞类型组成是帕金森氏病大脑中差异基因表达分析的主要混杂因素。考虑细胞类型比例会削弱许多以前与帕金森氏病相关的转录组特征，包括囊泡运输，突触传递，免疫和线粒体功能。相反，与内质网，脂质氧化和未折叠的蛋白反应有关的途径被加强，并成为帕金森氏病前额叶皮层中最主要的差异基因表达特征。我们的结果表明，帕金森氏病大脑组织中的差异基因表达特征明显地与细胞类型组成的潜在差异混淆。为了揭示代表帕金森氏病大脑中调节变化的转录组特征，因此建模细胞类型异质性至关重要，因此，更可能与潜在的疾病机制相关。