Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson’s disease

背景知识

此前研究结果表明，黑质致密部（SNpc）内多巴胺（DA）神经元的缺失是帕金森病（PD）的一个明确病理特征，这项研究中，研究人员就深入对大脑黑质中的DA神经细胞进行分析来找到哪些细胞会在帕金森疾病患者中死亡。

一，A molecular taxonomy of human SNpc DA neurons.

8名非帕金森病患者脑部黑质细胞

To address the sampling challenge associated with DA neuron profiling, we developed a protocol based on fluorescence-activated nuclei sorting

(FANS), to enrich midbrain DA neuron nuclei for use in snRNA-seq

2）发现了10种产生多巴胺的细胞亚型。

背景：  Sox6，CLAB1的表达区分了黑质背侧和腹侧偏倚多巴胺神经元，具有独特的特性和胚胎起源

 strong expression of genes that are essential for DA neurotransmission       Previously defined dopaminergic markers also showed strong expression

3）evolutionary conservation of our human DAneuron subtypes,

Cross-species analysis (Methods) identified eight clusters (Fig. 1g) that consistently followed the SOX6–CALB1 axis of variation (Extended Data Fig. 3a–c).

二，Localization of DA neurons in macaque midbrain by Slide-seq

背景：帕金森病黑质致密部(SNc)腹侧层多巴胺(DA)神经元明显退化，背侧层多巴胺(DA)神经元相对完好。

The strong ventral localization of the SOX6_AGTR1 population suggested that it may be especially susceptible to PD-associated degeneration.

三，Differentially vulnerable DA neurons in PD

To identify cell-type-specific molecular alterations in PD, we profiled an additional 202,810high-quality nuclei , including 6,364DA neurons, from ten age-matched and postmortem-interval-matched individuals with documented pathological midbrain DA neuron loss, and a clinical diagnosis of either PD or LBD.

Among the 68molecularly defined subpopulations, 11 showed significant proportional changes in association with PD/LBD

The largest statistically significant decline was in the SOX6_AGTR1 DA population, while clusters CALB1_GEM and CALB1_TRHR were proportionally increased.

We further developed a metric to visualize disease-associated enrichment or depletion within the low-dimensional embedding of jointly analyzed cell profiles, identifying a gradient of susceptibilit that correlated with the expression of AGTR1 and ORs from mixed-effects association of single cells (MASC).

We also confirmed selective depletion of the SOX6_AGTR1 subpopulation (Fig. 3e; Wilcoxon rank-sum test P<0.05, log2(fold

change−2.1)

四，Cellular localization of PD common variants.

We next sought to better understand the origins of the selective vulnerability of SOX6_AGTR1 cells to neurodegeneration in PD. One possibil ity is that the human genetic risk for PD—which is established at birth—selectively acts within the vulnerable population.

. a, Heatmap of expression of 26 familial genes, colored by AUC statistic (Presto; Methods). b, Bar plot of −log10-transformed P values from Fisher’s exact test comparing overlap between markers for major cell types (Methods) and familial variant genes. Red dashed line indicates Bonferroni significance threshold (P < 0.05)

The DA neuron gene set was the only one to show significant enrichment of genes that contained these familial variants , suggesting that a substantial fraction of these genes act within DA neurons to influence neurodegeneration.

Dot plot of −log10-transformed P values for MAGMA analysis of PD genetic risk in 68 transcriptionally defined SNpc clusters.

Using two different statistical methods, we found the largest and only statistically significant enrichment of PD genetic risk genes within

the SOX6_AGTR1 cell subtype .

总结：

1）DA神经元细胞分为了10个亚型。(以前的研究表明有2到3种将DA神经元细胞)

2）结果发现，在帕金森疾病患者中找到了一种极其脆弱的DA神经元细胞亚型。SOX6_AGTR1 亚型在帕金森患者机体中减少了。

3）这种脆弱的多巴胺神经元细胞，表达更多的遗传风险变异相关的基因，人类遗传学在这种细胞的易感性中起重要作用。

价值：

目前，治疗帕金森病的药物以各种方式促进多巴胺的分泌，但效果往往会随着时间的推移而减弱，因此需要更有效的治疗方法。上述发现找到了一种与帕金森疾病相关的DA亚型，有助于人们更好地理解帕金森病的病因，帮助评估潜在的治疗方法。也可用于在培养皿中培养该细胞用于测试新药。

严谨性：